
4001. microRNA suppresses prostate cancer stem cells and metastasis by inhibiting a cohort of pro-metastasis targets including CD44, Rho GTPases and EZH2
(Submitter supplied) microRNA plays important roles in tumor initiation and progression. Here we showed that, one of the miR-200 family member, miR-141 is drastically under-expressed in several prostate cancer stem cell populations in both xenograft and primary patient samples. Enforced expression of miR-141 in CD44+ PCa cells suppressed tumor initation and metastasis. Cancer stem cell related properties including clonal and sphere formation ability as well as migration and invasion abilites were blocked by miR-141. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 7 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71756/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA292016
Series		Accession: GSE71756	ID: 200071756

4002. An automatec microwell platform for large-scale single cell RNA-seq.
(Submitter supplied) We report an automated microwell array platform for single cell RNA-seq with significantly improved performance over previous implementations. We demonstrate cell capture efficiencies of >50%, compatibility with commercially available barcoded mRNA capture beads, and parallel expression profiling from thousands of individual cells. We apply our system to comprehensively assess heterogeneity in gene expression of patient-derived glioma neurospheres and uncover subpopulations similar to those observed in human glioma tissue.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL19415 GPL18573 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85575/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA338815
Series		Accession: GSE85575	ID: 200085575

4003. Effect of Hotair overexpression in human breast cancer cell lines
(Submitter supplied) Study of the transcriptome changes upon Hotair overexpression in wt and Ezh2-/- Human breast cancer cell lines
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72524/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA294267
Series		Accession: GSE72524	ID: 200072524

4004. The Chromatin-Looping Factor ZNF143 Engages at Looping Promoters to Favor the Estrogen Response in Breast Cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 16 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76460/
Series		Accession: GSE76460	ID: 200076460

4005. The Chromatin-Looping Factor ZNF143 Engages at Looping Promoters to Favor the Estrogen Response in Breast Cancer (RNA-seq)
(Submitter supplied) Estrogen signaling in breast cancer cells relies on long-range chromatin interactions connecting distal regulatory elements bound by the estrogen receptor 1 (ESR1) to target gene promoters. This ensures stimulus and subtype-specific transcriptional responses. Expanding on the function of CTCF and the cohesin complex in breast cancer, we demonstrate that the chromatin-looping factor ZNF143 binds the promoter of most early-response estrogen target genes connected to distal regulatory elements in ESR1-positive breast cancer cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76453/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA307350
Series		Accession: GSE76453	ID: 200076453

4006. Epigenomic remodeling of the PAX8 cistrome in high grade serous ovarian cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 46 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83101/
Series		Accession: GSE83101	ID: 200083101

4007. Epigenomic remodeling of the PAX8 cistrome in high grade serous ovarian cancer [RNA-Seq]
(Submitter supplied) We report mapping of the PAX8 cistrome in three high grade serous ovarian cancer cell lines (KURAMOCHI, OVSAHO, and JHOS4) compared to three benign immortalized fallopian tube cell lines (FT33, FT194, and FT246). We identified a highly conserved PAX8 binding pattern common across benign fallopian tube cell lines that was distinct from the unique PAX8 binding patterns seen in each cancer cell line.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 34 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83100/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA324760
Series		Accession: GSE83100	ID: 200083100

4008. Selective single cell isolation for genomics using microraft arrays
(Submitter supplied) Genomic methods are used increasingly to interrogate the individual cells that compose specific tissues. However, current methods for single cell isolation struggle to phenotypically differentiate specific cells in a heterogeneous population and rely primarily on the use of fluorescent markers. Many cellular phenotypes of interest are too complex to be measured by this approach, making it difficult to connect genotype and phenotype at the level of individual cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 120 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85183/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA336476
Series		Accession: GSE85183	ID: 200085183

4009. Biased Expression of the FOXP3Δ3 Isoform in Aggressive Bladder Cancer Mediates Differentiation and Cisplatin Chemotherapy Resistance
(Submitter supplied) This study shows for the first time that the FOXP3Δ3 isoform is preferentially expressed in bladder cancer and induces a more aggressive and luminal isoform is preferentially expressed in bladder cancer and induces a more aggressive and luminal regulation of cancer differentiation and the plasticity amongst cancer subtypes which can be leveraged to optimize therapeutic regimens. These findings also identify a novel molecular marker as a putative companion diagnostic to guide therapy and target to undermine chemotherapy resistance.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81157/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA320752
Series		Accession: GSE81157	ID: 200081157

4010. G-quadruplex structures mark human regulatory chromatin
(Submitter supplied) G-quadruplex (G4) structural motifs have been linked to transcription, replication and genome instability and are implicated in cancer and other diseases. However, it is crucial to demonstrate the bona fide formation of G4 structures within an endogenous chromatin context. Herein we address this through the development of G4 ChIP-seq, an antibody-based G4 chromatin immunoprecipitation and high-throughput sequencing approach. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platform: GPL18573 52 Samples
FTP download: GEO (NARROWPEAK, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76688/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA308317
Series		Accession: GSE76688	ID: 200076688

4011. A novel tumor-associated myeloid cell population inhibits antigen-specific immune responses in cancer patients
(Submitter supplied) Tumor progression is associated with an immunosuppressive microenvironment that consists of several elements, such as regulatory T cells, type 2 macrophages and myeloid-derived suppressor cells. Here, we identify for the first time a BDCA1+CD14+ population of immunosuppressive cells that resides both in the blood and tumor of melanoma patients. We demonstrated that the presence of these cells in dendritic cell (DC)-based anti-tumor vaccines significantly suppresses CD4+ T cells in an antigen-specific manner. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75042/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA302281
Series		Accession: GSE75042	ID: 200075042

4012. INO80 is required for oncogenic transcription and tumor growth in non-small cell lung cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (BEDGRAPH, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85119/
Series		Accession: GSE85119	ID: 200085119

4013. INO80 is required for oncogenic transcription and tumor growth in non-small cell lung cancer [RNA-seq]
(Submitter supplied) Epigenetic regulators are attractive targets for the development of new cancer therapies. Among them, the ATP-dependent chromatin remodeling complexes control the chromatin architecture and play important roles in gene regulation. They are often found to be mutated and de-regulated in cancers, but how they influence the cancer gene expression program during cancer initiation and progression is not fully understood. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85118/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA336230
Series		Accession: GSE85118	ID: 200085118

4014. Genome-wide expression screening discloses long noncoding RNAs involved in thyroid carcinogenesis
(Submitter supplied) Context: Long non-coding RNAs (lncRNAs) regulate pathological processes, yet their potential roles in papillary thyroid carcinoma (PTC) are poorly understood. Objective: To profile transcriptionally dysregulated lncRNAs in PTC and identify lncRNAs associated with clinicopathological characteristics.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 24 Samples
FTP download: GEO (GTF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83520/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA326252
Series		Accession: GSE83520	ID: 200083520

4015. A long noncoding RNA regulates sister chromatid cohesion
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL18573 GPL11154 GPL17586 15 Samples
FTP download: GEO (BEDGRAPH, CEL, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81602/
Series		Accession: GSE81602	ID: 200081602

4016. A long noncoding RNA regulates sister chromatid cohesion [RNA-seq]
(Submitter supplied) Long noncoding RNAs (lncRNAs) have appeared to be involved in the most diverse cellular processes through multiple mechanisms. Here we describe a previously uncharacterized human lncRNA, CONCR (cohesion regulator noncoding RNA), transcriptionally activated by MYC, which is upregulated in multiple cancer types. The expression of CONCR is cell cycle-regulated, and it is required for cell cycle progression and DNA replication. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81601/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA322065
Series		Accession: GSE81601	ID: 200081601

4017. Genome-wide mRNA sequencing of Panc-1 cells with or without fused IL-35 gene up-regulated
(Submitter supplied) To screen out the downstream genes of IL-35
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 2 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85050/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA336024
Series		Accession: GSE85050	ID: 200085050

4018. RNA sequencing of patient derived cell lines in pancreatic cancer
(Submitter supplied) Gene expression levels of pancreatic cell lines
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 73 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84023/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA327834
Series		Accession: GSE84023	ID: 200084023

4019. BASP1 modifies the Tamoxifen response
(Submitter supplied) We report that WT1 transcriptional repressor protein BASP1 interacts with oestrogen receptor alpha (Erα), and interaction which in enhanced in the presence of Tamoxifen. We utilised RNASeq to identify common BASP1 and ERα target genes as well as Tamoxifen responsive genes that are altered in the absence of BASP1.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78199/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA312917
Series		Accession: GSE78199	ID: 200078199

4020. Prox1 (Prosper-related homeobox  1)  transcription factor depletion effect on CGTH-W-1  cells.
(Submitter supplied) Analysis of CGTH-W-1  follicular thyroid carcinoma cells transcriptome following  48 hrs siRNA-mediated depletion of PROX1. PROX1 is a homeobox transcription factor. PROX1  depletion decreases  migratory ability, motility and invasivness and induces profound cytoskeleton changes of CGTH-W-1  cells.  Results provide insight into the role of PROX1 in the thyroid cancer.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 12 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80135/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA318015
Series		Accession: GSE80135	ID: 200080135

4021. Characterization of t(15;21) translocations in myeloid disorders
(Submitter supplied) We report on two novel t(15;21) alterations [t(15;21)(q24;q22) and t(15;21)(q21;q22)], which led to concurrent disruption of RUNX1 and two translocation partner genes encoding for transcription factors (SIN3A, TCF12)
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 2 Samples
FTP download: GEO (BEDPE) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71551/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA291497
Series		Accession: GSE71551	ID: 200071551

4022. Gene expression profiling of drug-tolerant persister BT474 breast cancer cells derived from lapatinib treatment
(Submitter supplied) Acquired drug resistance prevents targeted cancer therapy from achieving stable and complete responses. Emerging evidence implicates a key role for nonmutational mechanisms including changes in cell state during early stages of acquired drug resistance. Targeting nonmutational resistance may therefore present a therapeutic opportunity to eliminate residual surviving tumor cells and impede relapse. A variety of cancer cell lines harbor quiescent, reversibly drug-tolerant “persister” cells which survive cytotoxic drugs including targeted therapies and chemotherapies. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 5 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84896/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA335583
Series		Accession: GSE84896	ID: 200084896

4023. ZMYND8 reads the dual histone mark H3K4me1-H3K14ac to antagonize the expression of metastasis-linked genes
(Submitter supplied) Histone acetylation, including acetylated H3K14 (H3K14ac), is generally linked to gene activation. Monomethylated histone H3 lysine 4 (H3K4me1), together with other gene-activating marks, denotes active genes. In contrast to usual gene-activating functions of H3K14ac and H3K4me1, we here show that the dual histone modification mark H3K4me1-H3K14ac is recognized by ZMYND8 (also called RACK7) and functions to counteract gene expression. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL21290 GPL16791 35 Samples
FTP download: GEO (TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE82nnn/GSE82260/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA324450
Series		Accession: GSE82260	ID: 200082260

4024. Splicing towards noncoding isoforms in colorectal carcinoma is associated with tumor hypoxia and the DNA damage response
(Submitter supplied) Tumor hypoxia is associated with poor patient outcome and resistance to therapy. It is associated with a rapid decline in protein production mediated through mTOR signalling. Here we show that it also leads to widespread changes in splicing and a global shift towards the expression of noncoding isoforms, thus providing a novel and orthogonal mechanism by which cells can modulate protein expression.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81513/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA321835
Series		Accession: GSE81513	ID: 200081513

4025. Neoadjuvant chemotherapy modulates T cell responses in high-grade serous ovarian cancer metastases
(Submitter supplied) Our data suggest that neoadjuvant chemotherapy enhances anti-cancer responses of T cells in peritoneal metastases of patients with high-grade serous ovarian cancer but does not decrease levels of immune checkpoint molecules, providing a rationale for sequential chemo-immunotherapy.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 35 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71340/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA290924
Series		Accession: GSE71340	ID: 200071340

4026. An epigenetic mark of polycomb response elements implemented by Trx/MLL/COMPASS
(Submitter supplied) In Drosophila, Polycomb Response Elements (PREs) are identified as genomic sequences allowing the maintenance of transcriptional repression in the absence of the initiating signal. Although PREs in Drosophila are well characterized, the existence of mammalian PRE-like elements remains debated.  Accumulating evidence supports a model in which CpG islands function to recruit Polycomb-Group complexes (PcG), however, it is not evident which subclasses of CpG islands serve as PREs. more...
Organism:	Homo sapiens; Drosophila melanogaster
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL18573 GPL19132 GPL13304 87 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81795/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA322547
Series		Accession: GSE81795	ID: 200081795

4027. RNA-seq analysis of add-back rescued TALEN-mediated LATS2 knockout HeLa-S3 cells
(Submitter supplied) Chromatin modifying activities for construction of appropriate epigenetic landscapes by polycomb repressive complex 2 (PRC2) play an essential role in development and tumorigenesis. However, the spatiotemporal mechanisms by which PRC2 achieves diverse epigenomes for specific tissue or cellular contexts remain poorly understood. Here, we discovered that LATS2 knockout causes dysregulation of PRC2 and subsequent transcriptome changes for differentiation in both mouse and human cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66388/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA276702
Series		Accession: GSE66388	ID: 200066388

4028. RNA-seq analysis of TALEN-mediated LATS2 knockout HeLa-S3 cells
(Submitter supplied) Chromatin modifying activities for construction of appropriate epigenetic landscapes by polycomb repressive complex 2 (PRC2) play an essential role in development and tumorigenesis. However, the spatiotemporal mechanisms by which PRC2 achieves diverse epigenomes for specific tissue or cellular contexts remain poorly understood. Here, we discovered that LATS2 knockout causes dysregulation of PRC2 and subsequent transcriptome changes for differentiation in both mouse and human cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63537/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA268336
Series		Accession: GSE63537	ID: 200063537

4029. Modeling the Neuropathology of Tuberous Sclerosis with Human Stem Cells Reveals a Role for Inflammation and Angiogenic Growth Factors
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 72 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78961/
Series		Accession: GSE78961	ID: 200078961

4030. Modeling the Neuropathology of Tuberous Sclerosis with Human Stem Cells Reveals a Role for Inflammation and Angiogenic Growth Factors [Treatment]
(Submitter supplied) Tuberous sclerosis complex (TSC) is a rare genetic disease characterized by mTOR hyperfunction induced benign tumor growths in multiple organs and neurological symptoms. Because the molecular pathology is highly complex and the etiology poorly understood we employed a defined human neuronal model with a single mTOR activating mutation to dissect the disease-relevant molecular responses driving the neuropathology. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 48 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78960/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA314507
Series		Accession: GSE78960	ID: 200078960

4031. Modeling the Neuropathology of Tuberous Sclerosis with Human Stem Cells Reveals a Role for Inflammation and Angiogenic Growth Factors [Cell Model]
(Submitter supplied) Tuberous sclerosis complex (TSC) is a rare genetic disease characterized by mTOR hyperfunction induced benign tumor growths in multiple organs and neurological symptoms. Because the molecular pathology is highly complex and the etiology poorly understood we employed a defined human neuronal model with a single mTOR activating mutation to dissect the disease-relevant molecular responses driving the neuropathology. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78959/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA314508
Series		Accession: GSE78959	ID: 200078959

4032. Conversion of Human Gastric Epithelial Cells to Multipotent Endodermal Progenitors using Defined Small Molecules [gene expression]
(Submitter supplied) Endodermal stem/progenitor cells have diverse potential applications in research and regenerative medicine, so a readily available source could have widespread uses. Here we describe derivation of human induced endodermal progenitor cells (hiEndoPCs) from gastrointestinal epithelial cells using a cocktail of defined small molecules along with support from tissue-specific mesenchymal feeders. The hiEndoPCs show clonal expansion in culture and give rise to hepatocytes, pancreatic endocrine cells, and intestinal epithelial cells when treated with defined soluble molecules directing differentiation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL20795 GPL16791 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58557/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA252868
Series		Accession: GSE58557	ID: 200058557

4033. Adaptation of the Kinome Promotes Resistance to BET Bromodomain Inhibitors in Ovarian Cancer
(Submitter supplied) Small molecule BET bromodomain inhibitors (BETi) are actively being pursued in clinical trials for the treatment of a variety of cancers, however, the mechanisms of resistance to targeted BET protein inhibitors remain poorly understood. Using a novel mass spectrometry approach that globally measures kinase signaling at the proteomic level, we evaluated the response of the kinome to targeted BET inhibitor treatment in a panel of BRD4-dependent ovarian carcinoma (OC) cell lines. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE82nnn/GSE82329/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA324669
Series		Accession: GSE82329	ID: 200082329

4034. Spliced synthetic genes as internal controls in RNA sequencing experiments.
(Submitter supplied) RNA sequencing (RNA-seq) can be used to assemble spliced isoforms, quantify expressed genes and provide a global profile of the transcriptome. However, the size and diversity of the transcriptome, the wide dynamic range in gene expression and inherent technical biases confound RNA-seq analysis. We have developed a set of spike-in RNA standards, termed ‘sequins’ (sequencing spike-ins), that represent full-length spliced mRNA isoforms. more...
Organism:	Homo sapiens; synthetic construct
Type:		Expression profiling by high throughput sequencing
Platforms: GPL19604 GPL16791 10 Samples
FTP download: GEO (GTF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77072/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA309391
Series		Accession: GSE77072	ID: 200077072

4035. Nudt3 is a mRNA Decapping Enzyme That Modulates Cell Migration
(Submitter supplied) The Dcp2 and Nudt16 Nudix hydrolases, are mRNA decapping enzymes that preferentially modulate stability of a subset of mRNAs.  Here we report Nudt3 is a third Nudix protein that possess mRNA decapping activity in cells and is a modulator of cell migration in MCF-7 breast cancer cells.  Genome-wide analysis of Nudt3 compromised cells identified increases in mRNAs involved in cell motility including integrin β6, lipocalin-2 and fibronectin. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75146/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA302638
Series		Accession: GSE75146	ID: 200075146

4036. Distinct Function for ASCL1 and NEUROD1 in Pulmonary Neuroendocrine Tumors
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL10999 GPL9520 GPL13112 15 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69398/
Series		Accession: GSE69398	ID: 200069398

4037. Distinct Function for ASCL1 and NEUROD1 in Pulmonary Neuroendocrine Tumors (RNA-seq)
(Submitter supplied) Small cell lung carcinoma (SCLC) and large cell neuroendocrine carcinoma (LCNEC) are high-grade pulmonary neuroendocrine tumors. The neural basic helix-loop-helix (bHLH) transcription factors ASCL1 and NEUROD1 have been shown to play crucial roles in promoting the malignant behavior and survival of human SCLC cell lines. In this study, we find ASCL1 and NEUROD1 identify distinct neuroendocrine tumors, bind distinct genomic loci, and regulate mostly distinct genes. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL13112 GPL9520 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69393/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA285362
Series		Accession: GSE69393	ID: 200069393

4038. EZH2 and BCL6 cooperate to assemble CBX8-BCOR Polycomb complex to repress bivalent promoters, mediate germinal center formation and promote lymphomagenesis
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 20 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81705/
Series		Accession: GSE81705	ID: 200081705

4039. Development of Pathway Preferential Estrogens Affording Beneficial Metabolic and Vascular Actions without Reproductive Tissue Stimulation in Mice
(Submitter supplied) There is great medical need for estrogens having favorable pharmacological profiles, supporting desirable activities for menopausal women such as metabolic and vascular protection but lacking stimulatory activities on the breast or uterus. Here, we report the development of structurally novel estrogens with favorable target tissue-selective estrogenic activity. Through a process of structural alteration of the hormone estradiol that preserves essential chemical and physical features of estradiol but greatly moderates its binding affinity for the estrogen receptors (ERs), we obtained Pathway Preferential Estrogens (PaPEs) capable of having interaction with ER that is sufficient to activate the extranuclear-initiated signaling pathway preferentially over the direct nuclear-initiated pathway. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73663/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA297590
Series		Accession: GSE73663	ID: 200073663

4040. EZH2 and BCL6 cooperate to assemble CBX8-BCOR Polycomb complex to repress bivalent promoters, mediate germinal center formation and promote lymphomagenesis [RNA-seq]
(Submitter supplied) EZH2 mediates the humoral immune response and drives lymphomagenesis through de novo formation of bivalent chromatin domains and critical germinal center (GC) B cell promoters.  We show that such formation is dependent on the presense of BCL6 and the presence of non-canonical PRC1-BCOR complex.  We observe that BCL6 and EZH2 cooperate to accelerate diffuse large B cell lymphoma (DLBCL) development and combinatorial targeting of these repressors results in enhanced anti-lymphoma activity in vitro, in vivo, and in primary human DLBCLs.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73109/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA296397
Series		Accession: GSE73109	ID: 200073109

4041. HLA peptides derived from tumor antigens induced by inhibition of DNA methylation for development of drug-facilitated immunotherapy
(Submitter supplied) Treatment of cancer cells with anti-cancer drugs often fails to achieve complete remission. Yet, such drug treatments may induce alteration in the tumor’s gene expression patterns, including those of Cancer/Testis Antigens (CTA). The degradation products of such antigens can be presented as HLA peptides on the surface of the tumor cells and be developed into anti-cancer immunotherapeutics. For example, the DNA methyl transferase inhibitor, 5-aza-2'-deoxycytidine (Decitabine) has limited anti-tumor efficacy, yet it induces the expression of many genes, including CTAs that are normally silenced in the healthy adult tissues. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80137/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA318019
Series		Accession: GSE80137	ID: 200080137

4042. Deletion of DXZ4 on the human inactive X chromosome eliminates superdomains and impairs gene silencing
(Submitter supplied) During interphase, the inactive X chromosome (Xi) adopts an unusual 3D configuration known as the Barr body and is largely transcriptionally silent. Despite the importance of X inactivation, little is known about the 3D configuration of Xi and its relationship to gene silencing. We recently showed that in humans, Xi exhibits two distinctive structural features. First, Xi is partitioned into two huge intervals, called superdomains, such that pairs of loci in each superdomain show an enhanced contact frequency with one another. more...
Organism:	Macaca mulatta; Homo sapiens; Mus musculus
Type:		Other; Expression profiling by high throughput sequencing
5 related Platforms 101 Samples
FTP download: GEO (HIC, PDF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71831/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA292502
Series		Accession: GSE71831	ID: 200071831

4043. Glutamine Deficiency Occurs in Regions of Solid Tumours and Promotes Dedifferentiation through Inhibition of Histone Demethylation
(Submitter supplied) We sequenced mRNA from the core regions and the peripheral regions of  melanoma xenograft tumors
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81817/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA322625
Series		Accession: GSE81817	ID: 200081817

4044. Regulation of highly expressed hCINAP on translatome
(Submitter supplied) hCINAP is essential for human 18S rRNA processing and ribosome assembly. hCINAP is highly expressed in human cancers and promotes cancer cell growth. To connect the role of hCINAP in ribosome biogenesis and tumor growth, genome-wide polysome profiling was performed to detect the regulation of hCINAP on ribosome assembly and translation control. The results showed taht hihgly expressed hCINAP promotes ribosome biogenesis and selectively modulates cancer-associated translatome to promote malignancy. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81469/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA321727
Series		Accession: GSE81469	ID: 200081469

4045. TWIST1 drives cisplatin resistance and cell survival in an ovarian cancer model, via upregulation of GAS6, L1CAM, and Akt signalling
(Submitter supplied) We created two cell lines derived from Ovcar8 by stably transfecting with an eGFP-firefly luciferase fusion protein and either an additional copy of the gene TWIST1 or an shRNA against TWIST1, under the control of the CMV promoter. RNA sequencing was used to look for differential expression of genes that may impact cisplatin resistance in epithelial ovarian cancer.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84425/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA329127
Series		Accession: GSE84425	ID: 200084425

4046. High Resolution Mapping of RNA Polymerases Identifies Mechanisms of Sensitivity and Resistance to BET Inhibitors in t(8;21) AML
(Submitter supplied) Bromodomain and extra-terminal domain (BET) family inhibitors offer a new approach to treating hematological malignancies. We used precision nuclear run-on transcription sequencing (PRO-seq) to create high-resolution maps of active RNA polymerases across the genome in t(8;21) acute myeloid leukemia (AML) that are exceptionally sensitive to BET inhibitors. PRO-seq identified over 1400 genes showing impaired release of promoter-proximal paused RNA polymerases, including the stem cell factor receptor tyrosine kinase KIT that is mutated in t(8;21) AML. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms: GPL11154 GPL18573 22 Samples
FTP download: GEO (BEDGRAPH, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83660/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA326664
Series		Accession: GSE83660	ID: 200083660

4047. Identification of ZEB1-regulated gene expression changes in HCC827 human lung adenocarcinoma cells
(Submitter supplied) We performed next-generation RNA sequencing for HCC827 human lung adenocarcinoma cells that are stably transfected with pcDNA3.1-ZEB1 or an empty pcDNA3.1 vector plasmid, in triplicate for each of the two HCC827 cell transfectants. The goal of this experiment is to identify putative downstream mediators of ZEB1 in human lung cancer cells. By successfully acquiring about 25 million reads for each sample, we identified more than 1,700 transcripts that are significantly regulated by ZEB1 (increased or decreased by ZEB1; p < 0.05). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81167/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA320768
Series		Accession: GSE81167	ID: 200081167

4048. Hormone induced repression of genes requires BRG1-mediated H1.2 deposition at target promoters
(Submitter supplied) In this report we have discovered a new function of BRG1 during hormone-mediated gene repression. The ATPase BRG1 without the other subunits of the BAF complex is recruited by the hormone receptor to genomic sites marked by the pioneering factor FOXA1, where it remodels the target chromatin by interacting with linker histone H1.2 facilitating its deposition.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 20 Samples
FTP download: GEO (BED, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83785/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA326976
Series		Accession: GSE83785	ID: 200083785

4049. A conserved abundant cytoplasmic long noncoding RNA modulates repression of mRNAs by Pumilio proteins in human cells
(Submitter supplied) Thousands of long noncoding RNA (lncRNA) genes are encoded in the human genome, and hundreds of them are evolutionary conserved, but their functions and modes of action remain largely obscure. Particularly enigmatic lncRNAs are those that are exported to the cytoplasm, including NORAD - an abundant and highly conserved cytoplasmic lncRNA. Most of the sequence of NORAD is comprised of repetitive units that together contain at least 17 functional binding sites for the two Pumilio homologs in mammals. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL9115 GPL18573 26 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79804/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA317019
Series		Accession: GSE79804	ID: 200079804

4050. Different promoter affinities account for specificity in MYC-dependent gene regulation
(Submitter supplied) Enhanced expression of the MYC transcription factor is observed in the majority of tumors. Two seemingly conflicting models have been proposed for its function: one proposes that MYC enhances expression of all genes, while the other model suggests gene-specific regulation. Here, we have explored the hypothesis that specific gene expression profiles arise since promoters differ in affinity for MYC and high-affinity promoters are fully occupied by physiological levels of MYC. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL10999 GPL18573 22 Samples
FTP download: GEO (TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77356/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA310128
Series		Accession: GSE77356	ID: 200077356

4051. RNA-sequencing of tamoxifen resistant LY2 cells transfected with siRNA-HOXC11.
(Submitter supplied) To assess the global effects of HOXC11 in endocrine resistant breast cancer cells we performed RNA-seq on LY2 cells which were transfected with either siRNA targeting HOXC11 (siHOXC11) or a scrambled negative control siRNA (scrHOXC11) in the presence of 4-OH-tamoxifen (10-8M).  Knockdown was verified by Taq-man qRT-PCR prior to library preparation.  RNA (10µg) was extracted using an Oligotex mRNA kit (Qiagen) as per manufacturer’s instructions (n=4). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 8 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71139/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA290630
Series		Accession: GSE71139	ID: 200071139

4052. Aberrant downstream mechanisms following loss of KMT2C and KMT2D in Pancreatic Ductal Adenocarcinoma
(Submitter supplied) Genes encoding the histone H3 lysine 4 (H3K4) methyltransferases KMT2C and KMT2D are subject to deletion and mutation in pancreatic ductal adenocarcinomas (PDAC). We examined the functional and transcriptional consequences of loss of these methyltransferases in patients with PDAC. Patients with low KMT2C and KMT2D expression demonstrated a much-improved outcome compared with those expressing high levels. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75327/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA304108
Series		Accession: GSE75327	ID: 200075327

4053. INO80 governs super-enhancer-mediated oncogenic transcription and tumor growth in melanoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL15520 31 Samples
FTP download: GEO (BEDGRAPH, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE82nnn/GSE82334/
Series		Accession: GSE82334	ID: 200082334

4054. INO80 governs super-enhancer-mediated oncogenic transcription and tumor growth in melanoma [RNA-seq]
(Submitter supplied) Super-enhancers (SEs) are large genomic regions with high density of enhancer marks. In cancer, SEs are found near oncogenes and dictate cancer gene expression. However, how oncogenic SEs are regulated remains poorly understood. Here, we show that INO80, a chromatin remodeling complex, is required for SE-mediated oncogenic transcription and tumor growth in melanoma. The expression of Ino80, the SWI/SNF ATPase, is elevated in melanoma cells and patient melanomas compared to normal melanocytes and benign nevi. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE82nnn/GSE82333/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA328060
Series		Accession: GSE82333	ID: 200082333

4055. Multiple mechanisms disrupt let-7 miRNA biogenesis and function in neuroblastoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL18573 19 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81500/
Series		Accession: GSE81500	ID: 200081500

4056. Multiple mechanisms disrupt let-7 miRNA biogenesis and function in neuroblastoma [longRNA]
(Submitter supplied) The let-7 microRNA families are tumor suppressors often deregulated in cancer, yet the underlying mechanisms of let-7 disruption remain poorly understood. Neuroblastoma is defined in part by poor prognosis associated with genetic amplification of MYCN, itself a let-7  target. The let-7 biogenesis inhibitor LIN28B  has been implicated as a critical regulator of MYCN ; however, here we show that LIN28B is dispensable for both MYCN  protein expression and growth of MYCN amplified neuroblastoma cell lines despite robust de-repression of let-7 . more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 9 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81498/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA321946
Series		Accession: GSE81498	ID: 200081498

4057. Multiple mechanisms disrupt let-7 miRNA biogenesis and function in neuroblastoma [Let7Targets]
(Submitter supplied) The let-7 microRNA families are tumor suppressors often deregulated in cancer, yet the underlying mechanisms of let-7 disruption remain poorly understood. Neuroblastoma is defined in part by poor prognosis associated with genetic amplification of MYCN, itself a let-7  target. The let-7 biogenesis inhibitor LIN28B  has been implicated as a critical regulator of MYCN ; however, here we show that LIN28B is dispensable for both MYCN  protein expression and growth of MYCN amplified neuroblastoma cell lines despite robust de-repression of let-7 . more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81497/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA321947
Series		Accession: GSE81497	ID: 200081497

4058. RNA polymerase in pre-B-ALL cell lines
(Submitter supplied) [Gro-seq] Precursor B acute leukemia cells measured using global nuclear run-on sequencing [ChIP-Seq] The genome-wide occupancy of ser2 and ser5 phosphorylated RNA pol2 and H3K4me3 was measured in precursor B acute leukemia cells measured using chip-seq.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Third-party reanalysis; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 21 Samples
FTP download: GEO (BEDGRAPH, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67540/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA280216
Series		Accession: GSE67540	ID: 200067540

4059. MEIS2 is a novel oncogenic partner in AML1-ETO positive AML
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
4 related Platforms 36 Samples
FTP download: GEO (BEDGRAPH, CEL, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81330/
Series		Accession: GSE81330	ID: 200081330

4060. MEIS2 is a novel oncogenic partner in AML1-ETO positive AML [RNA-Seq human]
(Submitter supplied) MEIS2 collaborates with AML1-ETO in inducing acute myeloid leukemia in a murine bone marrow transplantation model
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81328/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA321307
Series		Accession: GSE81328	ID: 200081328

4061. mRNA-seq analysis of HCT116 cells following gene overexpression of IDO1 with or without Indole treatment
(Submitter supplied) To investigate the effect of indole on protection against colon injury and the role of IDO1 expression, we examined the effect of indole on hIDO1-overexpressing and empty vector control HCT116 cells by global gene expression profiling.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83939/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA327493
Series		Accession: GSE83939	ID: 200083939

4062. Ridaforolimus (MK-8669) synergizes with Dalotuzumab (MK-0646) in hormone-sensitive breast cancer
(Submitter supplied) Introduction: Mammalian target of rapamycin (mTOR) represents a key downstream intermediate for a myriad of oncogenic receptor tyrosine kinases. In the case of the insulin-like growth factor (IGF) pathway, the mTOR complex (mTORC1) mediates IGF-1 receptor (IGF-1R)-induced estrogen receptor alpha (ERα) phosphorylation/activation and leads to increased proliferation and growth in breast cancer cells. As a result, the prevalence of mTOR inhibitors combined with hormonal therapy has increased in recent years. Conversely, activated mTORC1 provides negative feedback regulation of IGF signaling via insulin receptor substrate (IRS)-1/2 serine phosphorylation and subsequent proteasomal degradation. Thus, the IGF pathway may provide escape (e.g. de novo or acquired resistance) from mTORC1 inhibitors. It is therefore plausible that combined inhibition of mTORC1 and IGF-1R for select subsets of ER-positive breast cancer patients presents as a viable therapeutic option.   Methods: Using hormone-sensitive breast cancer cells stably transfected with the aromatase gene (MCF-7/AC-1), works presented herein describe the in vitro and in vivo antitumor efficacy of the following compounds: dalotuzumab (DALO; “MK-0646”; anti-IGF-1R antibody), ridaforolimus (RIDA; “MK-8669”; mTORC1 small molecule inhibitor) and letrozole (“LET”, aromatase inhibitor).   Results: With the exception of MK-0646, all single agent and combination treatment arms effectively inhibited xenograft tumor growth, albeit to varying degrees. Correlative tissue analyses revealed MK-0646 alone and in combination with LET induced insulin receptor alpha A (InsR-A) isoform upregulation (both mRNA and protein expression), thereby further supporting a triple therapy approach.   Conclusion: These data provide preclinical rationalization towards the combined triple therapy of LET plus MK-0646 plus MK-8669 as an efficacious anti-tumor strategy for ER-positive breast tumors.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 46 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79492/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA315980
Series		Accession: GSE79492	ID: 200079492

4063. SPECtre: a spectral coherence-based classifier of actively translated transcripts from ribosome profiling sequence data
(Submitter supplied) Active protein translation can be assessed and measured using ribosome profiling sequencing strategies. Existing approaches make use of sequence fragment length or frame occupancy to differentiate between active translation and background noise, however they do not consider additional characteristics inherent to the technology which limits their overall accuracy. Here, we present an analytical tool that models the overall tri-nucleotide periodicity of ribosomal occupancy using a classifier based on spectral coherence. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 1 Sample
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75947/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA305807
Series		Accession: GSE75947	ID: 200075947

4064. Identification of Resistance Genes to BRAF Inhibitor in Melanoma by piggyBac Transposon Activation Mutagenesis Screen
(Submitter supplied) Genotype directed anti-cancer therapies such BRAF inhibitor in BRAF mutant melanoma can show remarkable clinical efficacy but resistance limits their benefit. We show that a transposon activation screen efficiently identifies resistance genes to BRAF and captures a number of previously uncharacterized resistance mechanisms, including an E3 ubiquitin ligase NEDD4L and the Hippo pathway effector WWTR1 (TAZ). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73470/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA297064
Series		Accession: GSE73470	ID: 200073470

4065. Genome-wide CRISPR-Cas9 screen identifies protein-coding genes and microRNAs important in FLT3-ITD+ AML (MV4-11) cellular growth
(Submitter supplied) The functional relevance of many microRNAs in the context of tumor biology remains unclear. Using CRISPR-Cas9 technology, we performed a global loss-of-function screen to test the impact of individual microRNAs on the growth of FLT3-ITD positive leukemia cells. This approach identified both evolutionarily conserved and non-conserved human microRNAs that function to suppress or promote tumor cell growth, revealing that microRNAs are extensively integrated into the molecular networks that control tumor cell physiology. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71539/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA291480
Series		Accession: GSE71539	ID: 200071539

4066. Time course of androgen-regulated transcripts in LNCaP cells
(Submitter supplied) Prostate cancer is the most common cancer in men and AR downstream signalings promote prostate cancer cell proliferation. To investigate the AR signaling, we performed RNA sequence analysis in AR positive prostate cancer cell line, LNCaP.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70150/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA287733
Series		Accession: GSE70150	ID: 200070150

4067. Human and mouse DRIP-seq and DRIPc-seq
(Submitter supplied) This study profiles RNA:DNA hybrid formation in human and mouse cell lines.
Organism:	Mus musculus; Homo sapiens
Type:		Other; Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms: GPL17021 GPL13112 GPL11154 13 Samples
FTP download: GEO (BED, BEDGRAPH, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70189/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA287823
Series		Accession: GSE70189	ID: 200070189

4068. RNASeq identified human transcriptome alterations in Chinese Nasopharyngeal Carcinoma
(Submitter supplied) Our study is the first transcriptome profiling of Chinese NPC patients. These results provide both molecular basis and therapeutic opportunities for Chinese NPC patients.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 46 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68799/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA283839
Series		Accession: GSE68799	ID: 200068799

4069. RNA-seq analysis of vorinostat-resistant HCT116 cells following gene knockdown of GLI1 or PSMD13 with or without vorinostat treatment
(Submitter supplied) Transcriptome analysis was conducted on vorinostat resistant HCT116 cells (HCT116-VR) upon knockdown of potential vorinostat resistance candidate genes in the presence and absence of vorinostat.  Potential vorinostat resistance candidate genes chosen for this study were GLI1 and PSMD13, which were identified through a genome-wide synthetic lethal RNA interference screen.  To understand the transcriptional events underpinning the effect of GLI1 and PSMD13 knockdown (sensitisation to vorinostat-induced apoptosis), cells were first subjected to gene knockdown, then to treatment with vorinsotat or the solvent control. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 42 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57871/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA248301
Series		Accession: GSE57871	ID: 200057871

4070. RNA-sequencing (RNA-seq) in breast cancer cell lines after ectopic manipulation of miR-26a expression
(Submitter supplied) RNA sequencing technology has been carried out in order to evaluate mRNA expression changes after manipulation of miR-26a in both MCF-7 and MDA-MB-231 breast cancer cell lines.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE43nnn/GSE43726/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA187476
Series		Accession: GSE43726	ID: 200043726

4071. Chromatin accessibility maps of chronic lymphocytic leukemia identify subtype-specific epigenome signatures and transcription regulatory networks
(Submitter supplied) Chronic lymphocytic leukemia (CLL) is characterized by substantial clinical heterogeneity, despite relatively few genetic alterations. To provide a basis for studying epigenome deregulation in CLL, we established genome-wide chromatin accessibility maps for 88 CLL samples from 55 patients using the ATAC-seq assay, and we also performed ChIPmentation and RNA-seq profiling for ten representative samples. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other
Platform: GPL21290 138 Samples
FTP download: GEO (BIGWIG, CSV, NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81274/
Series		Accession: GSE81274	ID: 200081274

4072. A Primate lncRNA Mediates Notch Signaling During Neuronal Development by Sequestering miRNA
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 70 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74210/
Series		Accession: GSE74210	ID: 200074210

4073. A Primate lncRNA Mediates Notch Signaling During Neuronal Development by Sequestering miRNA [single cell sequencing analysis]
(Submitter supplied) Long non-coding RNAs (lncRNAs) are a diverse category of transcripts with poor conservation and have expanded greatly in primates, particularly in their brain. We identified a lncRNA, which has acquired 16 microRNA response elements (MREs) for miR-143-3p in the Catarrhini branch of primates. This lncRNA termed LncND (neuro-development) gets expressed in neural progenitor cells and then declines in mature neurons. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 60 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74207/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA299330
Series		Accession: GSE74207	ID: 200074207

4074. A Primate lncRNA Mediates Notch Signaling During Neuronal Development by Sequestering miRNA [SHSY5Y cells]
(Submitter supplied) Long non-coding RNAs (lncRNAs) are a diverse category of transcripts with poor conservation and have expanded greatly in primates, particularly in their brain. We identified a lncRNA, which has acquired 16 microRNA response elements (MREs) for miR-143-3p in the Catarrhini branch of primates. This lncRNA termed LncND (neuro-development) gets expressed in neural progenitor cells and then declines in mature neurons. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73982/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA298642
Series		Accession: GSE73982	ID: 200073982

4075. JQ1 +/- Vemurafenib in BRAF mutant melanoma (A375)
(Submitter supplied) The combination of JQ1 and Vemurafenib acted synergistically in BRAF-mutant cell lines, resulting in marked apoptosis in vitro, with up-regulation of pro-apoptotic proteins. In vivo, combination treatment suppressed tumor growth and significantly improved survival compared to either drug alone. RNA sequencing of tumor tissues revealed almost four thousand genes that were uniquely modulated by the combination, with several anti-apoptotic genes significantly down-regulated.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83592/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA326440
Series		Accession: GSE83592	ID: 200083592

4076. Epigenomics Studies in Acute Myeloid Leukemia disease progression
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 427 Samples
FTP download: GEO (TAR) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83534/
Series		Accession: GSE83534	ID: 200083534

4077. Epigenomics Studies in Acute Myeloid Leukemia disease progression [RNAseq]
(Submitter supplied) We report the DNA methylation and transcriptional molecular features of paired diagnosis and relapsed Acute Myeloid Leukemia  samples
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 134 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83533/
Series		Accession: GSE83533	ID: 200083533

4078. microRNAs with an AAGUGC seed motif constitute an integral part of a signaling network driving NSCLC cell proliferation
(Submitter supplied) miR-372-3p target identification mRNA level
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81417/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA321508
Series		Accession: GSE81417	ID: 200081417

4079. RNASeq of MV4;11 cells transduced with scramble shRNA or BRD4 shRNA in combination with DMSO or SGC0946
(Submitter supplied) Central to the molecular pathogenesis of MLL leukaemia is the abnormal co-optation of members of transcription complexes including disrupter of telomeric silencing 1-like (DOT1L) and bromodomain containing protein 4 (BRD4). Consequently, targeted therapies against DOT1L and BRD4 are currently being evaluated in clinical trials. However, the mechanisms by which BRD4 and DOT1L regulate leukaemogenic transcription programs remain unclear. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81148/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA320733
Series		Accession: GSE81148	ID: 200081148

4080. RNASeq of 4SU labelled nascent RNA in MV4;11 cell treated with DMSO, I-BET, SGC0946 and combination of I-BET and SGC0946
(Submitter supplied) Central to the molecular pathogenesis of MLL leukaemia is the abnormal co-optation of members of transcription complexes including disrupter of telomeric silencing 1-like (DOT1L) and bromodomain containing protein 4 (BRD4). Consequently, targeted therapies against DOT1L and BRD4 are currently being evaluated in clinical trials. However, the mechanisms by which BRD4 and DOT1L regulate leukaemogenic transcription programs remain unclear. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81147/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA320734
Series		Accession: GSE81147	ID: 200081147

4081. Tumor-derived circulating endothelial cell clusters in colorectal cancer
(Submitter supplied) Circulating tumor cells (CTCs) are the subject of several translational studies and clinical trials because their examination could offer an insight into tumor progression and clinical outcomes. Circulating tumor microemboli (CTM) are clusters of CTCs that have been described as malignant entities for over 50 years, although a comprehensive characterization of these cells is still lacking. Contrary to current consensus, we demonstrate that CTM isolated from colorectal cancer patients are not cancerous, but represent a discrete population of tumor-derived endothelial cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 53 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74369/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA300264
Series		Accession: GSE74369	ID: 200074369

4082. Human glioblastoma-associated microglia/monocytes express a distinct RNA profile compared to human control and murine samples
(Submitter supplied) We used RNA sequencing to compare the expression profile of 8 CD11b+ human glioblastoma-associated microglia/monocytes (hGAMs) samples to 8 human non-tumor CD11b+ microglia samples. Hierarchical clustering and principal component analysis showed a clear separation of the two sample groups and we identified 334 significantly regulated genes in hGAMs. In comparison to human control microglia hGAMs up-regulate genes associated with mitotic cell cycle, cell migration, cell adhesion, and extracellular matrix organization.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80338/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA315145
Series		Accession: GSE80338	ID: 200080338

4083. Three different in vivo models of synovial sarcoma (xenograft: Fuji; PDX: CTG-0331 and CTG-0771) treated with or without the indicated dose of the EZH2 inhibitor, tazemetostat
(Submitter supplied) The catalytic activities of covalent and ATP-dependent chromatin remodeling are central to regulating the conformational state of chromatin and the resultant transcriptional output.  The enzymes that catalyze these activities are often contained within multiprotein complexes in nature.  Two such multiprotein complexes, the polycomb repressive complex 2 (PRC2) methyltransferase and the SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeler have been reported to act in opposition to each other during development and homeostasis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 57 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83479/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA326108
Series		Accession: GSE83479	ID: 200083479

4084. Robust inference of cell-to-cell expression variations from single- and k-cell profiling
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by RT-PCR; Expression profiling by high throughput sequencing
Platforms: GPL21782 GPL11154 350 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83451/
Series		Accession: GSE83451	ID: 200083451

4085. Robust inference of cell-to-cell expression variations from single- and k-cell profiling (RNA-Seq)
(Submitter supplied) Quantifying heterogeneity in gene expression among single cells can reveal information inaccessible to cell-population measurements. However, the levels of many transcripts in single cells fall below the detection limit of even the most sensitive technologies currently available. One proposed approach to overcome this challenge is to measure random pools of k cells (e.g., 10) to increase sensitivity, followed by computational deconvolution of cellular heterogeneity parameters (CHPs), such as the biological variance of single-cell expression levels. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83450/
Series		Accession: GSE83450	ID: 200083450

4086. A splicing switch of TEAD4 regulates Hippo-YAP signaling pathway to inhibit tumor proliferation
(Submitter supplied) Splicing dysregulations extensively occur in cancers, yet the biological consequences of such alterations are mostly undefined. Here we report that the Hippo-YAP signaling, a key pathway that regulates cell proliferation and organ size, is under control of a new splicing switch. We show that TEAD4, the transcription factor that mediates Hippo-YAP signaling, undergoes alternative splicing facilitated by the tumor suppressor RBM4, producing a truncated isoform, TEAD4-S, which lacks N-terminal DNA-binding domain but maintains YAP-interaction domain. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 5 Samples
FTP download: GEO (MATRIX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80372/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA318757
Series		Accession: GSE80372	ID: 200080372

4087. Comparative transcriptomic analysis of human and Drosophila extracellular vesicles reveals extensive conservation
(Submitter supplied) Extracellular vesicles (EVs) are membrane-enclosed nanoparticles containing specific repertoires of genetic material. In mammals, EVs can mediate the horizontal transfer of various cargos and signaling molecules, notably miRNA and mRNA species. Whether this form of intercellular communication prevails in other metazoans remains unclear. Here, we report the first parallel comparative morphologic and transcriptomic characterization of EVs from Drosophila and human cellular models. more...
Organism:	Drosophila melanogaster; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL13304 GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76173/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA306512
Series		Accession: GSE76173	ID: 200076173

4088. Image based identification and targeting of cancer stem cells in pancreatic adenocarcinoma (PDAC)
(Submitter supplied) Purpose: The goals of this study were to identify quantitative gene expression differences between wild type,  Musashi1 null, Msuashi2 null and Musashi1/Musashi2 null MIAPaCa2 pancreatic cancer cells
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75797/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA305397
Series		Accession: GSE75797	ID: 200075797

4089. Rocaglamide A converts RNA helicase eIF4A into a sequence-specific translational repressor
(Submitter supplied) Rocaglamide A (RocA) typifies a novel class of protein synthesis inhibitors that selectively kill aneuploid tumor cells and repress translation of specific mRNAs. RocA targets eukaryotic initiation factor 4A (eIF4A), the prototypical DEAD-box RNA helicase, and its mRNA selectivity is proposed to reflect highly structured 5′ UTRs that are very dependent on eIF4A-mediated unwinding. Here, we show that secondary structure in 5′ UTRs is only a minor determinant for RocA selectivity and RocA does not repress translation by reducing eIF4A activity. more...
Organism:	Homo sapiens; synthetic construct
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL11154 GPL15228 23 Samples
FTP download: GEO (FA, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70211/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA287879
Series		Accession: GSE70211	ID: 200070211

4090. The β-catenin/CBP-antagonist ICG-001 inhibits pediatric glioma tumorigenicity in a Wnt-independent manner
(Submitter supplied) In pediatric glioma cell lines, treatment with ICG-001 had no inhibitory effect on canonical Wnt-target genes but induced significant up regulation of various known β-catenin target genes in both cell lines and top 20 GO-annotations of down-regulated genes by ICG-001  were associated with biosynthetic and metabolic processes and cell cycle division processes.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83266/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA325456
Series		Accession: GSE83266	ID: 200083266

4091. PI3K/AKT signaling regulates H3K4 methylation in breast cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL11154 GPL18573 12 Samples
FTP download: GEO (BED, BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80594/
Series		Accession: GSE80594	ID: 200080594

4092. Messenger RNA expression after MK2206/DMSO treatment of T47D cells
(Submitter supplied) We performed RNA-seq in T47D cells after 24 hour treatment with the AKT inhibitor MK2206 or DMSO. We show that a group of transcripts is differentailly expressed after AKT inhibition.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80591/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA319399
Series		Accession: GSE80591	ID: 200080591

4093. miR-126 Orchestrates an Oncogenic Program in B-Cell Precursor Acute Lymphoblastic Leukemia
(Submitter supplied) MicroRNA (miRNA)-126 is a known regulator of hematopoietic stem cell quiescence. We engineered murine hematopoiesis to express miRNA-126 across all differentiation stages. Thirty percent of mice developed monoclonal B cell leukemia, which was prevented or regressed when a tetracycline-repressible miRNA-126 cassette was switched off. Regression was accompanied by upregulation of cell-cycle regulators and B cell differentiation genes, and downregulation of oncogenic signaling pathways. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL17021 36 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78078/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA312538
Series		Accession: GSE78078	ID: 200078078

4094. FUS KO mRNA sequencing and anti-FUS RNA immunoprecipitation sequencing
(Submitter supplied) The aim of our study is to identify the role of FUS in shaping the transcriptome. RNA-seq of two FUS KO clones was performed and compared to wt; for each, four replicates were sequenced. RNA molecules associated with the FUS protein were determined by means of a RNA immuno-precipitation, followed by high-throughput sequencing. Total RNA was used as a control. SH-SY5Y cells were used for both experiments.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL11154 GPL21290 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71812/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA292114
Series		Accession: GSE71812	ID: 200071812

4095.  Functional interdependency of BRD4 and DOT1L in MLL leukaemia
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 33 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71780/
Series		Accession: GSE71780	ID: 200071780

4096. RNASeq of MV4;11 cell treated with DMSO, I-BET, SGC0946 and combination of I-BET and SGC0946
(Submitter supplied) Central to the molecular pathogenesis of MLL leukaemia is the abnormal co-optation of members of transcription complexes including disrupter of telomeric silencing 1-like (DOT1L) and bromodomain containing protein 4 (BRD4). Consequently, targeted therapies against DOT1L and BRD4 are currently being evaluated in clinical trials. However, the mechanisms by which BRD4 and DOT1L regulate leukaemogenic transcription programs remain unclear. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71777/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA292066
Series		Accession: GSE71777	ID: 200071777

4097. Recurrent alterations of TNFAIP3 (A20) in T-cell large granular lymphocytic leukemia
(Submitter supplied) We identified a novel recurrent genetic lesion in T-LGL. Mutations of the tumour suppressor gene TNFAIP3 causing amino-acid exchanges or protein truncations were seen in 3/39 cases (8%).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69735/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA286292
Series		Accession: GSE69735	ID: 200069735

4098. RNA sequencing of pancreatic adenocarcinoma tumors yields novel expression patterns associated with long-term survival and reveals a role for *ANGPTL4*
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 65 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79670/
Series		Accession: GSE79670	ID: 200079670

4099. RNA sequencing of human pancreatic cancer cell lines
(Submitter supplied) RNA-seq profiling was conducted on human pancreatic cancer cell lines
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79669/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA316672
Series		Accession: GSE79669	ID: 200079669

4100. RNA-sequencing of human pancreatic adenocarcinoma cancer tissues
(Submitter supplied) RNA-seq profiling was conducted on clinically-annotated human pancreatic adenocarcinoma cancer tissues
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 51 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79668/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA316673
Series		Accession: GSE79668	ID: 200079668

4101. RNA sequencing analysis of NGFR ablation in both p53-positive and negative non-small-cell lung cancer cell lines
(Submitter supplied) We report the gene expression profiles by NGFR knockdown in H460 and H1299 cell lines and reveal that NGFR ablation activates p53 target gene expression.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 12 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79051/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA314813
Series		Accession: GSE79051	ID: 200079051

4102. Distinct gene regulatory programs define the inhibitory effects of LXRs and PPARG on cancer cell proliferation
(Submitter supplied) The liver x receptor (LXR) and peroxisome proliferator-activated receptor gamma (PPARG) nuclear receptor transcription factors (TFs) are master regulators of energy homeostasis that impact tumor cell metabolism and proliferation. To better define the underlying molecular processes governing the genetic control of cellular growth in response to extracellular metabolic signals, we performed a comprehensive, genome-wide characterization of the temporal regulatory cascades mediated by LXR and PPARG signaling in HT29 colorectal cancer cells. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 82 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77039/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA309305
Series		Accession: GSE77039	ID: 200077039

4103. Cellular androgen content influences enzalutamide agonism of F877L mutant androgen receptor
(Submitter supplied) Prostate cancer is the most commonly diagnosed and second-most lethal cancer among men in the United States. The vast majority of prostate cancer deaths are due to castration-resistant prostate cancer (CRPC) – the lethal form of the disease that has progressed despite therapies that interfere with activation of androgen receptor (AR) signaling. One emergent resistance mechanism to medical castration is synthesis of intratumoral androgens that activate the AR. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 30 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69896/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA287041
Series		Accession: GSE69896	ID: 200069896

4104. KSHV LANA upregulates the expression of EGFL7 proteins in BJAB cells
(Submitter supplied) The objective of this study was to determine the effects of LANA on the expressions of the cellular genes.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE82nnn/GSE82184/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA324265
Series		Accession: GSE82184	ID: 200082184

4105. A TGFbeta-PRMT5-MEP50 Axis Regulates Cancer Cell Invasion through Histone H3 and H4 Arginine Methylation Coupled Transcriptional Activation and Repression
(Submitter supplied) We sequenced mRNA from 3 biological replicates each of A549 lung adenocarcinoma cell lines expressing shRNA against GFP (control), PRMT5, or MEP50. We then determined differential gene expression.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 9 Samples
FTP download: GEO (TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80182/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA318251
Series		Accession: GSE80182	ID: 200080182

4106. NAD+ Analog-sensitive PARPs Reveal a Role for PARP-1 in Transcription Elongation
(Submitter supplied) The PARP family of proteins comprises 17 members, about two thirds of which are active mono- or poly(ADP-ribosyl)transferase enzymes that transfer the ADP-ribose moiety of NAD+ onto target proteins.  In many cases, ADP-ribosylation, which plays critical roles in human diseases (e.g., cancer, heart disease, and neuropathies) is associated with abrogation of the molecular functions of the target.  Discerning ADP-ribosylation events mediated by a specific PARP is challenging, since all PARPs use the same substrate (i.e., NAD+) and the available inhibitors lack the specificity needed to make such conclusions. more...
Organism:	Homo sapiens
Type:		Other; Expression profiling by high throughput sequencing
Platforms: GPL9052 GPL18573 11 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74142/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA299156
Series		Accession: GSE74142	ID: 200074142

4107. A positive regulatory loop between a Wnt-regulated non-coding RNA and ASCL2 controls intestinal stem cell fate
(Submitter supplied) The canonical Wnt pathway plays a central role in stem cell maintenance, differentiation and proliferation in the intestinal epithelium. Constitutive, aberrant activity of the TCF4/β-catenin transcriptional complex is the primary transforming factor in colorectal cancer. Despite significant recent inroads, the full complement of Wnt target genes and the mechanisms of regulation remain incompletely understood. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69036/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA284373
Series		Accession: GSE69036	ID: 200069036

4108. Comparison of HCC cell lines and primary HCCs-RNAseq data
(Submitter supplied) There are concerns about whether cancer cell lines could faithfully represent the matched primary cancer cells. Comparison of the HCC cell lines and primary HCCs demonstrated that, during long-term in vitro culture, cell lines retain the genetic landscape of the matched primary HCCs.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78236/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA312978
Series		Accession: GSE78236	ID: 200078236

4109. Modulated expression of specific tRNA species drives cancer progression
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Expression profiling by array
Platforms: GPL10558 GPL11154 GPL18573 66 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77401/
Series		Accession: GSE77401	ID: 200077401

4110. Targeting MTHFD2 in Acute Myeloid Leukemia
(Submitter supplied) Purpose:  Identify new targets in acute myeloid leukemia (AML). Methods:  MOLM-14 cells were transduced with lentivirus encoding shRNAs targeting MTHFD2 (shMTHFD2 hairpin TRCN0000036553, denoted M5) and control (LacZ, shControl TRCN0000072231). RNA from 6 samples, biological duplicates (LacZ1, LacZ2; M5-1, M5-2) and a technical replicate (LacZ3, M5-3) were sequenced as 50+50 bp paired-end reads using Illumina TruSeq strand specific library. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81062/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA320396
Series		Accession: GSE81062	ID: 200081062

4111. Transcriptome analysis of patient-derived xenograft models of HER2+ breast cancer brain metastases
(Submitter supplied) To gain insights into tumor heterogeneity in anti-cancer drug responses of patient-derived xenograft models of HER2+ breast cancer brain metastases, we performed transcriptome gene expression profiling by Ion AmpliSeq™ Transcriptome sequencing that targets more than 20,000 human genes. Our data found that all anti-cancer drugs responders have significantly higher expression levels of AKT-mTOR-dependent signature genes as compared to the non-responders, suggesting that most HER2+ breast cancer brain metastases are depend on the AKT-mTOR pathway
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 10 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80722/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA319811
Series		Accession: GSE80722	ID: 200080722

4112. NUPR1 maintains autolysosomal efflux by activating SNAP25 transcription in cancer cells
(Submitter supplied) In the advanced stages of cancer, autophagy is thought to promote tumor progression through its ability to mitigate various cellular stresses. However, the details of how autophagy is homeostatically regulated in such tumors are unknown. Here, we report that NUPR1 (nuclear protein 1, transcriptional regulator), a transcriptional coregulator, is aberrantly expressed in a subset of cancer cells and predicts low overall survival rates for lung cancer patients. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL10999 GPL11154 4 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68873/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA283956
Series		Accession: GSE68873	ID: 200068873

4113. SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells
(Submitter supplied) The packaging of DNA into chromatin plays an important role in transcriptional regulation and nuclear processes. Brahma related gene-1 SMARCA4 (also known as BRG1), the essential ATPase subunit of the mammalian SWI/SNF chromatin remodeling complex, uses the energy from ATP hydrolysis to disrupt nucleosomes at target regions. Although the transcriptional role of SMARCA4 at gene promoters is well-studied, less is known about its role in higher-order genome organization. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platform: GPL11154 12 Samples
FTP download: GEO (BED, BEDGRAPH, CSV, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74716/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA301233
Series		Accession: GSE74716	ID: 200074716

4114. A Co-repressor CBFA2T2 regulates pluripotency and germline development
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL11154 GPL13112 18 Samples
FTP download: GEO (BW, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71676/
Series		Accession: GSE71676	ID: 200071676

4115. PolyA RNAseq from HCT116 cells in normoxia and hypoxia
(Submitter supplied) To determine the effects of depleting TIP60, CDK8, or HIF1A on the transcriptional response to hypoxia, we performed RNAseq analysis of four HCT116 colorectal carcinoma cell lines (shNT, HIF1A-/-, shTIP60 and shCDK8) in normoxic and hypoxic (24hrs, 1% O2) conditions.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68297/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA282396
Series		Accession: GSE68297	ID: 200068297

4116. A Basal Stem Cell Signature Identifies Aggressive Prostate Cancer Phenotypes
(Submitter supplied) Aggressive cancers and normal stem cells often share similar molecular and functional traits. It is unclear if aggressive phenotypes of prostate cancer molecularly resemble normal stem cells residing within the human prostate. We performed high-throughput RNA sequencing on uncultured, highly purified epithelial populations from human prostates obtained after radical prostatectomy. We found the basal population to be defined by genes associated with developmental programs, epigenetic remodeling, and invasiveness. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 20 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE82nnn/GSE82071/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA323923
Series		Accession: GSE82071	ID: 200082071

4117. Human Cactin interacts with DHX8 and SRRM2 to assure efficient pre-mRNA splicing and sister chromatid cohesion.
(Submitter supplied) We analysed whole PolyA+ RNA from human osteosarcoma U2OS cells depleted for human Cactin or transfected with a control shRNA.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE82nnn/GSE82070/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA323919
Series		Accession: GSE82070	ID: 200082070

4118. Next Generation Sequencing (RNAseq) of non-small cell lung cancer
(Submitter supplied) Cancer testis antigens (CTAs) are of clinical interest as biomarkers and present valuable targets for immunotherapy. To comprehensively characterize the CTA landscape of non-small cell lung cancer (NSCLC), we compared RNAseq data of 199 NSCLC tissues to the normal transcriptome of 142 samples from 32 different normal organs. Of 232 CTAs currently annotated in the CTdatabase, 96 were confirmed in NSCLC. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 218 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81089/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA320473
Series		Accession: GSE81089	ID: 200081089

4119. Genomic agonism and phenotypic antagonism between estrogen and progesterone receptors in breast cancer. [cell models RNA-seq]
(Submitter supplied) Transcriptomic changes and estrogen and progesterone receptor binding in multiple ER+/PR+ models (eight ER+/PR+ patient tumors, various T47Ds, ZR75) and multiple ER+/PR-negative models (four ER+/PR- patient tuumors, PR-deficient T47D and MCF7 cells) treated with various hormone combinations. Results: In isolation, estrogen and progestin act as genomic agonists by regulating the expression of common target genes in similar directions, but at different levels. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 28 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80366/
Series		Accession: GSE80366	ID: 200080366

4120. Genomic agonism and phenotypic antagonism between estrogen and progesterone receptors in breast cancer. [tumor samples RNA-seq]
(Submitter supplied) Transcriptomic changes and estrogen and progesterone receptor binding in multiple ER+/PR+ models (eight ER+/PR+ patient tumors, various T47Ds, ZR75) and multiple ER+/PR-negative models (four ER+/PR- patient tuumors, PR-deficient T47D and MCF7 cells) treated with various hormone combinations. Results: In isolation, estrogen and progestin act as genomic agonists by regulating the expression of common target genes in similar directions, but at different levels. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 48 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80365/
Series		Accession: GSE80365	ID: 200080365

4121. Genomic agonism and phenotypic antagonism between estrogen and progesterone receptors in breast cancer.
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 102 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80098/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA317919
Series		Accession: GSE80098	ID: 200080098

4122. Lineage-specific and single cell chromatin accessibility charts human hematopoiesis and leukemia evolution
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL18573 GPL11154 GPL16791 787 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75384/
Series		Accession: GSE75384	ID: 200075384

4123. Generation of Patient-Matched Malignant and Normal Primary Cell Cultures from Clear Cell Renal Cell Carcinoma Patients
(Submitter supplied) Transcriptome profiling of de novo-derived ccRCC cell cultures and their matching parental tumours.  VHL-mutant and VHL wild-type cultures were established by isolating CA9+ and CA9- cells from tumor samples using FACS.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74958/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA302010
Series		Accession: GSE74958	ID: 200074958

4124. Unstranded RNA sequencing data
(Submitter supplied) A single hematopoietic stem cell can give rise to all blood cells with remarkable fidelity. Here, we define the chromatin accessibility and transcriptional landscape controlling this process in thirteen primary cell types that traverse the hematopoietic hierarchy. Exploiting the finding that enhancer landscapes better reflect cell identity than mRNA levels, we enable "enhancer cytometry" for accurate enumeration of pure cell types from complex populations. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL11154 81 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74246/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA299579
Series		Accession: GSE74246	ID: 200074246

4125. Modulation of Indoleamine 2, 3-dioxygenase 1 Expression by Activated Human T cells in Breast Cancer Cells is Controlled by DNA Promoter Methylation
(Submitter supplied) Tumor infiltrating lymphocytes (TILs) play a critical role in modulating the immunoediting features in certain malignancies like triple negative breast cancer (TNBC). Nevertheless, much is still unknown concerning the specific responses of tumors when challenged by lymphocyte infiltration.  Based on this void, we conducted a immuno-phenotype comparison using mRNA sequencing between the TNBC cell line MDA-MB-231 and the luminal breast cancer cell line MCF7 after both were co-cultured with activated human T-cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73527/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA297215
Series		Accession: GSE73527	ID: 200073527

4126. Patient-derived xenograft platform for metastatic melanoma: RNA sequencing of 4 melanoma PDX samples
(Submitter supplied) The therapeutic landscape of melanoma is rapidly changing. While targeted inhibitors yield significant responses, their clinical benefit is often limited by the early onset of drug resistance. This motivates the pursuit to establish more durable clinical responses, by developing combinatorial therapies. But while potential new combinatorial targets steadily increase in numbers, they cannot possibly all be tested in patients. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73737/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA297789
Series		Accession: GSE73737	ID: 200073737

4127. Patient-derived xenograft platform for metastatic melanoma: a model for studying resistance to targeted therapy.
(Submitter supplied) The therapeutic landscape of melanoma is rapidly changing. While targeted inhibitors yield significant responses, their clinical benefit is often limited by the early onset of drug resistance. This motivates the pursuit to establish more durable clinical responses, by developing combinatorial therapies. But while potential new combinatorial targets steadily increase in numbers, they cannot possibly all be tested in patients. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66539/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA277227
Series		Accession: GSE66539	ID: 200066539

4128. Myb-regulated transcriptome in pancreatic cancer
(Submitter supplied) To understand the global view of Myb-regulated genes and pathways in pancreatic cancer.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE61nnn/GSE61290/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA261015
Series		Accession: GSE61290	ID: 200061290

4129. miRNA-mediated expression switch of cell adhesion genes driven by microcirculation in chip
(Submitter supplied) Changes in cell adhesion molecule (CAM) expression and miRNAs regulating them are known to be involved in malignant progression in colon cancer. We investigated expression profiles of CAM genes and non-coding RNAs in CaCo2 colon cancer cells in static culture and under dynamic flow conditions perfused in microfluidic chip emulating physiological microenvironment. We incubated monolayers of CaCo2 cells in Transwell® units either under static conditions or under flow in a microfluidic chip. more...
Organism:	synthetic construct; Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by array
Platforms: GPL21572 GPL6244 12 Samples
FTP download: GEO (CEL, CHP) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81867/
Series		Accession: GSE81867	ID: 200081867

4130. shRNA RNA-seq from HepG2 (ENCSR998RZI)
(Submitter supplied) shRNA knockdown against TAF15 in HepG2 cells followed by RNA-seq. (TAF15-BGHLV12)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80952/
Series		Accession: GSE80952	ID: 200080952

4131. shRNA RNA-seq from HepG2 (ENCSR997FOT)
(Submitter supplied) shRNA knockdown against SUB1 in HepG2 cells followed by RNA-seq. (SUB1 BGHLV14)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80951/
Series		Accession: GSE80951	ID: 200080951

4132. shRNA RNA-seq from HepG2 (ENCSR995ZGJ)
(Submitter supplied) shRNA knockdown against SMNDC1 in HepG2 cells followed by RNA-seq. (SMNDC1 BGHLV14)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80950/
Series		Accession: GSE80950	ID: 200080950

4133. shRNA RNA-seq from K562 (ENCSR961YAG)
(Submitter supplied) shRNA knockdown against EIF4A3 in K562 cells followed by RNA-seq. (EIF4A3-LV08)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80949/
Series		Accession: GSE80949	ID: 200080949

4134. shRNA RNA-seq from K562 (ENCSR961WVL)
(Submitter supplied) shRNA knockdown against DDX21 in K562 cells followed by RNA-seq. (DDX21-LV11)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80948/
Series		Accession: GSE80948	ID: 200080948

4135. shRNA RNA-seq from HepG2 (ENCSR957EEG)
(Submitter supplied) shRNA knockdown against EIF4A3 in HepG2 cells followed by RNA-seq. (EIF4A3-BGHLV12)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80947/
Series		Accession: GSE80947	ID: 200080947

4136. shRNA RNA-seq from K562 (ENCSR952RRH)
(Submitter supplied) shRNA knockdown against IGF2BP2 in K562 cells followed by RNA-seq. (IGF2BP2-LV11)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80946/
Series		Accession: GSE80946	ID: 200080946

4137. shRNA RNA-seq from K562 (ENCSR947OIM)
(Submitter supplied) shRNA knockdown against RBM22 in K562 cells followed by RNA-seq. (RBM22-LV11)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80945/
Series		Accession: GSE80945	ID: 200080945

4138. shRNA RNA-seq from HepG2 (ENCSR945UYL)
(Submitter supplied) shRNA knockdown against G3BP2 in HepG2 cells followed by RNA-seq. (G3BP2-BGHLV12)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80944/
Series		Accession: GSE80944	ID: 200080944

4139. shRNA RNA-seq from HepG2 (ENCSR939ZRA)
(Submitter supplied) shRNA knockdown against RDBP in HepG2 cells followed by RNA-seq. (RDBP-BGHLV12)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80943/
Series		Accession: GSE80943	ID: 200080943

4140. shRNA RNA-seq from HepG2 (ENCSR927JXU)
(Submitter supplied) shRNA knockdown against FUS in HepG2 cells followed by RNA-seq. (FUS BGHLV14)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80942/
Series		Accession: GSE80942	ID: 200080942

4141. shRNA RNA-seq from K562 (ENCSR916WOI)
(Submitter supplied) shRNA knockdown against TRA2A in K562 cells followed by RNA-seq. (TRA2A-LV11)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80941/
Series		Accession: GSE80941	ID: 200080941

4142. shRNA RNA-seq from HepG2 (ENCSR914WQV)
(Submitter supplied) shRNA knockdown against CSTF2T in HepG2 cells followed by RNA-seq. (CSTF2T BGHLV14)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80940/
Series		Accession: GSE80940	ID: 200080940

4143. shRNA RNA-seq from K562 (ENCSR913CAE)
(Submitter supplied) Control shRNA against no target in K562 cells followed by RNA-seq. (Nontarget-LV08)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80939/
Series		Accession: GSE80939	ID: 200080939

4144. shRNA RNA-seq from HepG2 (ENCSR906WTM)
(Submitter supplied) shRNA knockdown against RTF1 in HepG2 cells followed by RNA-seq. (RTF1 BGHLV14)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80938/
Series		Accession: GSE80938	ID: 200080938

4145. shRNA RNA-seq from K562 (ENCSR906RHU)
(Submitter supplied) shRNA knockdown against SRSF5 in K562 cells followed by RNA-seq. (SRSF5-41-LV11)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80937/
Series		Accession: GSE80937	ID: 200080937

4146. shRNA RNA-seq from K562 (ENCSR904CJQ)
(Submitter supplied) shRNA knockdown against U2AF2 in K562 cells followed by RNA-seq. (U2AF2-LV08)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80936/
Series		Accession: GSE80936	ID: 200080936

4147. shRNA RNA-seq from K562 (ENCSR904BCZ)
(Submitter supplied) shRNA knockdown against RAVER1 in K562 cells followed by RNA-seq. (RAVER1-LV08)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80935/
Series		Accession: GSE80935	ID: 200080935

4148. shRNA RNA-seq from K562 (ENCSR895BTE)
(Submitter supplied) shRNA knockdown against CPSF6 in K562 cells followed by RNA-seq. (CPSF6-LV08)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80934/
Series		Accession: GSE80934	ID: 200080934

4149. shRNA RNA-seq from HepG2 (ENCSR861ENA)
(Submitter supplied) shRNA knockdown against EIF2S1 in HepG2 cells followed by RNA-seq. (EIF2S1-BGHLV12)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80933/
Series		Accession: GSE80933	ID: 200080933

4150. shRNA RNA-seq from HepG2 (ENCSR853ZJS)
(Submitter supplied) shRNA knockdown against HNRNPK in HepG2 cells followed by RNA-seq. (HNRNPK-BGHLV12)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80932/
Series		Accession: GSE80932	ID: 200080932

4151. shRNA RNA-seq from HepG2 (ENCSR850CKU)
(Submitter supplied) shRNA knockdown against KHSRP in HepG2 cells followed by RNA-seq. (KHSRP-BGHLV12)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80931/
Series		Accession: GSE80931	ID: 200080931

4152. shRNA RNA-seq from K562 (ENCSR849STR)
(Submitter supplied) shRNA knockdown against MAGOH in K562 cells followed by RNA-seq. (MAGOH-LV11)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80930/
Series		Accession: GSE80930	ID: 200080930

4153. shRNA RNA-seq from HepG2 (ENCSR840QFR)
(Submitter supplied) shRNA knockdown against DAZAP1 in HepG2 cells followed by RNA-seq. (DAZAP1 BGHLV14)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80929/
Series		Accession: GSE80929	ID: 200080929

4154. shRNA RNA-seq from K562 (ENCSR831YGP)
(Submitter supplied) shRNA knockdown against EWSR1 in K562 cells followed by RNA-seq. (EWSR1-LV08)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80928/
Series		Accession: GSE80928	ID: 200080928

4155. shRNA RNA-seq from K562 (ENCSR792XFP)
(Submitter supplied) shRNA knockdown against MATR3 in K562 cells followed by RNA-seq. (MATR3-06-LV11)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80927/
Series		Accession: GSE80927	ID: 200080927

4156. shRNA RNA-seq from K562 (ENCSR792CBM)
(Submitter supplied) shRNA knockdown against G3BP1 in K562 cells followed by RNA-seq. (G3BP1-LV11)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80926/
Series		Accession: GSE80926	ID: 200080926

4157. shRNA RNA-seq from K562 (ENCSR780YFF)
(Submitter supplied) shRNA knockdown against FXR1 in K562 cells followed by RNA-seq. (FXR1-LV08)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80925/
Series		Accession: GSE80925	ID: 200080925

4158. shRNA RNA-seq from HepG2 (ENCSR778AJO)
(Submitter supplied) shRNA knockdown against EIF3G in HepG2 cells followed by RNA-seq. (EIF3G BGHLV14)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80924/
Series		Accession: GSE80924	ID: 200080924

4159. shRNA RNA-seq from K562 (ENCSR774BXV)
(Submitter supplied) shRNA knockdown against EIF4B in K562 cells followed by RNA-seq. (EIF4B-LV08)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80923/
Series		Accession: GSE80923	ID: 200080923

4160. shRNA RNA-seq from HepG2 (ENCSR746EKS)
(Submitter supplied) shRNA knockdown against MAGOH in HepG2 cells followed by RNA-seq. (MAGOH-BGHLV12)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80922/
Series		Accession: GSE80922	ID: 200080922

4161. shRNA RNA-seq from HepG2 (ENCSR732IYM)
(Submitter supplied) shRNA knockdown against XRCC5 in HepG2 cells followed by RNA-seq. (XRCC5 BGHLV14)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80921/
Series		Accession: GSE80921	ID: 200080921

4162. shRNA RNA-seq from HepG2 (ENCSR716WZH)
(Submitter supplied) shRNA knockdown against FASTKD2 in HepG2 cells followed by RNA-seq. (FASTKD2 BGHLV14)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80920/
Series		Accession: GSE80920	ID: 200080920

4163. shRNA RNA-seq from HepG2 (ENCSR708GKW)
(Submitter supplied) shRNA knockdown against IGF2BP1 in HepG2 cells followed by RNA-seq. (IGF2BP1 BGHLV14)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80919/
Series		Accession: GSE80919	ID: 200080919

4164. shRNA RNA-seq from K562 (ENCSR694LKY)
(Submitter supplied) shRNA knockdown against TIA1 in K562 cells followed by RNA-seq. (TIA1-LV11)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80918/
Series		Accession: GSE80918	ID: 200080918

4165. shRNA RNA-seq from K562 (ENCSR648QFY)
(Submitter supplied) shRNA knockdown against PCBP2 in K562 cells followed by RNA-seq. (PCBP2-LV11)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80917/
Series		Accession: GSE80917	ID: 200080917

4166. shRNA RNA-seq from HepG2 (ENCSR637JLM)
(Submitter supplied) shRNA knockdown against DDX3X in HepG2 cells followed by RNA-seq. (DDX3X-BGHLV12)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80916/
Series		Accession: GSE80916	ID: 200080916

4167. shRNA RNA-seq from HepG2 (ENCSR635FRH)
(Submitter supplied) shRNA knockdown against PCBP1 in HepG2 cells followed by RNA-seq. (PCBP1-BGHLV12)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80915/
Series		Accession: GSE80915	ID: 200080915

4168. shRNA RNA-seq from K562 (ENCSR629EWX)
(Submitter supplied) shRNA knockdown against IGF2BP1 in K562 cells followed by RNA-seq. (IGF2BP1-LV11)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80914/
Series		Accession: GSE80914	ID: 200080914

4169. shRNA RNA-seq from K562 (ENCSR627NVU)
(Submitter supplied) shRNA knockdown against RBM15 in K562 cells followed by RNA-seq. (RBM15-LV08)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80913/
Series		Accession: GSE80913	ID: 200080913

4170. shRNA RNA-seq from HepG2 (ENCSR622MCX)
(Submitter supplied) shRNA knockdown against U2AF2 in HepG2 cells followed by RNA-seq. (U2AF2 BGHLV14)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80912/
Series		Accession: GSE80912	ID: 200080912

4171. shRNA RNA-seq from K562 (ENCSR611ZAL)
(Submitter supplied) shRNA knockdown against TAF15 in K562 cells followed by RNA-seq. (TAF15-LV08)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80910/
Series		Accession: GSE80910	ID: 200080910

4172. shRNA RNA-seq from HepG2 (ENCSR610AEI)
(Submitter supplied) shRNA knockdown against RBM25 in HepG2 cells followed by RNA-seq. (RBM25-BGHLV12)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80909/
Series		Accession: GSE80909	ID: 200080909

4173. shRNA RNA-seq from HepG2 (ENCSR603TCV)
(Submitter supplied) Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHLV12-93-94)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80908/
Series		Accession: GSE80908	ID: 200080908

4174. shRNA RNA-seq from HepG2 (ENCSR597XHH)
(Submitter supplied) shRNA knockdown against SRSF9 in HepG2 cells followed by RNA-seq. (SRSF9-BGHLV12)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80907/
Series		Accession: GSE80907	ID: 200080907

4175. shRNA RNA-seq from HepG2 (ENCSR597IYB)
(Submitter supplied) shRNA knockdown against EXOSC9 in HepG2 cells followed by RNA-seq. (EXOSC9 BGHLV14)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80906/
Series		Accession: GSE80906	ID: 200080906

4176. shRNA RNA-seq from K562 (ENCSR577XBW)
(Submitter supplied) shRNA knockdown against FXR2 in K562 cells followed by RNA-seq. (FXR2-LV08)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80905/
Series		Accession: GSE80905	ID: 200080905

4177. shRNA RNA-seq from HepG2 (ENCSR576GOW)
(Submitter supplied) shRNA knockdown against RAVER1 in HepG2 cells followed by RNA-seq. (RAVER1 BGHLV14)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80904/
Series		Accession: GSE80904	ID: 200080904

4178. shRNA RNA-seq from HepG2 (ENCSR572AMC)
(Submitter supplied) shRNA knockdown against RECQL in HepG2 cells followed by RNA-seq. (RECQL-BGHLV12)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80903/
Series		Accession: GSE80903	ID: 200080903

4179. shRNA RNA-seq from K562 (ENCSR561CBC)
(Submitter supplied) shRNA knockdown against KHSRP in K562 cells followed by RNA-seq. (KHSRP-LV11)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80902/
Series		Accession: GSE80902	ID: 200080902

4180. shRNA RNA-seq from K562 (ENCSR560AYQ)
(Submitter supplied) shRNA knockdown against RBM34 in K562 cells followed by RNA-seq. (RBM34-LV11)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80901/
Series		Accession: GSE80901	ID: 200080901

4181. shRNA RNA-seq from K562 (ENCSR546MBH)
(Submitter supplied) shRNA knockdown against EIF2S1 in K562 cells followed by RNA-seq. (EIF2S1-LV08)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80900/
Series		Accession: GSE80900	ID: 200080900

4182. shRNA RNA-seq from K562 (ENCSR545AIK)
(Submitter supplied) shRNA knockdown against PCBP1 in K562 cells followed by RNA-seq. (PCBP1-LV11)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80899/
Series		Accession: GSE80899	ID: 200080899

4183. shRNA RNA-seq from HepG2 (ENCSR533HXS)
(Submitter supplied) shRNA knockdown against EIF2C1 in HepG2 cells followed by RNA-seq. (EIF2C1 BGHLV14)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80898/
Series		Accession: GSE80898	ID: 200080898

4184. shRNA RNA-seq from HepG2 (ENCSR529QEZ)
(Submitter supplied) shRNA knockdown against PRPF6 in HepG2 cells followed by RNA-seq. (PRPF6 BGHLV14)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80897/
Series		Accession: GSE80897	ID: 200080897

4185. shRNA RNA-seq from K562 (ENCSR529JNJ)
(Submitter supplied) shRNA knockdown against HNRNPK in K562 cells followed by RNA-seq. (HNRNPK-LV11)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80896/
Series		Accession: GSE80896	ID: 200080896

4186. shRNA RNA-seq from K562 (ENCSR527IVX)
(Submitter supplied) shRNA knockdown against PTBP1 in K562 cells followed by RNA-seq. (PTBP1-LV11)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80895/
Series		Accession: GSE80895	ID: 200080895

4187. shRNA RNA-seq from HepG2 (ENCSR500WHE)
(Submitter supplied) shRNA knockdown against XRCC6 in HepG2 cells followed by RNA-seq. (XRCC BGHLV14)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80894/
Series		Accession: GSE80894	ID: 200080894

4188. shRNA RNA-seq from HepG2 (ENCSR492UFS)
(Submitter supplied) shRNA knockdown against MATR3 in HepG2 cells followed by RNA-seq. (MATR3 17-BGHLV12)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80893/
Series		Accession: GSE80893	ID: 200080893

4189. shRNA RNA-seq from HepG2 (ENCSR491FOC)
(Submitter supplied) Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT BGHLV14)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80892/
Series		Accession: GSE80892	ID: 200080892

4190. shRNA RNA-seq from HepG2 (ENCSR485ZTC)
(Submitter supplied) shRNA knockdown against DDX21 in HepG2 cells followed by RNA-seq. (DDX21 BGHLV14)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80891/
Series		Accession: GSE80891	ID: 200080891

4191. shRNA RNA-seq from HepG2 (ENCSR478FJK)
(Submitter supplied) shRNA knockdown against IGF2BP2 in HepG2 cells followed by RNA-seq. (IGF2BP2-BGHLV12)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80890/
Series		Accession: GSE80890	ID: 200080890

4192. shRNA RNA-seq from K562 (ENCSR464ADT)
(Submitter supplied) shRNA knockdown against SRSF7 in K562 cells followed by RNA-seq. (SRSF7-LV11)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80889/
Series		Accession: GSE80889	ID: 200080889

4193. shRNA RNA-seq from HepG2 (ENCSR455VZH)
(Submitter supplied) shRNA knockdown against PABPC4 in HepG2 cells followed by RNA-seq. (PABPC4-BGHLV12)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80888/
Series		Accession: GSE80888	ID: 200080888

4194. shRNA RNA-seq from HepG2 (ENCSR424YSV)
(Submitter supplied) shRNA knockdown against AATF in HepG2 cells followed by RNA-seq. (AATF BGHLV14)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80886/
Series		Accession: GSE80886	ID: 200080886

4195. shRNA RNA-seq from HepG2 (ENCSR410UHJ)
(Submitter supplied) shRNA knockdown against RPS10 in HepG2 cells followed by RNA-seq. (RPS10 BGHLV14)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80885/
Series		Accession: GSE80885	ID: 200080885

4196. shRNA RNA-seq from HepG2 (ENCSR398LZW)
(Submitter supplied) shRNA knockdown against SND1 in HepG2 cells followed by RNA-seq. (SND1 BGHLV14)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80884/
Series		Accession: GSE80884	ID: 200080884

4197. shRNA RNA-seq from K562 (ENCSR373KOF)
(Submitter supplied) shRNA knockdown against FUBP3 in K562 cells followed by RNA-seq. (FUBP3-LV08)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80883/
Series		Accession: GSE80883	ID: 200080883

4198. shRNA RNA-seq from K562 (ENCSR361LBE)
(Submitter supplied) shRNA knockdown against NCBP2 in K562 cells followed by RNA-seq. (NCBP2-LV08)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80882/
Series		Accession: GSE80882	ID: 200080882

4199. shRNA RNA-seq from K562 (ENCSR344XID)
(Submitter supplied) Control shRNA against no target in K562 cells followed by RNA-seq. (nontarget-LV08)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80881/
Series		Accession: GSE80881	ID: 200080881

4200. shRNA RNA-seq from K562 (ENCSR342EDG)
(Submitter supplied) shRNA knockdown against U2AF1 in K562 cells followed by RNA-seq. (U2AF1-LV08)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80880/
Series		Accession: GSE80880	ID: 200080880

4201. shRNA RNA-seq from K562 (ENCSR338CON)
(Submitter supplied) shRNA knockdown against AKAP1 in K562 cells followed by RNA-seq. (AKAP1-LV08)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80879/
Series		Accession: GSE80879	ID: 200080879

4202. shRNA RNA-seq from HepG2 (ENCSR330YOU)
(Submitter supplied) shRNA knockdown against QKI in HepG2 cells followed by RNA-seq. (QKI-BGHLV12)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80878/
Series		Accession: GSE80878	ID: 200080878

4203. shRNA RNA-seq from HepG2 (ENCSR318HAT)
(Submitter supplied) shRNA knockdown against RBM34 in HepG2 cells followed by RNA-seq. (RBM34 BGHLV14)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80876/
Series		Accession: GSE80876	ID: 200080876

4204. shRNA RNA-seq from HepG2 (ENCSR313CHR)
(Submitter supplied) shRNA knockdown against EIF4B in HepG2 cells followed by RNA-seq. (EIF4B-BGHLV12)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80875/
Series		Accession: GSE80875	ID: 200080875

4205. shRNA RNA-seq from K562 (ENCSR310VND)
(Submitter supplied) shRNA knockdown against RECQL in K562 cells followed by RNA-seq. (RECQL-LV08)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80874/
Series		Accession: GSE80874	ID: 200080874

4206. shRNA RNA-seq from K562 (ENCSR302JQA)
(Submitter supplied) shRNA knockdown against IGF2BP3 in K562 cells followed by RNA-seq. (IGF2BP3-LV11)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80873/
Series		Accession: GSE80873	ID: 200080873

4207. shRNA RNA-seq from HepG2 (ENCSR300IEW)
(Submitter supplied) shRNA knockdown against DDX24 in HepG2 cells followed by RNA-seq. (DDX24 BGHLV14)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80872/
Series		Accession: GSE80872	ID: 200080872

4208. shRNA RNA-seq from HepG2 (ENCSR295XKC)
(Submitter supplied) shRNA knockdown against GTF2F1 in HepG2 cells followed by RNA-seq. (GTF2F1 BGHLV14)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80871/
Series		Accession: GSE80871	ID: 200080871

4209. shRNA RNA-seq from K562 (ENCSR256PLH)
(Submitter supplied) shRNA knockdown against QKI in K562 cells followed by RNA-seq. (QKI-LV08)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80870/
Series		Accession: GSE80870	ID: 200080870

4210. shRNA RNA-seq from K562 (ENCSR253DCB)
(Submitter supplied) shRNA knockdown against ASCC1 in K562 cells followed by RNA-seq. (ASCC1-LV08)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80869/
Series		Accession: GSE80869	ID: 200080869

4211. shRNA RNA-seq from K562 (ENCSR246SOU)
(Submitter supplied) shRNA knockdown against G3BP2 in K562 cells followed by RNA-seq. (G3BP2-LV08)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80868/
Series		Accession: GSE80868	ID: 200080868

4212. shRNA RNA-seq from HepG2 (ENCSR237YZT)
(Submitter supplied) Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHLV12-01-02)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80867/
Series		Accession: GSE80867	ID: 200080867

4213. shRNA RNA-seq from HepG2 (ENCSR230ORC)
(Submitter supplied) shRNA knockdown against CIRBP in HepG2 cells followed by RNA-seq. (CIRBP-BGHLV12)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80866/
Series		Accession: GSE80866	ID: 200080866

4214. shRNA RNA-seq from K562 (ENCSR201WFU)
(Submitter supplied) shRNA knockdown against RDBP in K562 cells followed by RNA-seq. (RDBP-LV11)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80865/
Series		Accession: GSE80865	ID: 200080865

4215. shRNA RNA-seq from HepG2 (ENCSR193FFA)
(Submitter supplied) shRNA knockdown against ASCC1 in HepG2 cells followed by RNA-seq. (ASCC1-BGHLV12)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80864/
Series		Accession: GSE80864	ID: 200080864

4216. shRNA RNA-seq from HepG2 (ENCSR185JGT)
(Submitter supplied) shRNA knockdown against SLTM in HepG2 cells followed by RNA-seq. (SLTM BGHLV14)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80863/
Series		Accession: GSE80863	ID: 200080863

4217. shRNA RNA-seq from K562 (ENCSR149DMY)
(Submitter supplied) shRNA knockdown against RBM25 in K562 cells followed by RNA-seq. (RBM25-LV08)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80862/
Series		Accession: GSE80862	ID: 200080862

4218. shRNA RNA-seq from HepG2 (ENCSR148MQK)
(Submitter supplied) shRNA knockdown against SF3B4 in HepG2 cells followed by RNA-seq. (SF3B4-BGHLV12)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80861/
Series		Accession: GSE80861	ID: 200080861

4219. shRNA RNA-seq from HepG2 (ENCSR147ZBD)
(Submitter supplied) shRNA knockdown against DDX6 in HepG2 cells followed by RNA-seq. (DDX6-BGHLV12)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80860/
Series		Accession: GSE80860	ID: 200080860

4220. shRNA RNA-seq from K562 (ENCSR134JRE)
(Submitter supplied) shRNA knockdown against TARDBP in K562 cells followed by RNA-seq. (TARDBP-LV11)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80859/
Series		Accession: GSE80859	ID: 200080859

4221. shRNA RNA-seq from K562 (ENCSR129RWD)
(Submitter supplied) Control shRNA against no target in K562 cells followed by RNA-seq. (Nontarget-LV11)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80858/
Series		Accession: GSE80858	ID: 200080858

4222. shRNA RNA-seq from K562 (ENCSR119QWQ)
(Submitter supplied) shRNA knockdown against DDX6 in K562 cells followed by RNA-seq. (DDX6-LV08)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80857/
Series		Accession: GSE80857	ID: 200080857

4223. shRNA RNA-seq from K562 (ENCSR113HRG)
(Submitter supplied) shRNA knockdown against SRSF9 in K562 cells followed by RNA-seq. (SRSF9-LV11)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80856/
Series		Accession: GSE80856	ID: 200080856

4224. shRNA RNA-seq from HepG2 (ENCSR094KBY)
(Submitter supplied) shRNA knockdown against SRSF1 in HepG2 cells followed by RNA-seq. (SRSF1-BGHLV12)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80855/
Series		Accession: GSE80855	ID: 200080855

4225. shRNA RNA-seq from K562 (ENCSR081XRA)
(Submitter supplied) shRNA knockdown against SF3B4 in K562 cells followed by RNA-seq. (SF3B4-LV08)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80854/
Series		Accession: GSE80854	ID: 200080854

4226. shRNA RNA-seq from HepG2 (ENCSR081QQH)
(Submitter supplied) shRNA knockdown against ZRANB2 in HepG2 cells followed by RNA-seq. (ZRANB2 BGHLV14)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80853/
Series		Accession: GSE80853	ID: 200080853

4227. shRNA RNA-seq from K562 (ENCSR079IPT)
(Submitter supplied) shRNA knockdown against TBRG4 in K562 cells followed by RNA-seq. (TBRG4-LV08)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80852/
Series		Accession: GSE80852	ID: 200080852

4228. shRNA RNA-seq from HepG2 (ENCSR074UZM)
(Submitter supplied) shRNA knockdown against G3BP1 in HepG2 cells followed by RNA-seq. (G3BP1-BGHLV12)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80851/
Series		Accession: GSE80851	ID: 200080851

4229. shRNA RNA-seq from K562 (ENCSR067LLB)
(Submitter supplied) shRNA knockdown against DDX24 in K562 cells followed by RNA-seq. (DDX24-LV08)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80849/
Series		Accession: GSE80849	ID: 200080849

4230. shRNA RNA-seq from K562 (ENCSR066VOO)
(Submitter supplied) shRNA knockdown against SRSF1 in K562 cells followed by RNA-seq. (SRSF1-LV11)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80848/
Series		Accession: GSE80848	ID: 200080848

4231. shRNA RNA-seq from HepG2 (ENCSR064DXG)
(Submitter supplied) shRNA knockdown against PTBP1 in HepG2 cells followed by RNA-seq. (PTBP1-BGHLV12)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80847/
Series		Accession: GSE80847	ID: 200080847

4232. shRNA RNA-seq from HepG2 (ENCSR057GCF)
(Submitter supplied) shRNA knockdown against TIA1 in HepG2 cells followed by RNA-seq. (TIA1-BGHLV12)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80846/
Series		Accession: GSE80846	ID: 200080846

4233. shRNA RNA-seq from K562 (ENCSR056QEW)
(Submitter supplied) shRNA knockdown against CIRBP in K562 cells followed by RNA-seq. (CIRBP-LV11)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80845/
Series		Accession: GSE80845	ID: 200080845

4234. shRNA RNA-seq from K562 (ENCSR047EEG)
(Submitter supplied) shRNA knockdown against PABPC4 in K562 cells followed by RNA-seq. (PABPC4-LV08)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80844/
Series		Accession: GSE80844	ID: 200080844

4235. shRNA RNA-seq from HepG2 (ENCSR030GZQ)
(Submitter supplied) shRNA knockdown against TRA2A in HepG2 cells followed by RNA-seq. (TRA2A BGHLV14)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80843/
Series		Accession: GSE80843	ID: 200080843

4236. shRNA RNA-seq from HepG2 (ENCSR030ARO)
(Submitter supplied) shRNA knockdown against NCBP2 in HepG2 cells followed by RNA-seq. (NCBP2-BGHLV12)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80842/
Series		Accession: GSE80842	ID: 200080842

4237. shRNA RNA-seq from HepG2 (ENCSR028ITN)
(Submitter supplied) shRNA knockdown against PCBP2 in HepG2 cells followed by RNA-seq. (PCBP2 BGHLV14)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80841/
Series		Accession: GSE80841	ID: 200080841

4238. shRNA RNA-seq from HepG2 (ENCSR017PRS)
(Submitter supplied) shRNA knockdown against SRSF7 in HepG2 cells followed by RNA-seq. (SRSF7-BGHLV12)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80840/
Series		Accession: GSE80840	ID: 200080840

4239. shRNA RNA-seq from HepG2 (ENCSR016IDR)
(Submitter supplied) shRNA knockdown against AKAP1 in HepG2 cells followed by RNA-seq. (AKAP1-BGHLV12)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80839/
Series		Accession: GSE80839	ID: 200080839

4240. shRNA RNA-seq from HepG2 (ENCSR010ZMZ)
(Submitter supplied) shRNA knockdown against HLTF in HepG2 cells followed by RNA-seq. (HLTF BGHLV14)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80838/
Series		Accession: GSE80838	ID: 200080838

4241. shRNA RNA-seq from HepG2 (ENCSR009PPI)
(Submitter supplied) shRNA knockdown against FXR1 in HepG2 cells followed by RNA-seq. (FXR1-BGHLV12)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80837/
Series		Accession: GSE80837	ID: 200080837

4242. shRNA RNA-seq from HepG2 (ENCSR003EKR)
(Submitter supplied) Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT BGHLV14 1)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80836/
Series		Accession: GSE80836	ID: 200080836

4243. shRNA RNA-seq from K562 (ENCSR000KYM)
(Submitter supplied) shRNA knockdown against DDX3X in K562 cells followed by RNA-seq. (DDX3X-LV08)  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80835/
Series		Accession: GSE80835	ID: 200080835

4244. Expression profiling of MCF-7 cells with 10nM treatment of TCDD
(Submitter supplied) The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that is regulated by environmental toxicants that function as AHR agonists such as 2,3,7,8 tetrachlorodibenzo-p-dioxin (TCDD).  L-Type Amino Acid Transporter 1 (LAT1) is a leucine uptake transporter that is overexpressed in cancer.  The regulation of LAT1 by AHR in MCF-7 and MDA-MB-231 breast cancer cells (BCCs) was investigated in this report. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76608/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA308136
Series		Accession: GSE76608	ID: 200076608

4245. Transcription Profiles of Regulatory T Cells in Follicular Lymphoma Lymph Nodes, Normal Lymph Nodes and Reactive Lymph Nodes
(Submitter supplied) We have previously shown that Tregs infiltrating follicular lymphoma lymph nodes (FLN) are quantitatively and qualitatively different than those infiltrating normal and reactive nodes (NLN, RLN, respectively). To gain insight into how such Treg populations differ, we performed RNA sequence (RNAseq) analyses on flow sorted Tregs from all three sources. We identify several molecules that could contribute to the observed increased suppressive capacity of FLN tregs, including upregulation of CTLA-4, IL-10, and GITR, all confirmed by protein expression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL13393 27 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74102/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA299009
Series		Accession: GSE74102	ID: 200074102

4246. Patient-derived xenograft platform for metastatic melanoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL11154 18 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73738/
Series		Accession: GSE73738	ID: 200073738

4247. Fra-1 is a key driver of colon cancer metastasis and a Fra-1 classifier predicts disease-free survival
(Submitter supplied) Background and Aim: Fra-1 (Fos-related antigen-1) is a member of the AP1 (activator protein-1) family of transcription factors. We have recently shown that Fra-1 is necessary for breast cancer cells to metastasize in vivo, and that breast cancer outcome can be predicted by a classifier comprising genes that are expressed in a Fra-1-dependent fashion. Here, we show that Fra-1 plays an important role also in colon cancer progression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69415/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA285461
Series		Accession: GSE69415	ID: 200069415

4248. Transcriptome of RA-responsive and RA-resistant breast cancer cell lines
(Submitter supplied) Retinoic acid (RA), the main active vitamin A metabolite, controls multiple biological processes such as cell proliferation and differentiation through genomic programs and kinase cascades activation. Several breast cancer cells respond to the antiproliferative effects of RA, but others are RA-resistant. In several cases resistance has been correlated to the amplification of the erb-b2 receptor tyrosine kinase 2 (ERBB2) gene, but the overall signaling and transcriptional pathways that are altered in such cells have not been elucidated. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81814/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA322613
Series		Accession: GSE81814	ID: 200081814

4249. The lncRNA LUST promotes CCICs self-renewal stimulating the wnt/b-catenin signaling activation
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL9052 7 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69236/
Series		Accession: GSE69236	ID: 200069236

4250. The lncRNA LUST promotes CCICs self-renewal stimulating the wnt/b-catenin signaling activation [RNA-Seq]
(Submitter supplied) Comprehensive RNA-seq experiments in CD24bright/CD44bright (CCICs), CD24dim/CD44dim (more differentiated counterpart) cells and colonospheres delineate the role of the lncRNA LUST  in promoting CCICs self-renewal.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69233/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA284941
Series		Accession: GSE69233	ID: 200069233

4251. RNA-Seq of siRNA-mediated knockdown of the lncRNA SLNCR1 in WM1976 melanoma cells
(Submitter supplied) RNA-Seq was used to profile transcriptional changes induced by siRNA knockdown of the long non-coding RNA SLNCR1.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77902/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA311991
Series		Accession: GSE77902	ID: 200077902

4252. RNA-Seq of SLNCR1 over-expression in the melanoma cell line A375
(Submitter supplied) RNA-Seq was used to profile transcriptional changes induced by overexpression of the long non-coding RNA SLNCR1, as well as mutant version SLNCR1 delta conserved and SLNCR1 conserved.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77901/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA311990
Series		Accession: GSE77901	ID: 200077901

4253. HCT116 MYC 3' TBE1 (WT) and KO RNA-Seq
(Submitter supplied) mRNA was sequenced from HCT116 MYC 3' TBE1 (WT) and KO cells to identify genes differentially expressed after deletion of the MYC 3' TBE1
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70833/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA289658
Series		Accession: GSE70833	ID: 200070833

4254. RNA-Seq of over-expression and knockdown of the lncRNA SLNCR1 in melanoma cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77903/
Series		Accession: GSE77903	ID: 200077903

4255. DDX3X regulation of global translation is impaired by medulloblastoma-associated mutations
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL11154 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59096/
Series		Accession: GSE59096	ID: 200059096

4256. DDX3X regulation of global translation is impaired by medulloblastoma-associated mutations [RiboSeq]
(Submitter supplied) Whole-genome sequencing recently identified recurrent missense mutations in the RNA helicase DDX3X in pediatric medulloblastoma (MB) and other tumors. The normal function of DDX3X is poorly understood, and the consequences of its cancer-associated mutations have not been explored. Here we used genomic, biochemical, cell biological, and animal modeling approaches to investigate normal DDX3X function and the impact of cancer-associated DDX3X mutations. more...
Organism:	Homo sapiens
Type:		Other; Expression profiling by high throughput sequencing
Platform: GPL11154 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59095/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA254361
Series		Accession: GSE59095	ID: 200059095

4257. DDX3X regulation of global translation is impaired by medulloblastoma-associated mutations [RNA-Seq]
(Submitter supplied) Whole-genome sequencing recently identified recurrent missense mutations in the RNA helicase DDX3X in pediatric medulloblastoma (MB) and other tumors. The normal function of DDX3X is poorly understood, and the consequences of its cancer-associated mutations have not been explored. Here we used genomic, biochemical, cell biological, and animal modeling approaches to investigate normal DDX3X function and the impact of cancer-associated DDX3X mutations. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59093/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA254363
Series		Accession: GSE59093	ID: 200059093

4258. An extensive program of periodic alternative splicing linked to cell cycle progression
(Submitter supplied) Progression through the mitotic cell cycle requires periodic regulation of gene function at the levels of transcription, translation, protein-protein interactions, post-translational modification and degradation. However, the role of alternative splicing (AS) in the temporal control of cell cycle is not well understood. By sequencing the human transcriptome through two continuous cell cycles, we identify ~1,300 genes with cell cycle-dependent AS changes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL11154 22 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81485/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA321855
Series		Accession: GSE81485	ID: 200081485

4259. The Glioma-Infiltrating T Cell Receptor Repertoire
(Submitter supplied) While immune signaling has emerged as a defining feature of the glioma microenvironment, local selection of responding T cells and their anti-tumor potential as a population are difficult to measure directly in patients. High-throughput sequencing of T cell receptor repertoires (TCRseq) provides a population-wide statistical description of how T cells respond to disease.  Here, we define new immunophenotypes in glioma based on TCRseq and RNA-Seq of tumor tissue, non-neoplastic brain tissue, and peripheral blood from patients. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL11154 GPL15520 75 Samples
FTP download: GEO (TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79338/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA315543
Series		Accession: GSE79338	ID: 200079338

4260. Modeling genome-wide transcriptional cis-regulation in n LNCaP-abl cell line after siRNA knock down of a series of gene factors [RNA-seq]
(Submitter supplied) We describe, MARGE, Model-based Analysis of the Regulation of Gene Expression, a robust methodology that leverages a large library of genome-wide H3K27ac ChIP-seq profiles to predict key regulated genes and cis-regulatory regions in human or mouse. MARGE adopts a gene centric approach to define a regulatory potential that summarizes the aggregate activity of multiple cis-regulatory elements on each gene. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72534/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA294290
Series		Accession: GSE72534	ID: 200072534

4261. Transcriptional response to the HSP70 inhibitor MAL3-101 in parental rhabdomyosarcoma cells and isogenic acquired-resistance lines.
(Submitter supplied) We demonstrate that inhibition of HSP70 with MAL3-101 induces activation of the unfolded protein response, and that cells with acquired resistance upregulate a cytosolic HSP70 at the level of mRNA.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80525/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA319193
Series		Accession: GSE80525	ID: 200080525

4262. H3K36 mutations promote sarcomagenesis through genome-wide remodeling of H3K36 and H3K27 methylation [RNA_Chondroblastoma_H3K36M_H3WT]
(Submitter supplied) The goal of this study is to understand the genome-wide alterations in chromatin landscapy induced by a histone mutation (H3.3 K36M) derived from chondroblastomas
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75853/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA305540
Series		Accession: GSE75853	ID: 200075853

4263. Subtypes of HPV-positive head and neck cancers are associated with HPV characteristics, copy number variations, PIK3CA mutation, and pathway signatures.
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; SNP genotyping by SNP array; Genome variation profiling by SNP array
Platforms: GPL11154 GPL18900 GPL19699 108 Samples
FTP download: GEO (IDAT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74956/
Series		Accession: GSE74956	ID: 200074956

4264. Subtypes of HPV-positive head and neck cancers are associated with HPV characteristics, copy number variations, PIK3CA mutation, and pathway signatures. [RNA-Seq]
(Submitter supplied) Purpose: There is substantial heterogeneity within the human papillomavirus (HPV) positive head and neck cancer (HNC) tumors that predispose them to different outcomes, however this subgroup is poorly characterized due to various historical reasons.  Experimental Design: we perform unsupervised gene expression clustering on well-annotated HPV(+) HNC samples from two cohorts ( 84 total primary tumors), as well as 18 HPV(-) HNCs, to discover subtypes, and begin to characterize the differences between the subtypes in terms of their HPV characteristics, pathway activity, whole-genome somatic copy number variations and mutation frequencies. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 36 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74927/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA301936
Series		Accession: GSE74927	ID: 200074927

4265. H3K36 mutations promote sarcomagenesis through genome-wide remodeling of H3K36 and H3K27 methylation
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Drosophila melanogaster; Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL16791 GPL17021 GPL21227 69 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69291/
Series		Accession: GSE69291	ID: 200069291

4266. Functional characterization of RNA-binding protein IMP2 in primary Glioma cell lines
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by array
4 related Platforms 31 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73847/
Series		Accession: GSE73847	ID: 200073847

4267. Functional characterization of RNA-binding protein IMP2 in primary Glioma cell lines [HTS]
(Submitter supplied) Cancer stem cells (CSC) dictate tumor cell heterogeneity in diverse cancer types and arise, in part, from microRNA (miRNA)-dependent alteration of gene expression. The let-7 miRNA family induces differentiation by silencing genes that maintain stemness and is repressed by the RNA-binding proteins LIN28A/B, which preserve stemness in normal embryonic and malignant cells. Here, we observed that LIN28A/B is undetectable in glioma stem cells (GSC) whereas let-7 and, paradoxically, their target genes are highly expressed. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL19057 GPL18573 GPL16791 25 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73845/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA298216
Series		Accession: GSE73845	ID: 200073845

4268. Ileal pouch transcriptomics reveal shared pathogenesis between pouchitis and ulcerative colitis
(Submitter supplied) UC pouchitis is a potential model of UC. We prospectively examined the pouch transcriptomes of UC and familial adenomatous polyposis (FAP) IPAA patients to unveil molecular mechanisms of UC pouchitis susceptibility. Methods: Total RNA was isolated using the AllPrep DNA/RNA Mini Kit (QIAGEN, Cat No. 8020). RNA quality was evaluated using Bioanalyzer (Agilent, Santa Clara, CA). All RNA samples displayed RNA Integrity Number (RIN) >7. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 77 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81266/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA321131
Series		Accession: GSE81266	ID: 200081266

4269. Negative control of CSL gene transcription by stress/DNA damage response and p53 [RNA-Seq]
(Submitter supplied) CSL is a key transcription factor, mostly acting as a repressor. While known as main effector of Notch signaling, it can also play Notch-independent functions. Despite the wide interest in CSL, the mechanisms responsible for its own regulation have been little studied. We recently showed that CSL down-modulation in human dermal fibroblasts (HDFs) leads to conversion into cancer associated fibroblasts, which promote keratinocyte tumor development. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 46 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77370/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA310177
Series		Accession: GSE77370	ID: 200077370

4270. Next-Generation Sequencing reveals the effects of MYC silencing in gastric cancer cell lines from northern Brazil
(Submitter supplied) Purpose: In carcinogenesis, the stomach, the MYC gene is frequently amplified and its protein is overexpressed, which contributes to uncontrolled cell proliferation mucosal gástrica.Três cell lines were subjected to sequencing semiconductor Proton Ion before and after the silencing of MYC. These lines were originating from diffuse and intestinal histologic types and the third of a metastasis from a stomach tumor originating in a ascites. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17301 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81265/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJEB7457
Series		Accession: GSE81265	ID: 200081265

4271. Nfib promotes Metastasis through a Widespread Increase in Chromatin Accessibility
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL16417 GPL17021 GPL16791 91 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81258/
Series		Accession: GSE81258	ID: 200081258

4272. Transcriptional profiling of JEG3 cells with HLA-G ablation via deletion of Enhancer L
(Submitter supplied) HLA-G is a nonclassical HLA molecule expressed specifically in the placenta. While it is known to play a central role in maternal immune tolerance during pregnancy, the mechanism underlying its tissue-specific expression remains poorly understood. To elucidate this mechanism, we used a Massively Parallel Reporter Assay (MPRA) to systematically interrogate the HLA-G locus. This uncovered Enhancer L, a novel cis-regulatory element with enhancer activity 12kb upstream of HLA-G. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (DIFF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79779/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA316990
Series		Accession: GSE79779	ID: 200079779

4273. Disruption of Na+/H+ exchanger regulatory factor 2 scaffold suppresses colon cancer proliferation
(Submitter supplied) A key function of Na+/H+ exchanger regulatory factor 2 (NHERF2) is spatial organization of signaling proteins to facilitate signal transduction. The role of NHERF2 in cancer progress is not well understood. This study determines how loss of NHERF2 alter colon cancer progress.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 9 Samples
FTP download: GEO (TAR, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67931/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA281231
Series		Accession: GSE67931	ID: 200067931

4274. Transcriptome profiling of Caki2 cells re-expressing Polybromo-1 (PBRM1)
(Submitter supplied) PBRM1 is a component of the PBAF chromatin remodelling complex and has been observed to be deregulated in a significant proportion of patients with clear-cell Renal Cell Carcinoma (ccRCC). This study employs RNA-Seq to identify differentially expressed genes in cellular models of ccRCC by expressing PBRM1 in PBRM1-deficient Caki2 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76199/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA306616
Series		Accession: GSE76199	ID: 200076199

4275. Comparison of gene expression profiles between FRA1 knockdown and vector control Bel-7402 cells by RNA-sequencing
(Submitter supplied) The purpose of this experiment is to search for the transcriptional target of FRA1.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68005/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA281484
Series		Accession: GSE68005	ID: 200068005

4276. Comparative proteomics and transcriptomics study of signaling network proteins across multiple normal and cancer cell lines
(Submitter supplied) It is not known whether cancer cells generally show quantitative differences in the expression of signaling pathway proteins that could dysregulate signal transduction. To explore this issue, we first defined the primary components of the EGFR-MAPK pathway in normal human mammary epithelial cells, identifying 16 core proteins and 10 feedback regulators. We then quantified their absolute abundance at both the protein and mRNA level across a panel of normal and breast cancer cell lines. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9442 7 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81032/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA320318
Series		Accession: GSE81032	ID: 200081032

4277. RNA-seq of 50 paired hepatocellular carcinoma
(Submitter supplied) RNA-seq of Illumina sequencing of 50 paired normal and tumor samples
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 100 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77314/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA310012
Series		Accession: GSE77314	ID: 200077314

4278. Transcriptionally inactive ATF2 variant drives melanomagenesis
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL17303 GPL6885 14 Samples
FTP download: GEO (IDAT, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81014/
Series		Accession: GSE81014	ID: 200081014

4279. Cooperation of Nutlin-3a and a Wip1 inhibitor to induce p53 activity
(Submitter supplied) Targeting the Mdm2 oncoprotein by drugs has the potential of re-establishing p53 function and tumor suppression. However, Mdm2-antagonizing drug candidates, e. g. Nutlin-3a, often fail to abolish cancer cell growth sustainably. To overcome these limitations, we inhibited Mdm2 and simultaneously a second negative regulator of p53, the phosphatase Wip1/PPM1D. When combining Nutlin-3a with the Wip1 inhibitor GSK2830371 in the treatment of p53-proficient but not p53-deficient cells, we observed enhanced phosphorylation (Ser 15) and acetylation (Lys 382) of p53, increased expression of p53 target gene products, and synergistic inhibition of cell proliferation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80716/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA319792
Series		Accession: GSE80716	ID: 200080716

4280. mRNA expression of breast cancer cell lines across different densities [SCRB-Seq]
(Submitter supplied) mRNA expression profiles for 3 breast cancer cell lines seeded at different density and grown for different duration
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 87 Samples
FTP download: GEO (DAT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80297/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA318513
Series		Accession: GSE80297	ID: 200080297

4281. RBPJ Maintains Brain Tumor Initiating Cells through CDK9-mediated Transcriptional Elongation
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL18573 GPL16791 18 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79736/
Series		Accession: GSE79736	ID: 200079736

4282. RNA-seq Profiles in RBPJ Maintains Brain Tumor Initiating Cells through CDK9-mediated Transcriptional Elongation
(Submitter supplied) Glioblastomas coopt stem cell regulatory pathways to maintain brain tumor initiating cells (BTICs), also known as cancer stem cells.  Notch signaling has been a molecular target in BTICs, but Notch antagonists have demonstrated limited efficacy in clinical trials.  RBPJ is considered a central transcriptional mediator of Notch activity. Here, we report that pharmacologic Notch inhibitors were less effective than targeting RBPJ in suppressing tumor growth. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79735/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA316861
Series		Accession: GSE79735	ID: 200079735

4283. Sensitivity and engineered resistance of myeloid leukemia cells to BRD9 inhibition
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL11154 GPL13112 47 Samples
FTP download: GEO (BIGWIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79391/
Series		Accession: GSE79391	ID: 200079391

4284. Sensitivity and engineered resistance of myeloid leukemia cells to BRD9 inhibition (RNA-seq)
(Submitter supplied) Our study shows that acute myeloid leukemia (AML) cells require the BRD9 subunit of the SWI/SNF chromatin remodeling complex to sustain MYC transcription, rapid cell proliferation, and a block in differentiation. Based on these observations, we derived small-molecule inhibitors of the BRD9 bromodomain, which selectively suppressed the proliferation of mouse and human AML cell lines. To establish these effects as on-target, we engineered a bromodomain-swap allele of BRD9, which retains functionality despite a radically altered bromodomain pocket. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL13112 33 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79284/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA315563
Series		Accession: GSE79284	ID: 200079284

4285. Targetting super enhancer associated oncogenes in esophageal squamous cell carcinoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 16 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76861/
Series		Accession: GSE76861	ID: 200076861

4286. Targetting super enhancer associated oncogenes in esophageal squamous cell carcinoma [RNA-seq]
(Submitter supplied) Esophageal squamous cell carcinoma (ESCC) is an aggressive malignancy and the major histological subtype of esophageal cancer. Although recent large-scale genomic analysis has improved the description of the genetic abnormalities of ESCC, few targetable genomic lesions were identified and no molecular-based therapy is available. To identify druggable candidates in this tumor, we performed high-throughput small-molecule inhibitor screening. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76860/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA308805
Series		Accession: GSE76860	ID: 200076860

4287. H2O2-treated and untreated HCT116 cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75964/
Series		Accession: GSE75964	ID: 200075964

4288. RNA-seq Generated Transcriptional Profile of H2O2 Treated HCT116 vs. Untreated HCT116
(Submitter supplied) Oxidative stress, is considered to be a key risk state for a variety of human diseases, which can upregulate transcriptional expression of DNA repair genes. However, it remains elusive whether all or just a portion of DNA repair genes can be upregulated in response to oxidative stress. Therefore, the changes in expression pattern of DNA repair genes and how they are regulated in response to oxidative stress need to be elucidated. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75962/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA305863
Series		Accession: GSE75962	ID: 200075962

4289. Neuronal cell lines as model dorsal root ganglion neurons: a transcriptomic comparison
(Submitter supplied) Aim: Dorsal root ganglion neuron-derived immortal cell lines including ND7/23 and F-11 cells have been used extensively as in vitro model systems of native peripheral sensory neurons. However, while it is clear that some sensory neuron-specific receptors and ion channels are present in these cell lines, a systematic comparison of the molecular targets expressed by these cell lines with intact peripheral neurons is lacking. more...
Organism:	Homo sapiens; Rattus rattus; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL21221 GPL11154 GPL13112 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75811/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA305415
Series		Accession: GSE75811	ID: 200075811

4290. Genes regulated by dimethyl-2-ketoglutarate (DKG) in breast cancer cells
(Submitter supplied) We report the gene expression profile of DKG-treated MDA-MB-231 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74031/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA298777
Series		Accession: GSE74031	ID: 200074031

4291. U1 snRNP regulates alternative polyadenylation in DNA damage response
(Submitter supplied) The DNA damage response (DDR) involves coordinated control of gene expression and DNA repair. Using deep sequencing we found widespread changes of  alternative cleavage and polyadenylation (APA) site usage upon UV-treatment in mammalian cells. APA regulation in the 3’ untranslated region (3’UTR) is substantial, leading to both shortening and lengthening of 3’UTRs. Interestingly, a strong activation of intronic APA sites is detected, resulting in widespread expression of truncated transcripts. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL9115 3 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71801/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA292106
Series		Accession: GSE71801	ID: 200071801

4292. Gene expression analysis of human cell lines established from normal patient's fibroblast and BWS patients with known mutations in the CDKN1C and KCNQ1OT1
(Submitter supplied) Gene expression profiling was carried out in one normal human fibroblast cell line established from normal people and three different cell lines established from BWS patients to characterize the molecular mechanisms relevant to the etiology of BWS and tumor development. Whole-transcriptome sequencing of three BWS fibroblastic cell lines was established from patients with mutation in the CDKN1C mutation (CDKN1C+ cell line), and loss of methylation in the KCNQ1OT1 region (KvDMR+ cell line: with KvDMR molecular defect, and KvDMR- cell line: absence of KvDMR molecular defect but it had some clinical signs of BWS)
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69737/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA286305
Series		Accession: GSE69737	ID: 200069737

4293. Transcriptionally inactive ATF2 variant drives melanomagenesis [Seq]
(Submitter supplied) Characterized by striking metastatic propensity and chemoresistance, melanoma is among the most lethal cutaneous malignancies. The transcription factor ATF2 was shown to elicit oncogenic activities in melanoma, and its inhibition attenuates melanoma development. Here, a mouse model engineered to express a transcriptionally inactive form of Atf2 (Atf2?8,9) was found to be sufficient to induce nevi formation and, when crossed with BrafV600E animals, to promote melanoma development. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79917/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA317371
Series		Accession: GSE79917	ID: 200079917

4294. Proteasome machinery is instrumental in a common gain-of-function program of the p53 missense mutants in cancer.
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL10558 GPL11154 30 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68249/
Series		Accession: GSE68249	ID: 200068249

4295. Proteasome machinery is instrumental in a common gain-of-function program of the p53 missense mutants in cancer.
(Submitter supplied) Mutant p53 proteins, resulting from the missense mutations of the TP53 tumor suppressor gene, possess gain-of-function activities and are among the most robust oncoproteins in human tumors. They are potentially important therapeutic targets. No studies to date have distinguished common, therapeutically relevant mutant p53 gain-of-function effects from effects specific to different mutant variants and cell backgrounds. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68248/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA282134
Series		Accession: GSE68248	ID: 200068248

4296. Fixed tissue ChIP-Seq (FiT-Seq) of archived clinical samples reveals chromatin dynamics and tumor-specific enhancer profiles
(Submitter supplied) Analysis of cancer epigenomes has revealed important insights into key lineage determinants and oncogenic drivers. Chromatin immune-precipitation followed by next generation sequencing (ChIP-seq) has allowed the comprehensive mapping of transcription factor cistromes and histone modifications in fresh or frozen cells and tissues. It has not been possible, however, to apply ChIP-seq to the vast majority of clinical tissue samples, owing to the very extensive tissue fixation and cross-linking introduced during routine pathological processing. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 109 Samples
FTP download: GEO (BW, FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73398/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA296916
Series		Accession: GSE73398	ID: 200073398

4297. FBXO10 deficiency and BTK activation upregulate BCL2 expression in mantle cell lymphoma
(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to identify BTK targets by RNA-seq and high-throughput data analysis and verify these genes by quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods Methods: mino/z138 sc4/shbtk stable cell lines were generated with tet-on system vector, small hairpins were induced for 48 hours after doxycycline addition, mRNA was exacted and used for RNA sequencing. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80563/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA319310
Series		Accession: GSE80563	ID: 200080563

4298. RNA-Seq following PCR-based sorting reveals rare cell transcriptional signatures
(Submitter supplied) Background: Rare cell subtypes can profoundly impact the course of human health and disease, yet their presence within a sample is often missed with bulk molecular analysis.  Single-cell analysis tools such as FACS, FISH-FC and single-cell barcode-based sequencing can investigate cellular heterogeneity; however, they have significant limitations that impede their ability to identify and transcriptionally characterize many rare cell subpopulations. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80551/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA319253
Series		Accession: GSE80551	ID: 200080551

4299. ChIP-seq and RNA-seq analysis of KMT2D-silenced metastatic melanoma cells
(Submitter supplied) Purpose: Study of the mechanism trough which KTM2D regulates chromatin modification and transcription in a xenograft model of human metatstatic melanoma Methods: We generated patient derived xenografts (PDXs) from metastatic melanoma (MM) biopsies of three different patients.  The MMs carry NRASQ61L, NRASQ61Q or BRAFV600 mutations. Cells from secondary PDX (PDX2) were transduced with lentiviral vectors carrying Luciferase (shLuc) and KMT2D (shKMT2D) hairpins and mRNA profiles and genome-wide chromatin-state maps were generated by deep sequencing using Illumina HiSeq2000. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 40 Samples
FTP download: GEO (BIGWIG, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71854/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA292318
Series		Accession: GSE71854	ID: 200071854

4300. RNA sequencing of siSNRNP40 in breast cancer cells
(Submitter supplied) To identify gene expression profile changes upon SNRNP40 depletion, RNA-sequencing was performed on breast cancer cells transfected with siRNAs targeting SNRNP40.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78527/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA313216
Series		Accession: GSE78527	ID: 200078527

4301. Genome-wide definition of regulatory elements in hematopoietic stem cell differentiation [RNA-seq (CAGE)]
(Submitter supplied) The rapidly expanding information on the structural and functional characteristics of the human genome allows the development of genome-wide approaches to investigate the molecular circuitry wiring the genetic and epigenetic programs of clinically relevant stem/progenitor cells. Here, we define the transcriptional and epigenetic profile of human hematopoietic stem/progenitor cells (HSPC) and their committed, early myeloid and erythroid progeny. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70674/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA270570
Series		Accession: GSE70674	ID: 200070674

4302. Human Induced Pluripotent Stem Cells Recapitulate Breast Cancer Patients’ Predilection to Doxorubicin-Induced Cardiotoxicity
(Submitter supplied) Doxorubicin (Adriamycin) is an anthracycline chemotherapy agent effective in treating a wide range of malignancies1 with a well-established dose-response cardiotoxic side-effect that can lead to heart failure2-4. Even at relatively low cumulative doses of 200–250 mg/m2, the risk of cardiotoxicity is estimated at 7.8% to 8.8%4,5. Doxorubicin-induced cardiotoxicity (DIC) can range from asymptomatic reductions in left ventricular ejection fraction (LVEF) to highly symptomatic heart failure6,7. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76314/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA306880
Series		Accession: GSE76314	ID: 200076314

4303. BRD4 connects enhancer remodeling to senescence immune surveillance (RNA-seq)
(Submitter supplied) Cellular senescence is a homeostatic program associated with tumor suppression, wound healing, and certain age related pathologies. Senescent cells display a repressive chromatin configuration thought to stably silence proliferation-promoting genes, while at the same time activate an unusual form of immune surveillance involving a secretory program referred to as the senescence-associated secretory phenotype (SASP). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 72 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74324/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA299683
Series		Accession: GSE74324	ID: 200074324

4304. Mutation of cancer driver MLL2 results in transcription stress and genome instability
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing
Platforms: GPL17301 GPL16331 GPL13112 62 Samples
FTP download: GEO (BED, RPKM) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73130/
Series		Accession: GSE73130	ID: 200073130

4305. EGFRvIII/STAT3 targets in glioblastoma pathogenesis
(Submitter supplied) Next generation sequencing platforms were used to identify STAT3 targets in the background of EGFRvIII expresssion
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL13112 GPL11002 GPL10999 14 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE51nnn/GSE51281/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA222297
Series		Accession: GSE51281	ID: 200051281

4306. Study of Topoisomerase I in human
(Submitter supplied) We report a mechanism through which the transcription machinery directly controls topoisomerase 1 (TOP1) activity to adjust DNA topology throughout the transcription cycle. By comparing TOP1 occupancy using ChIP-Seq, versus TOP1 activity using TOP1-Seq, a method reported here to map catalytically engaged TOP1, TOP1 bound at promoters was discovered to become fully active only after pause-release. This transition coupled the phosphorylation of the carboxyl-terminal-domain (CTD) of RNA polymerase II (RNAPII) with stimulation of TOP1 above its basal rate, enhancing its processivity. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL9115 GPL9520 27 Samples
FTP download: GEO (TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57628/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA246370
Series		Accession: GSE57628	ID: 200057628

4307. HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells
(Submitter supplied) We used the myelogenous leukemia line K562 as a model of HDACi-induced differentiation to investigate chromatin accessibility (DNase-seq) and expression (RNA-seq) changes associated with this process. We identified several thousand specific regulatory elements (~10% of total DHS sites) that become significantly more or less accessible with sodium butyrate or suberanilohydroxamic acid (SAHA) 72-hour treatments. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL10999 GPL11154 76 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74999/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA302159
Series		Accession: GSE74999	ID: 200074999

4308. Integrin signaling regulates YAP/TAZ to control skin homeostasis
(Submitter supplied) The skin is a squamous epithelium that is continuously renewed by a population of basal layer stem/progenitor cells and can heal wounds. Here, we show that the transcription regulators YAP and TAZ localise to the nucleus in the basal layer of skin and are elevated upon wound healing. Skin-specific deletion of both YAP and TAZ in adult mice slows proliferation of basal layer cells, leads to hair loss and impairs regeneration after wounding. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80082/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA317776
Series		Accession: GSE80082	ID: 200080082

4309. Gene signature in sessile serrated polyps identifies colon cancer subtype
(Submitter supplied) RNA sequencing analysis of gene expression in serrated colon polyps, uninvolved colon and control colon
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 86 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76987/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA309180
Series		Accession: GSE76987	ID: 200076987

4310. Epigenomic profiling reveals the key function of histone H3K9 methylation during tumor transformation process
(Submitter supplied) To understand transcriptome and epigenome profilings alteration during breast cancer initiation and development, we constructed a in vitro breast cancer transformation model. And then, we use mRNA-Seq to uncover differential expression genes during breast cancer transformation process. For epigenomic profilings, we specificly analysis genome wide H3K9me2, H3K9me3,H3K4me3 and H3K27me3 modifications using ChIP-Seq. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 34 Samples
FTP download: GEO (TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64367/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA270845
Series		Accession: GSE64367	ID: 200064367

4311. HEXIM1 is induced by DHODH inhibition to suppress melanoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL11154 GPL16791 12 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57432/
Series		Accession: GSE57432	ID: 200057432

4312. HEXIM1 is induced by DHODH inhibition to suppress melanoma [Gro-Seq]
(Submitter supplied) Recent evidence suggests that leflunomide, a DHODH inhibitor, disrupts neural crest development and melanoma pathogenesis via inhibiting transcription elongation. Here, we provide evidence that a transcriptional regulator, HEXIM1, is upregulated in response to leflunomide. HEXIM1 is assembled into the 7SK snRNP complex to sequester and inhibit the kinase P-TEFb. P-TEFb triggers elongation by phosphorylating RNA polymerase II and pausing factors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57430/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA246459
Series		Accession: GSE57430	ID: 200057430

4313. G9a-Mediated Methylation of ERα Links the PHF20/MOF Histone Acetyltransferase Complex to Hormonal Gene Expression
(Submitter supplied) The euchromatin histone methyltransferase 2 (EHMT2, aka G9a) methylates histone H3K9 to repress gene expression, but it also acts as a coactivator for some nuclear receptors.  The molecular mechanisms underlying this activation remain elusive.  Here we show that G9a functions as a bona fide coactivator of the endogenous estrogen receptor α (ERα) in breast cancer cells in a histone methylation-independent manner. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76507/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA307589
Series		Accession: GSE76507	ID: 200076507

4314. A Surveillance System of Active Enhancers by a RACK7-histone Demethylase Complex (RNA-Seq II)
(Submitter supplied) Primed enhancers are marked by histone H3K4 mono-methylation (H3K4me1), and the conversion to active enhancers involves acetylation of histone H3K27 (H3K27Ac). However, whether active enhancers are regulated remains unclear. Here we report a biochemical complex consisting of a potential chromatin reader (RACK7) and a histone demethylase (KDM5C) that occupies many active enhancers in a breast cancer cell line. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (BEDGRAPH, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71326/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA290902
Series		Accession: GSE71326	ID: 200071326

4315. A Surveillance System of Active Enhancers by a RACK7-histone Demethylase Complex (RNA-Seq I)
(Submitter supplied) Primed enhancers are marked by histone H3K4 mono-methylation (H3K4me1), and the conversion to active enhancers involves acetylation of histone H3K27 (H3K27Ac). However, whether active enhancers are regulated remains unclear. Here we report a biochemical complex consisting of a potential chromatin reader (RACK7) and a histone demethylase (KDM5C) that occupies many active enhancers in a breast cancer cell line. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71325/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA290903
Series		Accession: GSE71325	ID: 200071325

4316. Comparative analysis of human and mouse transcriptomes of Th17 cell priming.
(Submitter supplied) Uncontrolled Th17 cell activity is associated with cancer and autoimmune and inflammatory diseases. To validate the potential relevance of mouse models of targeting the Th17 pathway in human diseases we used RNA sequencing to compare the expression of coding and non-coding transcripts during the priming of Th17 cell differentiation in both human and mouse. In addition to already known targets, several transcripts not previously linked to Th17 cell polarization were found in both species. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL13112 GPL11154 114 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE52nnn/GSE52260/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA227306
Series		Accession: GSE52260	ID: 200052260

4317. A large microRNA cluster on chromosome 19 is a transcriptional hallmark of WHO type A and AB thymomas
(Submitter supplied) Thymomas are one of the most rarely diagnosed malignancies. To better understand its biology and to identify therapeutic targets, we performed next-generation RNA sequencing.  The RNA was sequenced from 13 thymic malignancies and 3 normal thymus glands. Validation of microRNA expression was performed on a separate set of 35 thymic malignancies. For cell-based studies, a thymoma cell line was used. Hierarchical clustering revealed 100% concordance between gene expression clusters and WHO subtype. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL18723 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79978/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA317556
Series		Accession: GSE79978	ID: 200079978

4318. ATXN7L3 And ENY2 Coordinate Activity Of Multiple H2B Deubiquitinases Important For Cellular Proliferation And Tumor Growth
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 20 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79967/
Series		Accession: GSE79967	ID: 200079967

4319. ATXN7L3 And ENY2 Coordinate Activity Of Multiple H2B Deubiquitinases Important For Cellular Proliferation And Tumor Growth [RNA-Seq]
(Submitter supplied) We report that H2B deubiquitinating enzymes USP22, USP27x and USP51 have both unique and overlapping target loci.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79861/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA317531
Series		Accession: GSE79861	ID: 200079861

4320. Determination of a comprehensive alternative splicing regulatory network and the combinatorial regulation by key factors during Epithelial-to-Mesenchymal Transition
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 36 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75492/
Series		Accession: GSE75492	ID: 200075492

4321. Determination of a comprehensive alternative splicing regulatory network and the combinatorial regulation by key factors during Epithelial-to-Mesenchymal Transition [RBM47 KD]
(Submitter supplied) RBM47 is a RNA binding protein that is known to regulate alternative splicing. To study the genome wide regulatory role of RBM47 in alternative splicing and determine the potential function of RBM47 during EMT, we used lentiviral shRNAs to knockdown RBM47 in H358 cells and performed RNA-seq in biological triplicates.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75491/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA304418
Series		Accession: GSE75491	ID: 200075491

4322. Determination of a comprehensive alternative splicing regulatory network and the combinatorial regulation by key factors during Epithelial-to-Mesenchymal Transition [ESRP KD]
(Submitter supplied) Epithelial specific splicing regulatory protein 1 and 2 (ESRP1 and ESRP2) are important regulators of alternative splicing during EMT. To study the alternative splicing events regulated by ESRP1/2 at a genome wide scale, we used lentiviral shRNAs to knockdown ESRP1/2 in H358 cells and performed RNA-seq in biological triplicates.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75489/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA304419
Series		Accession: GSE75489	ID: 200075489

4323. Determination of a comprehensive alternative splicing regulatory network and the combinatorial regulation by key factors during Epithelial-to-Mesenchymal Transition [EMT.time course]
(Submitter supplied) The epithelial to mesenchymal transition (EMT) is an essential biological process during embryonic development and has also been implicated in cancer metastasis. Previous studies have characterized transcriptional regulation and key transcription factors that impact EMT. However, the role of alternative splicing (AS) regulation in EMT has only recently emerged and remains relatively uncharacterized. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 24 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75487/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA304414
Series		Accession: GSE75487	ID: 200075487

4324. Single cell RNA-seq analysis of melanoma
(Submitter supplied) To understand the diversity of expression states within melanoma tumors, we obtained freshly resected samples, dissagregated the samples, sorted into single cells and profiled them by single-cell RNA-seq.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 4645 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72056/
Series		Accession: GSE72056	ID: 200072056

4325. Regulation of poly(A) tail and translation during the somatic cell cycle
(Submitter supplied) Poly(A) tails are critical for mRNA stability and translation. However, recent studies have challenged this view, showing that poly(A) tail length and translation efficiency are decoupled in non-embryonic cells. Using TAIL-seq and ribosome profiling, we investigate poly(A) tail dynamics and translational control in the somatic cell cycle. We find dramatic changes in poly(A) tail lengths of cell cycle regulatory genes like CDK1, TOP2A, and FBXO5, explaining their translational repression in M phase. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL11154 18 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79664/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA316618
Series		Accession: GSE79664	ID: 200079664

4326. Three-dimensional disorganisation of the cancer genome occurs coincident with long range genetic and epigenetic alterations
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms: GPL16791 GPL11154 22 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73785/
Series		Accession: GSE73785	ID: 200073785

4327.  Three-dimensional disorganisation of the cancer genome occurs coincident with long range genetic and epigenetic alterations [RNA-seq]
(Submitter supplied) A three-dimensional chromatin state underpins the structural and functional basis of the genome by bringing regulatory elements and genes into close spatial proximity to ensure proper, cell-type specific gene expression profiles. Here, we perform HiC chromosome conformation, ChIP-seq and RNA-seq to investigate how the three-dimensional organization of the cancer genome is disrupted in the context of epigenetic remodelling and atypical gene expression programs.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73784/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA297885
Series		Accession: GSE73784	ID: 200073784

4328. Dissecting stages of human kidney development and Tumorigenesis with surface markers affords simple prospective Purification of nephron stem cells
(Submitter supplied) When assembling a nephron during development a multipotent stem cell pool becomes restricted as differentiation ensues. A faulty differentiation arrest in this process leads to transformation and initiation of a Wilms' tumor. Mapping these transitions with respective surface markers affords accessibility to specific cell subpopulations. NCAM1 and CD133 have been previously suggested to mark human renal progenitor populations. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 3 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78502/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA313148
Series		Accession: GSE78502	ID: 200078502

4329. Wiskott-Aldrich Syndrome-causative mutations disrupt alternative splicing and promote gene networks predisposed to hematologic malignancies
(Submitter supplied) Wiskott-Aldrich syndrome (WAS) is characterized by X-linked thrombocytopenia, eczema, immunodeficiency, recurrent infections and increased risk of autoimmunity and malignancies. WAS is caused by mutations in the WAS gene, which encodes the exclusively hematopoietic WAS protein (WASp) that is classically characterized as aν actin nucleator. However, disruption of F-actin polymerization by WAS mutations can not account for many aspects of WAS pathogenesis. more...
Organism:	Homo sapiens; unidentified plasmid
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL21375 14 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77253/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA309863
Series		Accession: GSE77253	ID: 200077253

4330. Transposon mutagenesis reveals fludarabine-resistance mechanisms in chronic lymphocytic leukemia
(Submitter supplied) Purpose:To identify resistance mechanisms for the chemotherapeutic drug fludarabine in chronic lymphocytic leukemia (CLL), as innate and acquired resistance to fludarabine-based chemotherapy represents a major challenge for long-term disease control. Methods: We employed piggyBac transposon-mediated mutagenesis, combined with next-generation sequencing, to identify genes that confer resistance to fludarabine in a human CLL cell line. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75844/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA305520
Series		Accession: GSE75844	ID: 200075844

4331. The DNA methylation landscape of human melanoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 24 Samples
FTP download: GEO (BEDGRAPH, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71748/
Series		Accession: GSE71748	ID: 200071748

4332. The DNA methylation landscape of human melanoma [RNA-Seq]
(Submitter supplied) Melanoma genomes are often characterized by large numbers of sunlight-induced mutations. However, epigenetic alterations, in the form of aberrant DNA methylation patterns, are also abundant. Using MIRA-seq, we have carried out a comprehensive characterization of the DNA methylome in a series of metastatic melanoma samples and catalogued the methylation changes relative to normal melanocytes, the presumed cells of origin for these tumors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 20 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71747/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA291993
Series		Accession: GSE71747	ID: 200071747

4333. A mechanism of resistance to gefitinib mediated by cellular reprogramming and the acquisition of an FGF2-FGFR1 autocrine growth loop
(Submitter supplied) Despite initial and often dramatic responses of epidermal growth factor receptor (EGFR)-addicted lung tumors to the EGFR-specific tyrosine kinase inhibitors (TKIs), gefitinib and erlotinib, nearly all develop resistance and relapse. To explore novel mechanisms mediating acquired resistance, we employed non-small-cell lung cancer (NSCLC) cell lines bearing activating mutations in EGFR and rendered them resistant to EGFR-specific TKIs through chronic adaptation in tissue culture. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79688/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA316712
Series		Accession: GSE79688	ID: 200079688

4334. Transcriptomic and Epigenetic analysis of cell line derivatives from H2087 and HCC1954 cell lines
(Submitter supplied) We profiled the transcriptomes of latency-competent cells derived from the human cancer cell lines H2087 (lung adenocarcinoma) and HCC1954 (breast adenocarcinoma) in mitogen-rich and mitogen-low media (MRM and MLM, respectively). In addition, we analyzed the epigenetic landscape of these cell lines under MLM conditions. 
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL11154 GPL16791 43 Samples
FTP download: GEO (TDF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72956/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA295409
Series		Accession: GSE72956	ID: 200072956

4335. Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome variation profiling by SNP array; Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms: GPL11154 GPL10999 GPL6801 37 Samples
FTP download: GEO (CEL, CNCHP) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE46nnn/GSE46598/
Series		Accession: GSE46598	ID: 200046598

4336. Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer
(Submitter supplied) To understand epigenetic changes in the distal regulatory as well as proximal regions, we performed RNA-seq, MBD-seq, and H3K27ac ChIP-seq on gastric tissues and cell lines.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL10999 GPL11154 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE46nnn/GSE46597/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA201423
Series		Accession: GSE46597	ID: 200046597

4337. XX-650-23, an inhibitor of CREB-CBP interaction, effect on acute myeloid leukemia cell line
(Submitter supplied) Analysis of acute myeloid leukemia KG1 cells treated with XX-650-23 (5 mM) for 12hrs. XX-650-23 inhibits proliferation of KG1 cells. Results provides insight into the molecular mechanisms underlying by the inhibitory activity of XX-650-23 on acute leukemia.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74928/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA301935
Series		Accession: GSE74928	ID: 200074928

4338. CLIC5: a novel ETV6 target gene in childhood acute lymphoblastic leukemia
(Submitter supplied) Background: The most common rearrangement in childhood precursor B-cell acute lymphoblastic leukemia (pre-B ALL) is the t(12;21)(p13;q22) translocation resulting in the ETV6-AML1 fusion gene. A frequent concomitant event is the loss of the residual ETV6 allele suggesting a critical role for the ETV6 transcriptional repressor in the etiology of pre-B ALL. However, the precise mechanism through which loss of functional ETV6 contributes to disease pathogenesis is still unclear Results: To investigate the impact of ETV6 loss on the transcriptional network and identify new transcriptional targets of ETV6, we used whole transcriptome analysis of both pre-B leukemic cell lines and pre-B ALL patients combined with chromatin immunoprecipitation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16558 GPL16791 25 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79373/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA315627
Series		Accession: GSE79373	ID: 200079373

4339. polyA mRNA RNA-seq from HepG2 (ENCSR985KAT)
(Submitter supplied) RNA Evaluation HepG2 Long Poly-A+ from Graveley  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78686/
Series		Accession: GSE78686	ID: 200078686

4340. total RNA-seq from HT-29 (ENCSR971GPJ)
(Submitter supplied) The libraries contained in this experiment come from independent growths of cell line HT-29, a colorectal adenocarcinoma from a 44 year old female.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78684/
Series		Accession: GSE78684	ID: 200078684

4341. total RNA-seq from M059J (ENCSR696SMK)
(Submitter supplied) The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line M059J. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78666/
Series		Accession: GSE78666	ID: 200078666

4342. total RNA-seq from SK-MEL-5 (ENCSR669KQU)
(Submitter supplied) The libraries contained in this experiment come from independent growths of cell line SK-MEL-5, a metastatic malignant melanoma from a 24 year old female.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78664/
Series		Accession: GSE78664	ID: 200078664

4343. total RNA-seq from MCF-7 (ENCSR667JTA)
(Submitter supplied) RNA Evaluation MCF7 Long Total from Graveley  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78663/
Series		Accession: GSE78663	ID: 200078663

4344. polyA mRNA RNA-seq from NCI-H460 (ENCSR625QJI)
(Submitter supplied) The libraries contained in this experiment come from nuclear fractions of immortalized cell line NCI-H460 derived from a large cell lung carcinoma of a 37 year old male.  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78661/
Series		Accession: GSE78661	ID: 200078661

4345. polyA mRNA RNA-seq from NCI-H460 (ENCSR586SEE)
(Submitter supplied) The libraries contained in this experiment come from cytoplasmic fractions of immortalized cell line NCI-H460 derived from a large cell lung carcinoma of a 37 year old male.  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 1 Sample
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78659/
Series		Accession: GSE78659	ID: 200078659

4346. polyA mRNA RNA-seq from SK-N-DZ (ENCSR569JKX)
(Submitter supplied) The libraries contained in this experiment come from cytoplasmic fractions of a neuroblastoma immortalized cell line SK-N-DZ erived from a metastatic site in the bone marrow of a 2 year old female. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78656/
Series		Accession: GSE78656	ID: 200078656

4347. total RNA-seq from SJCRH30 (ENCSR568YRP)
(Submitter supplied) The libraries contained in this experiment come from independent growths of cell line SJCRH30, a metastatic rhabdomyosarcoma from a 17 year old male.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78655/
Series		Accession: GSE78655	ID: 200078655

4348. total RNA-seq from HT1080 (ENCSR535VTR)
(Submitter supplied) The libraries contained in this experiment come from independent growths of cell line HT-1080, a connective tissue fibrosarcoma from a 35 year old male.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78653/
Series		Accession: GSE78653	ID: 200078653

4349. total RNA-seq from A375 (ENCSR504VXC)
(Submitter supplied) The libraries contained in this experiment come from independent growths of cell line A375, a malignant melanoma from a 54 year old female.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78652/
Series		Accession: GSE78652	ID: 200078652

4350. total RNA-seq from HepG2 (ENCSR468ION)
(Submitter supplied) RNA Evaluation HepG2 Long Total from Graveley  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78650/
Series		Accession: GSE78650	ID: 200078650

4351. total RNA-seq from PC-3 (ENCSR420NLC)
(Submitter supplied) The libraries contained in this experiment come from independent growths of cell line PC-3, a metastatic prostate grade IV adenocarcinoma from a 62 year old male.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78648/
Series		Accession: GSE78648	ID: 200078648

4352. total RNA-seq from RPMI-7951 (ENCSR320BRR)
(Submitter supplied) The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line RPMI-7951. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78643/
Series		Accession: GSE78643	ID: 200078643

4353. total RNA-seq from Karpas-422 (ENCSR314LXG)
(Submitter supplied) The libraries contained in this experiment come from independent growths of cell line Karpas-422, a B cell from a 73 year old female with non-Hodgkins Lymphoma.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78642/
Series		Accession: GSE78642	ID: 200078642

4354. polyA mRNA RNA-seq from MCF-7 (ENCSR310FIS)
(Submitter supplied) RNA Evaluation MCF7 Long Poly-A+ from Graveley  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78641/
Series		Accession: GSE78641	ID: 200078641

4355. polyA mRNA RNA-seq from SK-MEL-5 (ENCSR291DJH)
(Submitter supplied) The libraries contained in this experiment come from cytoplasmic fractions of a malignant melonoma immortalized cell line SK-MEL-5 derived from a metastatic axillary node of a 24 year old female. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78639/
Series		Accession: GSE78639	ID: 200078639

4356. polyA mRNA RNA-seq from SK-N-DZ (ENCSR255NYQ)
(Submitter supplied) The libraries contained in this experiment come from nuclear fractions of a neuroblastoma immortalized cell line SK-N-DZ derived from a metastatic site in the bone marrow of a 2 year old female. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78637/
Series		Accession: GSE78637	ID: 200078637

4357. polyA mRNA RNA-seq from SK-MEL-5 (ENCSR201WVA)
(Submitter supplied) The libraries contained in this experiment come from nuclear fractions of a malignant melonoma immortalized cell line SK-MEL-5 derived from a metastatic axillary node of a 24 year old female. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78632/
Series		Accession: GSE78632	ID: 200078632

4358. polyA mRNA RNA-seq from HT1080 (ENCSR166QLP)
(Submitter supplied) The libraries contained in this experiment come from cytoplasmic fractions of a fibrosarcoma immortalized cell line HT1080 derived from the connective tissue from a 35 year old male. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78629/
Series		Accession: GSE78629	ID: 200078629

4359. total RNA-seq from NCI-H460 (ENCSR164OCT)
(Submitter supplied) The libraries contained in this experiment come from independent growths of cell line NCI-H460, a male large cell lung carcinoma.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78628/
Series		Accession: GSE78628	ID: 200078628

4360. total RNA-seq from SK-N-DZ (ENCSR136WGP)
(Submitter supplied) The libraries contained in this experiment come from independent growths of cell line SK-N-DZ, a metastatic neuroblastoma from a 2 year old female.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78627/
Series		Accession: GSE78627	ID: 200078627

4361. total RNA-seq from K562 (ENCSR109IQO)
(Submitter supplied) RNA Evaluation K562 Long Total from Graveley  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78625/
Series		Accession: GSE78625	ID: 200078625

4362. polyA mRNA RNA-seq from HT1080 (ENCSR067UNX)
(Submitter supplied) The libraries contained in this experiment come from nuclear fractions of a fibrosarcoma immortalized cell line HT1080 derived from the connective tissue from a 35 year old male. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78624/
Series		Accession: GSE78624	ID: 200078624

4363. total RNA-seq from OCI-LY7 (ENCSR001HHK)
(Submitter supplied) The libraries contained in this experiment come from independent growths of cell line Oci-Ly-7, a peripherial blood sample from a 48 year old male with Non-Hodgkin lymphoma.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78621/
Series		Accession: GSE78621	ID: 200078621

4364. polyA mRNA RNA-seq from K562 (ENCSR000AEQ)
(Submitter supplied) RNA Evaluation K562 Long Poly-A+ RNA-seq from Wold  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78561/
Series		Accession: GSE78561	ID: 200078561

4365. total RNA-seq from K562 (ENCSR000AEP)
(Submitter supplied) RNA Evaluation K562 Long Total RNA-seq from Wold  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78560/
Series		Accession: GSE78560	ID: 200078560

4366. polyA mRNA RNA-seq from K562 (ENCSR000AEO)
(Submitter supplied) RNA Evaluation K562 Long Poly-A+  from Graveley  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78559/
Series		Accession: GSE78559	ID: 200078559

4367. total RNA-seq from K562 (ENCSR000AEN)
(Submitter supplied) RNA Evaluation K562 Long Total from Graveley  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78558/
Series		Accession: GSE78558	ID: 200078558

4368. polyA mRNA RNA-seq from K562 (ENCSR000AEM)
(Submitter supplied) The libraries contained in this experiment come from independent growths of cell line K562.  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.  These data were collected as part of the RNA Evaluation Study.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78557/
Series		Accession: GSE78557	ID: 200078557

4369. total RNA-seq from K562 (ENCSR000AEL)
(Submitter supplied) The libraries contained in this experiment come from independent growths of cell line K562.  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.  These data were collected as part of the RNA Evaluation Study.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78556/
Series		Accession: GSE78556	ID: 200078556

4370. small RNA-seq from NCI-H460 (ENCSR968YZV)
(Submitter supplied) The libraries contained in this experiment come from cytoplasmic fractions of immortalized cell line NCI-H460 derived from a large cell lung carcinoma of a 37 year old male.  They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted TAP pretreated Total RNA < 200 nucleotides in size.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78492/
Series		Accession: GSE78492	ID: 200078492

4371. small RNA-seq from SK-MEL-5 (ENCSR964EPR)
(Submitter supplied) The libraries contained in this experiment come from nuclear fractions of a malignant melonoma immortalized cell line SK-MEL-5 derived from a metastatic axillary node of a 24 year old female. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted TAP pretreated Total RNA < 200 nucleotides in size.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78491/
Series		Accession: GSE78491	ID: 200078491

4372. small RNA-seq from Karpas-422 (ENCSR905KHW)
(Submitter supplied) The libraries contained in this experiment come from independent growths of cell line, Karpas-422. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size that was pre-treated with TAP prior to cloning.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78476/
Series		Accession: GSE78476	ID: 200078476

4373. small RNA-seq from HT1080 (ENCSR855CYO)
(Submitter supplied) The libraries contained in this experiment come from nuclear fractions of a fibrosarcoma immortalized cell line HT1080 derived from the connective tissue from a 35 year old male. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted TAP pretreated RNA < 200 nucleotides in size.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78470/
Series		Accession: GSE78470	ID: 200078470

4374. small RNA-seq from HT-29 (ENCSR807KQN)
(Submitter supplied) The libraries contained in this experiment come from independent growths of cell line, HT-29. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size that was pre-treated with TAP prior to cloning.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78459/
Series		Accession: GSE78459	ID: 200078459

4375. small RNA-seq from OCI-LY7 (ENCSR740DKM)
(Submitter supplied) The libraries contained in this experiment come from independent growths of cell line, Oci-Ly-7. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size that was pre-treated with TAP prior to cloning.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78446/
Series		Accession: GSE78446	ID: 200078446

4376. small RNA-seq from SK-N-DZ (ENCSR626WAX)
(Submitter supplied) The libraries contained in this experiment come from nuclear fractions of a neuroblastoma immortalized cell line SK-N-DZ derived from a metastatic site in the bone marrow of a 2 year old female. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted TAP pretreated Total RNA < 200 nucleotides in size.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78422/
Series		Accession: GSE78422	ID: 200078422

4377. small RNA-seq from SK-N-DZ (ENCSR610CDO)
(Submitter supplied) The libraries contained in this experiment come from cytoplasmic fractions of a neuroblastoma immortalized cell line SK-N-DZ derived from a metastatic site in the bone marrow of a 2 year old female. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted TAP pretreated Total RNA < 200 nucleotides in size.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78418/
Series		Accession: GSE78418	ID: 200078418

4378. small RNA-seq from SK-MEL-5 (ENCSR571FTT)
(Submitter supplied) The libraries contained in this experiment come from cytoplasmic fractions of a malignant melonoma immortalized cell line SK-MEL-5 derived from a metastatic axillary node of a 24 year old female. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted TAP pretreated Total RNA < 200 nucleotides in size.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78411/
Series		Accession: GSE78411	ID: 200078411

4379. small RNA-seq from A375 (ENCSR376XXO)
(Submitter supplied) The libraries contained in this experiment come from independent growths of cell line, A375. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size that was pre-treated with TAP prior to cloning.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78382/
Series		Accession: GSE78382	ID: 200078382

4380. small RNA-seq from NCI-H460 (ENCSR211PJW)
(Submitter supplied) The libraries contained in this experiment come from nuclear fractions of immortalized cell line NCI-H460 derived from a large cell lung carcinoma of a 37 year old male.  They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted TAP pretreated Total RNA < 200 nucleotides in size.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78344/
Series		Accession: GSE78344	ID: 200078344

4381. small RNA-seq from K562 (ENCSR000AES)
(Submitter supplied) The libraries contained in this experiment come from independent growths of cell line K562.  They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.  These data were collected as part of the RNA Evaluation Study.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78289/
Series		Accession: GSE78289	ID: 200078289

4382. mRNA expressions in pre-treatment melanomas undergoing anti-PD-1 checkpoint inhibition therapy
(Submitter supplied) PD-1 immune checkpoint blockade provides significant clinical benefits for cancer patients. However, factors influencing innate sensitivity remain incompletely catalogued. We analyzed the somatic mutanomes and transcriptomes of pretreatment melanoma biopsies. Mutations in cell adhesion genes and the DNA repair gene BRCA2 were enriched in responding tumors, and a high mutational load associated with improved survival. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 28 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78220/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA312948
Series		Accession: GSE78220	ID: 200078220

4383. Gene expression in human glioblastoma specimens
(Submitter supplied) We assessed global gene expression changes in 32 human glioblastoma specimens
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 32 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77530/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA310727
Series		Accession: GSE77530	ID: 200077530

4384. GAS5 controls Nodal autocrine in Human Embryonic Stem Cells Self-Renewal through competing endogenous mechanism
(Submitter supplied) Long non-coding RNAs (lncRNAs) are recently characterized players that are involved in the regulatory circuitry of self-renewal in human embryonic stem cells (hESCs). However, the specific roles of lncRNAs in this circuitry are poorly understood. Here, we determined that growth-arrest-specific transcript 5 (GAS5), which is a known tumor suppressor and growth arrest gene, is abundantly expressed in the cytoplasm of hESCs and essential for hESC self-renewal. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms: GPL11154 GPL17303 7 Samples
FTP download: GEO (XLS, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66993/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA278657
Series		Accession: GSE66993	ID: 200066993

4385. IGF2BP3 controls cancer cell invasiveness by modulation RISC function
(Submitter supplied) The goal of this study was to determine IGF2BP3 regulation of RNA targets in human pacreatic ductal adenocarcinoma cell lines
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other; Non-coding RNA profiling by high throughput sequencing
Platforms: GPL11154 GPL15520 26 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79147/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA315017
Series		Accession: GSE79147	ID: 200079147

4386. An Integrated Metabolic Atlas of Clear Cell Renal Cell Carcinoma
(Submitter supplied) Changes in cellular metabolism contribute to the development and progression of tumors, and can render tumors vulnerable to interventions. However, studies of human cancer metabolism remain limited due to technical challenges of detecting and quantifying small molecules, the highly interconnected nature of metabolic pathways, and the lack of designated tools to analyze and integrate metabolomics with other –omics data. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74734/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA301435
Series		Accession: GSE74734	ID: 200074734

4387. ROR-γ drives androgen-receptor expression and represents a therapeutic target in castration-resistant prostate cancer
(Submitter supplied) The androgen receptor (AR) is overexpressed and hyperactivated in human castration-resistant prostate cancer (CRPC). However, the determinants of AR overexpression in CRPC are poorly defined. Here we show that retinoic acid receptor–related orphan receptor γ (ROR-γ) is overexpressed and amplified in metastatic CRPC tumors, and that ROR-γ drives AR expression in the tumors. ROR-γ recruits nuclear receptor coactivator 1 and 3 (NCOA1 and NCOA3, also known as SRC-1 and SRC-3)  to an AR–ROR response element (RORE) to stimulate AR gene transcription. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72483/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA294140
Series		Accession: GSE72483	ID: 200072483

4388. Characterizing the heterogeneity of triple-negative breast cancers using RNA Sequencing
(Submitter supplied) Triple-negative breast cancers (TNBCs) are a heterogeneous set of tumors defined by an absence of actionable therapeutic targets (ER, PR, and HER-2). Microdissected normal ductal epithelium from healthy volunteers represents a novel comparator to reveal insights into TNBC heterogeneity and to inform drug development. Using RNA-sequencing data from our institution and The Cancer Genome Atlas (TCGA) we compared the transcriptomes of 94 TNBCs, 20 microdissected normal breast tissues from healthy volunteers from the Susan G. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9520 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78918/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA314351
Series		Accession: GSE78918	ID: 200078918

4389. RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes in Human Normal and Cancerous Tissues
(Submitter supplied) Circular RNAs (circRNAs) represent a novel class of widespread and diverse endogenous RNAs that may regulate gene expression in eukaryotes. However, the regulation and function of human circRNAs remain largely unknown. Here we generate ribosomal-depleted RNA sequencing data from six normal tissues and seven cancers, and detect at least 27,000 circRNA candidates.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL11154 26 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77661/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA311161
Series		Accession: GSE77661	ID: 200077661

4390. miRNA-1343 attenuates pathways of fibrosis by targeting the TGF-beta receptors [RNA-seq]
(Submitter supplied) miRNA-1343 is an uncharacterized miRNA predicted to target a number of genes involved in epithelial cell function including TGF-beta signaling, cell adhesion, and cell proliferation. We transiently overexpressed miRNA-1343 or a non-targeting control miRNA in A549 and 16HBE14o- human airway cell lines. As predicted, RNA-seq following miRNA-1343 overexpression showed significant downregulation of genes involved in these pathways. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 16 Samples
FTP download: GEO (DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75591/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA304643
Series		Accession: GSE75591	ID: 200075591

4391. RNA-Seq profiling of Ewing's sarcoma and MSC cell lines
(Submitter supplied) Comparison of expression profile of Ewing's sarcoma with cell of origin, mesenchymal stem cells with the goal of identifying novel therapeutic targets.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 5 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73610/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA297425
Series		Accession: GSE73610	ID: 200073610

4392. Expression data (micro-array and RNA-seq, frozen tumors and FFPE blocks) from various sarcomas
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Expression profiling by array
Platforms: GPL570 GPL11154 489 Samples
FTP download: GEO (CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71121/
Series		Accession: GSE71121	ID: 200071121

4393. RNA-seq performed on FFPE sarcoma blocks
(Submitter supplied) We validated the technological and material transfers of the CINSARC signature.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 41 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71120/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA287206
Series		Accession: GSE71120	ID: 200071120

4394. RNA-seq performed on sarcomas to identify various alterations
(Submitter supplied) We validated the technological and material transfers of the CINSARC signature.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 136 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71119/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA282597
Series		Accession: GSE71119	ID: 200071119

4395. The genomic landscape of pediatric T-cell acute lymphoblastic leukemia reveals novel X-linked somatic mutations associated with apoptosis resistance.
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL16558 GPL16791 63 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78786/
Series		Accession: GSE78786	ID: 200078786

4396. The genomic landscape of pediatric T-cell acute lymphoblastic leukemia reveals novel X-linked somatic mutations associated with apoptosis resistance. [RNA-Seq]
(Submitter supplied) Background. T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy with a dismal prognosis. It represents 15% of pediatric ALL and has a threefold higher incidence among males. T-cell transformation is a multi-step process involving cooperating events leading to altered T-cell signaling, proliferation, differentiation and survival. Many recurrent alterations have been identified and help define molecular subgroups of T-ALL, however the full range of events involved in driving transformation remain to be defined. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL16558 13 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78785/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA313769
Series		Accession: GSE78785	ID: 200078785

4397. Transcriptional profile changes by Prox1 expression in thyroid cancer cells
(Submitter supplied) Human thyroid cancer cell line BCPAP was engineered for doxycyclin-mediated inducible expressoin of Prox1 and next generation sequcing was performed to study the transcriptional regulation by Prox1
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75059/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA302305
Series		Accession: GSE75059	ID: 200075059

4398. The effect of knockdown Abl kinases on breast cancer cells' global transcriptome
(Submitter supplied) To gain insight into the signaling pathway(s) required for ABL1/ABL2-dependent bone metastasis, we evaluated the consequences of single or double inactivation of ABL1 and ABL2 on the transcriptome of breast cancer cells. Double ABL1/ABL2 knockdown was required to decrease the levels of p-CrKL by more than 90%, indicative of inactivation of the endogenous ABL kinases. To examine the consequences of depleting the ABL kinases on the transcriptome of metastatic breast cancer cells we employed next generation sequencing (RNAseq) analysis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69125/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA284608
Series		Accession: GSE69125	ID: 200069125

4399. Interactions of aCPs with Cytosine-rich Polypyrimidine Tracts Enhance Splicing of Cassette Exons
(Submitter supplied) Alternative splicing comprises a robust generator of mammalian transcriptome complexity. Splice site specification and activity are controlled by interactions of cis-acting determinants on a transcript with specific RNA binding proteins. A major subset of these interactions comprises interactions localized to the intronic U-rich polypyrimidine tract located immediately 5’ to the majority of splice acceptors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71569/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA291524
Series		Accession: GSE71569	ID: 200071569

4400. Single Cell triple omics sequencing reveals genetic and epigenetic heterogeneity in hepatocellular carcinoma
(Submitter supplied) Single cell genome, DNA methylome, and transcriptome sequencing has been achieved separately. However, to analyze the regulation of RNA expression by genetic and epigenetic factors within an individual cell, it is necessary to analyze these omics simultaneously from the same single cell. Here we developed a single cell triple omics sequencing technique- scTrio-seq, to analyze the genome, DNA methylome, and transcriptome concurrently of a mammalian cell.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
4 related Platforms 95 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE65nnn/GSE65364/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA273802
Series		Accession: GSE65364	ID: 200065364

4401. Reduced expression of RBM47 enhances Nrf2 activity to promote tumor growth in A549 lung adenocarcinoma cells
(Submitter supplied) We identified RNA binding motif protein 47 (RBM47) as a target gene of transforming growth factor (TGF)-beta in mammary gland epithelial cells (NMuMG cells) that have undergone the epithelial-to-mesenchymal transition (EMT). TGF-beta repressed RBM47 expression in NMuMG cells and lung cancer cell lines. Expression of RBM47 correlated with good prognosis in patients with lung, breast, and gastric cancer. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL17303 8 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE61nnn/GSE61910/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA262663
Series		Accession: GSE61910	ID: 200061910

4402. Loss of 5-hydroxymethylcytosine is linked to gene body hypermethylation in kidney cancer
(Submitter supplied) Aberrant DNA methylation is common in cancer. To associate DNA methylation with gene function, we performed RNAseq upon tumor  tissue and matched normal tissues of two ccRCC (clear cell renal cell carcinoma) patients. To quantify 5mC and 5hmC level in each CG site at genome-wide level, we performed BS-seq and TAB-seq upon tumor  tissue and matched normal tissues of two ccRCC (clear cell renal cell carcinoma) patients, respectively.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63183/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA266915
Series		Accession: GSE63183	ID: 200063183

4403. Loss of CSL unlocks a hypoxic response and enhanced tumor growth potential in breast cancer cells
(Submitter supplied) Notch signaling is an important regulator of stem cell differentiation. All canonical Notch signaling is transmitted through the DNA-binding protein CSL and hyperactivated Notch signaling is associated with tumor development; thus it may be anticipated that CSL deficiency should reduce tumor growth. In contrast, we report that genetic removal of CSL in breast tumor cells caused accelerated growth of xenografted tumors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 404 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77308/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA310000
Series		Accession: GSE77308	ID: 200077308

4404. 24hr CA treatment vs. DMSO in HCT116 cells (from 'Identification of CDK8 and CDK19 substrates in human cells using cortistatin A and quantitative phosphoproteomics')
(Submitter supplied) Cortistatin A (CA) is a highly selective inhibitor of the Mediator kinases CDK8 and CDK19. Using CA, we report here the first large-scale identification of Mediator kinase substrates in human cells (HCT116).  Among over 16,000 quantified phosphosites, we identified 78 high-confidence Mediator kinase targets within 64 proteins, including DNA-binding transcription factors and proteins associated with chromatin, DNA repair, and RNA polymerase II. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78506/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA313158
Series		Accession: GSE78506	ID: 200078506

4405. RNA-seq of pre-treatment and post-relapse matched samples from melanoma patients
(Submitter supplied) RNA-seq of pre-treatment and post-relapse matched samples from melanoma patients
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77940/
Series		Accession: GSE77940	ID: 200077940

4406. MLL1 is essential for the senescence-associated secretory phenotype [RNA-Seq]
(Submitter supplied) Oncogene-induced senescence (OIS) and therapy-induced senescence (TIS), while tumor-suppressive, also promote procarcinogenic effects by activating the DNA damage response (DDR), which in turn induces inflammation. This inflammatory response prominently includes an array of cytokines known as the senescence-associated secretory phenotype (SASP). Previous observations link the transcription-associated methyltransferase and oncoprotein MLL1 to the DDR, leading us to investigate the role of MLL1 in SASP expression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78138/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA312767
Series		Accession: GSE78138	ID: 200078138

4407. MLL1 is essential for the senescence-associated secretory phenotype
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.  Oncogene-induced senescence (OIS) and therapy-induced senescence (TIS), while tumor-suppressive, also promote procarcinogenic effects by activating the DNA damage response (DDR), which in turn induces inflammation. This inflammatory response prominently includes an array of cytokines known as the senescence-associated secretory phenotype (SASP). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL18573 GPL11154 20 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78142/
Series		Accession: GSE78142	ID: 200078142

4408. Role of the histone demethylase KDM2B in hematopoietic homeostasis and malignancies
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
4 related Platforms 40 Samples
FTP download: GEO (BED, CEL, CHP) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70729/
Series		Accession: GSE70729	ID: 200070729

4409. Measure transcript integrity using RNA-seq data
(Submitter supplied) Achieved biospecimens annotated with patient clinical characteristics are unique resources for translational research. However, RNA extracted from the achieved tissues is often degraded. RNA degradation can have a significant impact on the measure of transcript abundance that can lead to an increase rate of erroneous differentially expressed genes.  Here, we are presenting the transcript integrity number (TIN) algorithm to measure the RNA degradation at transcript level. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 20 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70285/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA288159
Series		Accession: GSE70285	ID: 200070285

4410. Comprehensive mutational analysis of primary and relapse acute promyelocytic leukemia
(Submitter supplied) Acute promyelocytic leukemia (APL) is a subtype of myeloid leukemia characterized by   differentiation block at the promyelocyte stage. Besides the presence of chromosomal   rearrangement t(15;17) leading to formation of PML-RARA fusion, other genetic   alterations have also been implicated in APL. Here, we performed comprehensive   mutational analysis of primary and relapse APL to identify somatic alterations which   cooperate with PML-RARA in the pathogenesis of APL. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 3 Samples
FTP download: GEO (FPKM_TRACKING, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77946/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA312173
Series		Accession: GSE77946	ID: 200077946

4411. nELAVL HITS-CLIP and RNA-seq in Alzheimer's Disease patients and IMR-32 neuroblastoma cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL10999 GPL16791 GPL15520 64 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53699/
Series		Accession: GSE53699	ID: 200053699

4412. RNAseq in IMR-32 neuroblastoma cells
(Submitter supplied) IMR-32 cells were subjected to lentiviral YRNA infection or nELAVL RNAi and/or UV stress followed by RNAseq analysis to monitor RNA level changes
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 21 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53698/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA232668
Series		Accession: GSE53698	ID: 200053698

4413. nELAVL HITS-CLIP in IMR-32 neuroblastoma cells
(Submitter supplied) Non-stressed and UV-stressed IMR-32 cells were subjected to HITS-CLIP to monitor nELAVL binding changes during AD progression
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53696/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA232670
Series		Accession: GSE53696	ID: 200053696

4414. Activation of the P-TEFb Complex by Lethal Prostate Cancer-Associated Enhancer RNAs
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL11154 GPL16791 36 Samples
FTP download: GEO (BEDGRAPH, BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE55nnn/GSE55032/
Series		Accession: GSE55032	ID: 200055032

4415. Activation of the P-TEFb Complex by Lethal Prostate Cancer-Associated Enhancer RNAs [RNA-Seq]
(Submitter supplied) Castration resistant prostate cancer (CRPC) is a lethal disease1-4.  Aberrant activation of the androgen receptor (AR) becomes a central mechanism contributing to the resistance of endocrine therapies2,3.  Here we demonstrate that non-coding RNAs transcribed from the AR bound-enhancers RNAs (AR-eRNAs) are upregulated in human CRPC cells in vitro, xenografts in vivo and patient tissues.  Expression of a subset of genes with elevated AR-eRNAs, including TLE1 and HTR3A, is inversely correlated with biochemical recurrence-free survival of CRPC patients. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE55nnn/GSE55030/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA238295
Series		Accession: GSE55030	ID: 200055030

4416. Histone H3 Lysine4 Acetylation-Methylation Dynamics Define Breast Cancer Subtypes
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18460 27 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75169/
Series		Accession: GSE75169	ID: 200075169

4417. Histone H3 lysine 4 acetylation-methylation dynamics define breast cancer subtypes [RNA-seq]
(Submitter supplied) The onset and progression of breast cancer are linked to genetic and epigenetic changes that alter the normal programming of cells. Epigenetic modifications of DNA and histones contribute to chromatin structure that results in the activation or repression of gene expression. Several epigenetic pathways have been shown to be highly deregulated in cancer cells. Targeting specific histone modifications represents a viable strategy to prevent oncogenic transformation, tumor growth or metastasis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75168/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA302668
Series		Accession: GSE75168	ID: 200075168

4418. The RNAseq of 79 small cell lung cancer (sclc) and 7 normal control
(Submitter supplied) Even though small cell lung cancer (SCLC) has entered the age of broad genomic analysis, platinum-based chemotherapy remains the standard care for SCLC. Topotecan is the only approved agent for recurrent or progressive SCLC (1).  In the absence of well-defined genomic biomarkers, clinical efficacy signals in genomically distinct subsets of SCLC could have been missed. Serine/Arginine Splicing Factor 1 (SRSF1) is a member of SR protein family. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 86 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE60nnn/GSE60052/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA257389
Series		Accession: GSE60052	ID: 200060052

4419. Chimeric RNA profiling demonstrates an association of alveolar rhabdomyosarcoma with specific stages of normal myogenesis
(Submitter supplied) Total RNA extracted from differentiated mesenchymal stem cells at four time points (T1,T2,T3,T4) and sequenced using Illumina Hi-seq 2000 platform to generate RNA sequencing with 101bp in read length. Nearly 50 million raw reads were yielded from each sample respectively. We used FastQC to confirm the quality of raw fastq sequencing data, and SOAPfuse software to detect fusion transcripts.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 5 Samples
FTP download: GEO (FPKM_TRACKING, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64032/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA269918
Series		Accession: GSE64032	ID: 200064032

4420. Genome-wide and experimental resolution of relative translation elongation speed at individual gene level in human cells
(Submitter supplied) In the process of translation, ribosomes first bind to mRNAs (translation initiation) and then move along the mRNA (elongation) to synthesize proteins. Elongation pausing is deemed highly relevant to co-translational folding of nascent peptides and the functionality of protein products, which positioned the evaluation of elongation speed as one of the central questions in the field of translational control. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL11154 GPL16791 7 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE46nnn/GSE46613/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA201228
Series		Accession: GSE46613	ID: 200046613

4421. Expression profiling by high throughput sequencing of tumors derived from human prostate epithelial cells transformed with the oncogenes N-Myc and myrAKT1.
(Submitter supplied) MYCN amplification and overexpression are common in neuroendocrine prostate cancer (NEPC). However, the impact of aberrant N-Myc expression in prostate tumorigenesis and the cellular origin of NEPC have not been established. We define N-Myc and activated AKT1 as oncogenic components sufficient to transform human prostate epithelial cells to prostate adenocarcinoma and NEPC including the small cell prostate carcinoma (SCPC) variant with phenotypic and molecular features of aggressive, late-stage human disease. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77624/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA311066
Series		Accession: GSE77624	ID: 200077624

4422. Identifying DEK-dependent transcriptional signatures in HPV+ and HPV- head and neck squamous cell carcinoma (HNSCC)
(Submitter supplied) We report the first RNA-Seq experiments profiling the effects of DEK loss in HNSCC. Our data also incorporates HPV+ and HPV- tumors to idenfity HPV-dependent and -independent gene signatures.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70462/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA288722
Series		Accession: GSE70462	ID: 200070462

4423. Suppression of NAF-1 in Breast Cancer Cells Reduces their Tumorigenicity by Interfering with Cellular Iron Distribution and Metabolism and Ensuing ROS Formation and Apoptosis
(Submitter supplied) Nutrient autophagy factor 1 (NAF-1) is an iron-sulfur protein found on the outer mitochondrial membrane and the ER. Recent studies highlighted an important role for NAF-1 in regulating autophagy via interaction with BCL-2. We recently reported that the level of NAF-1 is elevated in cancer cells and that NAF-1 is required for tumor growth. Here we report that shRNA suppression of NAF-1 results in the activation of apoptosis in xenograft tumors and cancer cells grown in culture. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TAR, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66158/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA275982
Series		Accession: GSE66158	ID: 200066158

4424. The Polycomb protein BMI1 induces an invasive gene expression signature in melanoma that promotes metastasis and chemoresistance.
(Submitter supplied) The epigenetic regulator BMI1 is upregulated in many human malignancies and has been implicated in cell migration, but the impact on autochthonous tumor progression is unexplored. Our analyses of human expression data show that BMI1 levels increase with progression in melanoma. We find that BMI1 expression in melanoma cells does not influence cell proliferation or primary tumor growth. In contrast, BMI1 levels are a key determinant of melanoma metastasis, whereby deletion impairs and overexpression enhances dissemination. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71890/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA292416
Series		Accession: GSE71890	ID: 200071890

4425. Differential RNA-seq analysis comparing APC-defective and APC-restored SW480 colorectal cancer cells
(Submitter supplied) Identify genes that are differentially regulated as a consequence of restoration of full-length functional APC in a colorectal cancer cell lines.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76307/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA306863
Series		Accession: GSE76307	ID: 200076307

4426. Tumor cells can follow distinct evolutionary paths to become resistant to epidermal growth factor receptor inhibition
(Submitter supplied) Although mechanisms of acquired resistance of EGFR mutant non-small cell lung cancers to EGFR inhibitors have been identified, little is known about how resistant clones evolve during drug therapy. Here, we observe that acquired resistance caused by the T790M gatekeeper mutation can occur either by selection of pre-existing T790M clones or via genetic evolution of initially T790M-negative drug tolerant cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 22 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75602/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA304927
Series		Accession: GSE75602	ID: 200075602

4427. A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Danio rerio; Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by array
4 related Platforms 48 Samples
FTP download: GEO (BW, NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75356/
Series		Accession: GSE75356	ID: 200075356

4428. A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation [human cell line RNA-seq]
(Submitter supplied) We report gene expression data for human melanoma cell lines using RNAseq.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 10 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75354/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA304002
Series		Accession: GSE75354	ID: 200075354

4429. Gene expression profiling in metabolically heterogeneous human lung tumors
(Submitter supplied) To investigate the impact of genetic and environmental factors that influence cancer cell metabolism in vivo, we conducted intra-operative 13C-glucose infusions in NSCLC patients. We determined that regional glucose metabolism was correlated with tumor perfusion as assessed by pre-surgical dynamic gadolinium enhancement.  Tumors or tumor regions showing high or low perfusion were collected and subjected to RNA-seq analysis.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74484/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA300542
Series		Accession: GSE74484	ID: 200074484

4430. A Dual Molecular Analog Tuner for Dissecting Mammalian Protein Function
(Submitter supplied) Loss-of-function studies are fundamental for dissecting gene function. Yet, methods to rapidly and effectively perturb genes in mammalian cells are scarce. We present a novel system, deliverable with only two lentiviral vectors, which enables simultaneous control over two different proteins in the same cell. By harnessing the plant auxin and jasmonate hormone-induced degradation pathways, combined with RNA interference, this system allows constitutive depletion of two endogenous proteins and their replacement with two exogenous proteins whose degradation is rapidly and reversibly induced by external ligands, representing a dual analog molecular tuner. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74457/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA300451
Series		Accession: GSE74457	ID: 200074457

4431. Gene expression in TAL1-driven T-cell ALL in response to TAL1-KD, UTX-KD, and GSKJ4 treatment
(Submitter supplied) T-cell Acute Lymphoblastic Leukemia (T-ALL) is a heterogeneous group of hematological tumors composed of distinct subtypes that vary in their genetic abnormalities, gene expression signatures and prognoses. However, it remains unclear whether T-ALL subtypes differ at the functional level, and as such T-ALL treatments are uniformly applied across subtypes leading to variable responses between patients. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (R, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72299/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA293697
Series		Accession: GSE72299	ID: 200072299

4432. Differential expression in LNCaP cells expressing the wild-type androgen receptor (AR-WT) or the ligand-independent AR-V7 splice variant
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71336/
Series		Accession: GSE71336	ID: 200071336

4433. mRNA differential expression in LNCaP cells expressing the wild-type androgen receptor (AR-WT) or the ligand-independent AR-V7 splice variant
(Submitter supplied) Constitutively active AR variants are truncated proteins lacking the c-terminal region containing the ligand binding domain (LBD) and the activation function 2 (AF-2). The expression of these AR variants in CRPC was also associated with the resistance to novel therapies such as enzalutamide and abiraterone acetate. These variants are also involved in tumor progression.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71334/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA290918
Series		Accession: GSE71334	ID: 200071334

4434. 7SK-BAF axis controls pervasive transcription at enhancers
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other
4 related Platforms 74 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69143/
Series		Accession: GSE69143	ID: 200069143

4435. Distinct epigenomes in CD4+ T cells of newborns, middle-ages and centenarians.
(Submitter supplied) To reveal dynamic changes in networks of gene expression and epigenetic regulation during healthy human T cell aging.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms: GPL10999 GPL11154 27 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE65nnn/GSE65515/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA274258
Series		Accession: GSE65515	ID: 200065515

4436. Mastermind-like 3 controls proliferation and differentiation in neuroblastoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 18 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69183/
Series		Accession: GSE69183	ID: 200069183

4437. Mastermind-like 3 controls proliferation and differentiation in neuroblastoma (RNA-seq)
(Submitter supplied) Neuroblastoma cell lines can differentiate upon retinoic acid (RA) treatment, a finding that provided the basis for the clinical use of RA to treat neuroblastoma. However, resistance to RA is often observed, which limits its clinical utility. Using a gain-of-function genetic screen we identify the transcriptional coactivator Mastermind-like 3 (MAML3) as a gene whose ectopic expression confers resistance to RA. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69121/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA284759
Series		Accession: GSE69121	ID: 200069121

4438. RNA-Seq to assess the transcriptional effects of G quadruplex stabilization by the G4 ligand PhenDC3 in HT-1080 cells
(Submitter supplied) G-quadruplex motifs are frequently located near TSS and in the first introns of transcribed genes. We investigated the role that G4 structures play in transcription by stabilizing G4 DNA with the selective G4 ligand PhenDC3 in the HT-1080 human fibrosarcoma cell line. After treatment of triplicate samples with PhenDC3 or a negative control (DMSO carrier only), we performed RNA-Seq after poly-dT selection to assess changes in gene expression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (DIFF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE60nnn/GSE60630/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA259163
Series		Accession: GSE60630	ID: 200060630

4439. mRNA profiling  of Hepatocellular carcinoma (HCC)
(Submitter supplied) We did mRNA profiling and  showed that an interferon-inducible gene's deletion and under-expression is significantly associated with shorter time to tumor recurrence, shorter progression-free survival, and shorter overall survival in  HCC patients.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 42 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE56nnn/GSE56545/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA243866
Series		Accession: GSE56545	ID: 200056545

4440. GATA3-mediated chromatin reprogramming in breast cancer cells
(Submitter supplied) Pioneer transcription factors bind to silent chromatin, and initiate cell fate conversion. One potential pioneer factor, GATA3, is a critical component for multiple cellular programs. GATA3 is of particular interest as it regulates gene expression in breast cancers, and low expression correlates with poor prognosis. Here we demonstrate the pioneering activity of GATA3 utilizing a cellular reprogramming system (the mesenchymal-epithelial transition) in breast cancer cells. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL11154 GPL15520 80 Samples
FTP download: GEO (BED, BIGWIG, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72141/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA293191
Series		Accession: GSE72141	ID: 200072141

4441. Gene expression analysis following JQ1 treatments in colon cancer lines
(Submitter supplied) RNAseq is performed (50bp single end reads) on SW480, HT-29, HCT-15, HCT-116, COLO 205, and COLO 320 cell lines after DMSO or JQ1 treatment
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 36 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73318/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA296592
Series		Accession: GSE73318	ID: 200073318

4442. Ambient O2 pressure induces NF-kB1/RelA related inflammatory response in human lung epithelial cells in vitro
(Submitter supplied) Purpose: Oxygen (O2) levels in cell culture conditions is typically 2-5 fold higher than the physiological O2 levels that most tissues experience in vivo. The ambient atmospheric O2 (21%) is known to induce cell proliferation defects and cellular senescence in stem cell and primary cell cultures. Therefore, culturing these cells under lower O2 levels (2-9%) is currently a standard practice. However, the non-cancerous immortalized cells and cancer cells, which evade cellular senescence are normally cultured under 21% O2 levels and the effects of higher O2 levels on these cells are not fully understood. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68378/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA282543
Series		Accession: GSE68378	ID: 200068378

4443. Bioreactor-engineered cancer tissues mimic phenotypes, gene expression profiles and drug resistance mechanisms detectable in xenografts and clinical specimens.
(Submitter supplied) Cancer tissue-like structures were developed by using established human tumor cell lines in perfusion-based bioreactor systems. In colorectal cancer (CRC) cell lines, perfusion allowed more homogeneous scaffold seeding than tri-dimensional (3D) static cultures and significantly (13.7 fold, p<0.0001) higher proliferation. Resulting tissues exhibited morphology and phenotypes similar to xenografts generated in immunodeficient mice. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57961/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA248557
Series		Accession: GSE57961	ID: 200057961

4444. Distinct expression profiles of soft tissue sarcomas
(Submitter supplied) Soft tissue sarcomas (STTs) are neoplasms of mesenchymal cells, and are composed of more than 60 subtypes. Although many of these STTs could be distinguished from each other by morphology and limited IHC biomarkers, the precise diagnosis of STTs with similar morphology is still difficult to achieve. Therefore developing novel diagnosis biomarker and molecular signatures will be very helpful to pathologist in clinic.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 45 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE54nnn/GSE54734/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA237519
Series		Accession: GSE54734	ID: 200054734

4445. E2F1 transcription factor knockdown effect on gene expression in LNCaP-abl cells
(Submitter supplied) Our computational approach identified E2F1 as a potential collaborator of EZH2 in androgen-independent prostate cancer. This experiment is to designed to validate the crosstalking of E2F1 and EZH2 pathways. We showed that majority of the EZH2-induced genes in androgen-independent prostate tumor cells are in downstream of E2F1, providing insight into the EZH2-E2F1 collaborative regulatory pathway.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE56nnn/GSE56331/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA242934
Series		Accession: GSE56331	ID: 200056331

4446. Newly constructed network models of different WNT signaling cascades applied to breast cancer expression data
(Submitter supplied) RNA-Seq profiling of MCF-7 and MDA-MB-231. We profiled RNA expression in the estrogen-receptor-positive (ER+) MCF-7 and the triple-negative MDA-MB-231 breast cancer cells. The objective was to find genes differentially expressed between these cell lines as potential drivers of invasiveness of the triple-negative MDA-MB-231. We further utilized the identified differential genes to validate expression-responsive module of non-canonical Wnt signaling pathway.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 5 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73857/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA298248
Series		Accession: GSE73857	ID: 200073857

4447. p53 deficiency linked to BTG2 loss enhances metastatic potential by promoting tumor growth in primary and metastatic sites in PDX models of triple negative breast cancer
(Submitter supplied) We performed differential expression analyses from RNA-seq data derived from isogenic p53 wild-type and p53-knockdown triple negative breast tumors
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 7 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76433/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA307273
Series		Accession: GSE76433	ID: 200076433

4448. BPTF is required for c-MYC-induced remodelling of target chromatin and transcriptional activation [RNA-Seq]
(Submitter supplied) The c-MYC oncogene is a key transcription factor deregulated in most human tumors. Histone marks associated with transcriptionally active genes in euchromatic islands define the set of high-affinity c-MYC targets. The mechanisms involved in their recognition by c-MYC are not known but likely involve chromatin-remodelling and chromatin-modifying complexes. Here, we show that c-MYC interacts with BPTF, a core subunit of the NURF complex that binds active chromatin. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 4 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE65nnn/GSE65545/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA274338
Series		Accession: GSE65545	ID: 200065545

4449. Dissection of transcriptional and cis-regulatory control of differentiation in human pancreatic cancer.
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 79 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64560/
Series		Accession: GSE64560	ID: 200064560

4450. Dissection of transcriptional and cis-regulatory control of differentiation in human pancreatic cancer [RNA-seq]
(Submitter supplied) The histological grade of carcinomas describes the ability of tumor cells to organize differentiated epithelial structures and has prognostic impact. Molecular control of differentiation in normal and cancer cells relies on lineage-determining transcription factors (TFs) that activate the repertoire of cis-regulatory elements controlling cell type-specific transcriptional outputs. TF recruitment to cognate genomic DNA binding sites results in the deposition of histone marks characteristic of enhancers and other cis-regulatory elements. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 29 Samples
FTP download: GEO (DIFF, FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64558/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA271301
Series		Accession: GSE64558	ID: 200064558

4451. The RNA binding protein IGF2BP3 promotes hematopoietic progenitor cell proliferation by targeting leukemogenic pathways
(Submitter supplied) The goal of this study was to determine IGF2BP3 RNA targets in human B-cell Acute Lymphocitic Leukemia cell models.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL11154 12 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76931/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA308961
Series		Accession: GSE76931	ID: 200076931

4452. Epigenomic profiling of Non-small-cell Lung Cancer (NSCLC) cells with or without Eed
(Submitter supplied) Polycomb repressive complexes (PRC) are frequently implicated in human cancer acting either as oncogenes or tumor suppressors. Here we show that PRC2 is a critical regulator of Kras-driven non-small-cell lung cancer (NSCLC) progression. Modulation of PRC2 by either Ezh2 overexpression or Eed deletion enhances Kras-driven adenomagenesis and inflammation, respectively. Eed-loss-driven inflammation leads to massive macrophage recruitment and marked decline in tissue function. more...
Organism:	Mus musculus; Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL13112 GPL17021 GPL16791 31 Samples
FTP download: GEO (BED, BIGWIG, BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE61nnn/GSE61190/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA260490
Series		Accession: GSE61190	ID: 200061190

4453. The Functional Genomic Landscape of Human Breast Cancer Drivers, Vulnerabilities, and Resistance (RNASeq)
(Submitter supplied) Large-scale genomic studies have identified multiple somatic aberrations in breast cancer, including copy number alterations, translocations, and point mutations. Still, identifying causal variants and emergent vulnerabilities that arise as a consequence of genetic alterations remain major challenges. We performed whole genome shRNA “dropout screens” on 77 breast cancer cell lines. Using a new hierarchical linear regression algorithm to score our screen results and integrate them with accompanying detailed genetic and proteomic information, we identify novel vulnerabilities in breast cancer, including new candidate “drivers,” and reveal general functional genomic properties of cancer cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 82 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73526/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA297219
Series		Accession: GSE73526	ID: 200073526

4454. Integrative analysis identifies targetable CREB1/FoxA1 transcriptional co-regulation as a predictor of prostate cancer recurrence
(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this work is comprehensive analysis of target genes co-regulated by CREB1 and FoxA1 in prostate cancer cell models, tissues, and circulating tumor cells (CTCs). Expression of CREB1/FoxA1 target genes corresponds with disease recurrence and aggressive clinical features. Methods: LNCaP cells between passage number 32-34 and abl between 62-64 were used for assay. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 17 Samples
FTP download: GEO (BED, BW, TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63034/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA266510
Series		Accession: GSE63034	ID: 200063034

4455. The Histone Methyltransferases MLL1 and DOT1L Cooperate with Meningioma-1 to Induce AML
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL13112 GPL11154 27 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76750/
Series		Accession: GSE76750	ID: 200076750

4456. The Histone Methyltransferases MLL1 and DOT1L Cooperate with Meningioma-1 to Induce AML [Human RNA-seq]
(Submitter supplied) Purpose: To characterize transcriptional changes associated with inhibition of Dot1l in 2 inv(16) patient AML samples Methods: We sequenced mRNA from patient samples that were exposed to 5 uM EPZ004777 or DMSO control for 7  days. Results: Inhibition of Dot1l leads to gene expression changes in genes related to cell growth and cell cycle.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76747/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA308493
Series		Accession: GSE76747	ID: 200076747

4457. Effects on the transcriptome upon deletion of distal elements are not correlated with the size of H3K27Ac peaks in human cells
(Submitter supplied) Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with increased risk for colorectal cancer (CRC). A molecular understanding of the functional consequences of this genetic variation is complicated because most GWAS SNPs are located in non-coding regions. After identifying H3K27Ac peaks in HCT116 colon cancer cells that harbor SNPs associated with an increased risk for CRC, we used CRISPR/Cas9 nuclease to delete 2 CRC risk-associated H3K27Ac peaks (E7 and E24), a peak that is not associated with CRC risk (18qE) and a region that doesn?t have H3K27Ac peak (18qNE) from HCT116 cells and analyzed effects on the transcriptome and epigenome. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms: GPL18573 GPL11154 32 Samples
FTP download: GEO (TXT, ZIP) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72631/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA294738
Series		Accession: GSE72631	ID: 200072631

4458. Combinatorial targeting of nuclear export and translation of RNA inhibits aggressive B-cell lymphoma
(Submitter supplied) Aggressive double and triple hit (DH/TH) DLBCL feature activation of Hsp90 stress pathways.  Herein, we show that Hsp90 controls post-transcriptional dynamics of key mRNA species including those encoding BCL6, MYC and BCL2. Using a proteomics approach, we found that Hsp90 binds to and maintains activity of eIF4E (eukaryotic translation initiation factor 4E). EIF4E drives nuclear export and translation of BCL6, MYC and BCL2 mRNA. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63265/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA267117
Series		Accession: GSE63265	ID: 200063265

4459. Transcriptome Sequencing (RNAseq) enables utilization of Formalin-Fixed, Paraffin-Embedded Biopsies with Clear Cell Renal Cell Carcinoma for Exploration of Disease Biology and Biomarker Development
(Submitter supplied) Formalin-fixed, paraffin-embedded (FFPE) tissues are an underused resource for molecular analyses. This proof of concept study aimed to compare RNAseq results from FFPE biopsies with the corresponding RNAlater® (Qiagen, Germany) stored samples from clear cell renal cell carcinoma (ccRCC) patients, to enable the decision of whether or not it is feasible to apply RNAseq technology to archival tissue. Core biopsies were obtained with a 16g needle from 16 patients undergoing partial or full nephrectomy. The RNA sequencing libraries were generated applying the new Illumina TruSeq® Access library preparation protocol. 
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 64 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76207/
Series		Accession: GSE76207	ID: 200076207

4460. Coordinated control of senescence by lncRNA UCA1 and a novel CAPERα/TBX3 co-repressor
(Submitter supplied) Coordination of a complex series of transcriptional, structural and signaling events culminates in cellular senescence, a crucial tumor suppressor mechanism. We have discovered a repressor complex composed of TBX3 and CAPERa which functions upstream of the RB and p53 effector pathways and is required to prevent senescence of primary cells and in mouse embryos. TBX3/ CAPERa directly binds and represses transcription and chromatin structure of genes in multiple senescence pathways and the LncRNA UCA1, which we have identified as a novel tumor suppressor. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 10 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76572/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA308072
Series		Accession: GSE76572	ID: 200076572

4461. The apoptotic network and expression of BH3-containing proteins predict phenotypic response to BET bromodomain inhibitors
(Submitter supplied) Small molecule inhibitors of the bromodomain and extraterminal (BET) family of proteins are in clinical trials for a variety of cancers, but patient selection strategies are limited.  This is due in part to the heterogeneity of response following BET inhibition (BETi), which includes differentiation, senescence, and cell death in subsets of cancer cell lines.  To elucidate the dominant features defining response to BETi, we carried out phenotypic and gene expression analysis of both treatment naïve cell lines and engineered tolerant lines. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 26 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69383/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA285337
Series		Accession: GSE69383	ID: 200069383

4462. Response and resistance to BET bromodomain inhibitors in triple negative breast cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL18573 65 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63584/
Series		Accession: GSE63584	ID: 200063584

4463. Response and resistance to BET bromodomain inhibitors in triple negative breast cancer [RNA-Seq]
(Submitter supplied) Triple negative breast cancer (TNBC) is a heterogeneous and clinically aggressive disease for which there is no targeted therapy. Here we report the preferential and high sensitivity of TNBCs to BET bromodomain inhibitors such as JQ1 manifested by cell cycle arrest in early G1, apoptosis, and induction of markers of luminal epithelial differentiation in vitro and in vivo. The sensitivity of TNBC and other tumor types to BET inhibition establishes a rationale for clinical investigation, and a motivation to understand mechanisms of resistance. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL11154 28 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63582/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA268320
Series		Accession: GSE63582	ID: 200063582

4464. Bromodomain inhibition of the transcriptional coactivators CBP/EP300 as a therapeutic strategy to target the IRF4 network in multiple myeloma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 21 Samples
FTP download: GEO (TDF, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71911/
Series		Accession: GSE71911	ID: 200071911

4465. Next generation sequencing of A375 melanoma cell line revealed a complex regulatory network when IGFBP5 overexpressed
(Submitter supplied) IGFBP5, a critical regulators of insulin-like growth factors, has been reported to be involved in many kinds of carcinogenesis and cancer metastases. The role of IGFBP5 in human malignant melanoma (MM), however, remains largely unknown. In this study, we demonstrated that IGFBP5 was aberrantly expressed in human melanoma cells and cancer tissues. Overexpression of IGFBP5 dramatically inhibited the proliferation, migration and invasion of human melanoma cells, whereas knockdown of IGFBP5 by shRNA resulted in the opposite effects, enhanced the cell proliferation, migration and metastasis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17301 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64693/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA271653
Series		Accession: GSE64693	ID: 200064693

4466. Bromodomain inhibition of the transcriptional coactivators CBP/EP300 as a therapeutic strategy to target the IRF4 network in multiple myeloma (RNA-Seq)
(Submitter supplied) Pharmacological inhibition of chromatin co-regulatory factors represents a clinically validated strategy to modulate oncogenic signaling through selective attenuation of gene expression. Here, we demonstrate that CBP/EP300 bromodomain inhibition preferentially abrogates the viability of multiple myeloma cell lines. Phenotypic effects are preceded by the direct transcriptional suppression of the lymphocyte-specific transcription factor IRF4 and the subsequent down-regulation of the IRF4 transcriptional program. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64317/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA270740
Series		Accession: GSE64317	ID: 200064317

4467. A designed inhibitor of p53 aggregation rescues p53 tumor-suppression in ovarian carcinomas
(Submitter supplied) Half of all human cancers lose p53 function by missense mutations, with an unknown fraction of these containing p53 in a self-aggregated, amyloid-like state. Here we show that a cell-penetrating peptide, ReACp53, designed to inhibit p53 amyloid formation, rescues p53 function in cancer cell lines and in organoids derived from high-grade serous ovarian carcinomas (HGSOC), an aggressive cancer characterized by ubiquitous p53 mutations. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74550/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA300686
Series		Accession: GSE74550	ID: 200074550

4468. Expression profiles of cultured human epididymis cells reveal the functional diversity of caput, corpus and cauda regions.
(Submitter supplied) Purpose: To compare the transcriptome profiles (RNA-seq) of cultured human epididymis cells and tissue from the caput, corpus and cauda regions of the human epididymis. Methods: Human epididymis tissue was obtained with Institutional Review Board approval from 3 patients (UC05, UC06, UC09, range: 22 - 36 years) undergoing inguinal radical orchiectomy for a clinical diagnosis of testicular cancer. None of the epididymides had extension of the testicular cancer. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72986/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA295529
Series		Accession: GSE72986	ID: 200072986

4469. MAGE-A1 Promotes Proliferation, Migration and Invasion of Human Melanoma Cells through RNA-SEQ Analysis via Affecting C-JUN-IL8-ARHGAP29 Network
(Submitter supplied) To define the role of MAGE-A1 in melanoma growth and metastasis, we performed RNA-seq analysis on MAGE-A1 overexpression (OE) and knockdown (KD) models in A375 human melanoma cell line. Our results revealed that overexpression of MAGE-A1 dramatically promoted proliferation, migration, and invasion of human melanoma cells in vitro and down-regulated of MAGE-A1 inhibited tumor cell proliferation and invasion. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17301 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66859/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA278118
Series		Accession: GSE66859	ID: 200066859

4470. RNA-seq 1,25(OH)2D3 time course in THP-1 cells
(Submitter supplied) gene expression profiling by RNA-seq in THP-1 cells treated with 1,25(OH)2D3 for 2.5-24 h
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 18 Samples
FTP download: GEO (DIFF, TDF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69284/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA285092
Series		Accession: GSE69284	ID: 200069284

4471. METTL3 promotes translation in human cancer cells
(Submitter supplied) we find METTL3 associates with polyribosomes and promotes translation. METTL3 depletion inhibits translation, and both wild-type and catalytically inactive METTL3 promote translation when tethered to the 3' untranslated region (UTR) of a reporter mRNA. Mechanistically, METTL3 enhances mRNA translation through an interaction with the translation initiation machinery.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL11154 11 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76367/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA307106
Series		Accession: GSE76367	ID: 200076367

4472. A novel RAF kinase inhibitor with DFG-out binding mode: high efficacy in BRAF-mutant tumor xenograft models in the absence of normal tissue hyperproliferation
(Submitter supplied) Purpose: Seek for differential gene expression in vemurafenib-resistant A375 tumors vs. untreated controls to provide a rationale for resistance mechanism Methods: mRNA profiles of vemurafenib-resistant A375 tumors and untreated control tumors were generated by transcriptome sequencing of A375 melanoma bearing mice. Since our xenograft samples contain a mixture of human and mouse RNAs we mapped RNASeq reads against a hybrid human/mouse genome. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74729/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA301353
Series		Accession: GSE74729	ID: 200074729

4473. 1,25(OH)2D3 time course in THP-1 cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL9115 35 Samples
FTP download: GEO (TDF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69303/
Series		Accession: GSE69303	ID: 200069303

4474. Assessment of ability of hTSLP to maintain primary CRLF2 B-ALL cells in a xenograft model in a state more similar to the parent leukemia
(Submitter supplied) Xenograft models represent an excellent method for expanding primary leukemias, but their ability to preserve the gene expression profile of the parent leukemia may also depend on providing microenvironmental factors that are not cross-reactive between human and mouse. Here we focused on leukemias with a CRLF2 mutation, and the ability of human TSLP to stimulate these cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 5 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74339/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA299771
Series		Accession: GSE74339	ID: 200074339

4475. Genome-wide profiling of histone H3 lysine 27 and lysine 4 trimethylation in multiple myeloma reveals the importance of Polycomb gene targeting and highlights EZH2 as a potential therapeutic target
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL16558 GPL17586 22 Samples
FTP download: GEO (BED, CEL, TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69253/
Series		Accession: GSE69253	ID: 200069253

4476. BMAL1 Activates Clock Gene Expression by Regulating Transcription Initiation
(Submitter supplied) We showed that Bmal1 mainly regulates clock gene initiation, with this functioning being highly conserved across species.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL10999 GPL16791 GPL17021 27 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68416/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA282679
Series		Accession: GSE68416	ID: 200068416

4477. Genome-wide mapping of TEL-AML1 targets in acute leukemia
(Submitter supplied) Around 20-25% of childhood acute lymphoblastic leukemias carry the TEL-AML1 (TA) fusion gene. It is a fusion of two central hematopoietic transcription factors, TEL (ETV6) and AML1 (RUNX1). Despite its prevalence, the exact genomic targets of TA have remained elusive. We evaluated gene loci and enhancers targeted by TA genome-wide in precursor B acute leukemia cells  using global nuclear run-on sequencing (GRO-seq).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67519/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA280122
Series		Accession: GSE67519	ID: 200067519

4478. The RNA-Seq transcriptome of human prostate cancer cell line depleted of CIC
(Submitter supplied) To identify which genes were regulated by CIC in human prostate cancer cell, the effect of CIC knockdown on PC3 cell transcriptome was determined
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 4 Samples
FTP download: GEO (DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64025/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA269778
Series		Accession: GSE64025	ID: 200064025

4479. Genome-wide profiling of histone H3 lysine 27 and lysine 4 trimethylation in multiple myeloma reveals the importance of Polycomb gene targeting and highlights EZH2 as a potential therapeutic target [Seq]
(Submitter supplied) Multiple myeloma (MM) is a hematopoietic malignancy characterised by the accumulation of neoplastic post-germinal centre, isotype-switched, long-lived plasma cell within the bone marrow. In genetic and clinical terms MM is highly heterogeneous and remains fatal. Here we present the first epigenomic map of MM derived from freshly isolated bone marrow plasma cells from four patients. Using ChIP- and RNA-sequencing we define a set of silent H3K27me3 targets, active genes bearing H3K4me3, and bivalent genes.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL16558 16 Samples
FTP download: GEO (BED, TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53215/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA231147
Series		Accession: GSE53215	ID: 200053215

4480. LncRNA DINO guides DNA damage signaling
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by array; Other; Expression profiling by high throughput sequencing
4 related Platforms 56 Samples
FTP download: GEO (BED, NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76420/
Series		Accession: GSE76420	ID: 200076420

4481. Expression data for KDM1B knockdown in Glioma-Initiating Cells (GICs)
(Submitter supplied) Glioblastoma (GBM) is the most common and aggressive primary brain tumor in adults, with glioma initiating cells (GICs) implicated to be critical for tumor progression and resistance to therapy. KDM1B is involved in regulating GICs' responses to hypoxia, since over-expression of KDM1B delays the cell growth under hypoxia while knocking-down of KDM1B in GICs promotes their survival and tumorigenic abilities.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73573/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA297346
Series		Accession: GSE73573	ID: 200073573

4482. Profiling of three leiomyosarcoma molecular subtypes with RNA-sequencing
(Submitter supplied) Leiomyosarcoma (LMS) is a malignant neoplasm with smooth muscle differentiation, and there are three molecular subtypes of LMS which have been defined previously by our lab. To further validate these subtypes and identify potential therapeutic targets in each subtype, we profiled the LMS cases from each subtype with RNA-Seq technology.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 54 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62544/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA264379
Series		Accession: GSE62544	ID: 200062544

4483. FOXD3 is a novel tumor suppressor in lung cancer
(Submitter supplied) The transcription factor forkhead box D3 (FoxD3) is a transcriptional factor which belongs to forkhead box (Fox) transcription factor family. The functions of FOXD3 in embryogenesis and in the development of neural crest cells have been clearly defined. Its tumor suppressor function hasbeen found in many types of cancer in recent years. However, the study about its roles in lung cancerdevelopment is still lacking. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64513/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA271162
Series		Accession: GSE64513	ID: 200064513

4484. Truncation of LOC100288798 (SLC38A4-AS) lncRNA in human haploid KBM7 cell line
(Submitter supplied) Many thousand long non-coding (lnc) RNAs are mapped in the human genome. Time consuming studies using reverse genetic approaches by post-transcriptional knock-down or genetic modification of the locus demonstrated diverse biological functions for a few of these transcripts. The Human Gene Trap Mutant Collection in haploid KBM7 cells is a ready-to-use tool for studying protein-coding gene function. As lncRNAs show remarkable differences in RNA biology compared to protein-coding genes, it is unclear if this gene trap collection is useful for functional analysis of lncRNAs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71284/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA290802
Series		Accession: GSE71284	ID: 200071284

4485. Identifying transcription start sites and active enhancer elements using BruUV-seq
(Submitter supplied) BruUV-seq utilizes UV light to introduce transcription-blocking DNA lesions randomly in the genome prior to bromouridine-labeling and deep sequencing of nascent RNA. By inhibiting transcription elongation, but not initiation, pre-treatment with UV light leads to a redistribution of transcription reads resulting in the enhancement of nascent RNA signal towards the 5′-end of genes promoting the identification of transcription start sites (TSSs). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75398/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA304151
Series		Accession: GSE75398	ID: 200075398

4486. CRISPR-Cas9 combinatorial KO of epigenetic regulators in human ovarian cancer cells
(Submitter supplied) We sequenced polyA mRNA from OVCAR8-ADR-Cas9 cells in which one or two of 3 epigenetic regulators (BRD4, KDM4C, KDM6B) had been knocked out to examine how global gene expression was affected and evaluate potential synergistic effects at a molecular level.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71074/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA290313
Series		Accession: GSE71074	ID: 200071074

4487. Identification of MEF2B, EBF1, and IL6R as chromosome bound targets of EBNA1 essential for EBV infected B-lymphocyte survival
(Submitter supplied) EBNA1 is the EBV-encoded nuclear antigen required for viral episome maintenance during latency.  EBNA1 is a sequence specific DNA binding protein with high affinity binding sites for the viral genome, especially OriP.  EBNA1 can also bind sequence specifically to a large number of sites in the host cellular genome, but the function of these binding sites has remained elusive.  EBNA1 is also known to provide a host cell survival function, but the molecular mechanisms accounting for this function are not completely understood. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL9115 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73887/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA298334
Series		Accession: GSE73887	ID: 200073887

4488. Competition between DNA methylation and transcription factors determines binding of NRF1
(Submitter supplied) Eukaryotic transcription factors (TFs) are key determinants of gene activity, yet they bind only a fraction of their corresponding DNA sequence motifs in any given cell type. Chromatin has the potential to restrict accessibility of binding sites; however, in which context chromatin states are instructive for TF binding remains mainly unknown. To explore the contribution of DNA methylation to constrained TF binding, we mapped DNase-I-hypersensitive sites in murine stem cells in the presence and absence of DNA methylation. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms: GPL17021 GPL16791 48 Samples
FTP download: GEO (BW, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67867/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA281090
Series		Accession: GSE67867	ID: 200067867

4489. HSB-2 cells stably expressing LDB1 or mutant LDB1 proteins
(Submitter supplied) LMO2 is a component of multisubunit DNA-binding transcription factor complexes that regulate gene expression in hematopoietic stem and progenitor cell development. Enforced expression of LMO2 causes leukemia by inducing hematopoietic stem cell-like features in T-cell progenitor cells, but the biochemical mechanisms of LMO2 function have not been fully elucidated.  In this study we systematically dissected the LMO2/LDB1 binding interface to investigate the role of this interaction in T-cell leukemia. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75839/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA305514
Series		Accession: GSE75839	ID: 200075839

4490. Combined Genome and Transcriptome Sequencing to Identify Allelic Selection in Epithelial Ovarian Cancer
(Submitter supplied) Identifying genes where a variant allele is preferentially expressed in tumors could lead to a better understanding of cancer biology and optimization of targeted therapy. However, tumor sample heterogeneity complicates standard approaches for detecting preferential allele expression. We therefore developed a novel approach combining genome and transcriptome sequencing data from the same sample that corrects for sample heterogeneity and identifies significant preferentially expressed alleles. more...
Organism:	Homo sapiens
Type:		Genome variation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL10999 GPL11154 GPL16791 28 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75935/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA305745
Series		Accession: GSE75935	ID: 200075935

4491. Downregulation of LATS kinases alters p53 to promote cell migration
(Submitter supplied) p53 is a pivotal tumor suppressor and a major barrier against cancer. We now report that silencing of the Hippo pathway tumor suppressors LATS1 and LATS2 in non-transformed mammary epithelial cells reduces p53 phosphorylation and increases its association with the p52 NF-?B subunit. Moreover, it partly shifts p53’s conformation and transcriptional output towards a state resembling cancer-associated p53 mutants, and endow p53 with the ability to promote cell migration. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74493/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA300555
Series		Accession: GSE74493	ID: 200074493

4492. RNA-Seq of human astrocytes
(Submitter supplied) Astrocytes were purified from fetal and adult human brain tissue using an immunopanning method with the HepaCAM antibody. Samples were taken from otherwise 'healthy' pieces of tissue, unless otherwise specified.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL19057 45 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73721/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA297760
Series		Accession: GSE73721	ID: 200073721

4493. RNA Polymerase II-associated factor 1 regulates the release and phosphorylation of paused RNA Polymerase II
(Submitter supplied) Release of promoter-proximal paused RNA polymerase II (Pol II) during early elongation is a critical step in transcriptional regulation in metazoan cells. Paused Pol II release is thought to require the kinase activity of cyclin-dependent kinase 9 (CDK9) for the phosphorylation of DRB sensitivity-inducing factor, negative elongation factor, and C-terminal domain (CTD) serine-2 of Pol II. We found that Pol II-associated factor 1 (PAF1) is a critical regulator of paused Pol II release, that positive transcription elongation factor b (P-TEFb) directly regulates the initial recruitment of PAF1 complex (PAF1C) to genes, and that the subsequent recruitment of CDK12 is dependent on PAF1C. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL11154 GPL16791 32 Samples
FTP download: GEO (BEDGRAPH, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62171/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA263366
Series		Accession: GSE62171	ID: 200062171

4494. AKT Inhibition Promotes Non-autonomous Cancer Cell Survival
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Protein profiling by protein array; Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other
Platforms: GPL20791 GPL11154 GPL20790 40 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71901/
Series		Accession: GSE71901	ID: 200071901

4495. AKT Inhibition Promotes Non-autonomous Cancer Cell Survival [RNA-Seq]
(Submitter supplied) Small-molecule inhibitors of AKT signaling are being in evaluated in patients with various cancer types, but have so far proven therapeutically disappointing for reasons that remain unclear. Here, we treat cancer cells with sub-therapeutic doses of Akti-1/2, an allosteric small molecule AKT inhibitor, in order to experimentally model pharmacologic inhibition of AKT signaling in vitro. We then apply a combined RNA, protein, and metabolite profiling approach to develop an integrated, multi-scale, molecular snapshot of this “AKTlow” cancer cell state. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71900/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA292420
Series		Accession: GSE71900	ID: 200071900

4496. AKT Inhibition Promotes Non-autonomous Cancer Cell Survival [GRO-Seq]
(Submitter supplied) Small-molecule inhibitors of AKT signaling are being in evaluated in patients with various cancer types, but have so far proven therapeutically disappointing for reasons that remain unclear. Here, we treat cancer cells with sub-therapeutic doses of Akti-1/2, an allosteric small molecule AKT inhibitor, in order to experimentally model pharmacologic inhibition of AKT signaling in vitro. We then apply a combined RNA, protein, and metabolite profiling approach to develop an integrated, multi-scale, molecular snapshot of this “AKTlow” cancer cell state. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71898/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA292421
Series		Accession: GSE71898	ID: 200071898

4497. TET-catalyzed 5-hydroxymethylcytosine regulates gene expression in differentiating colonocytes and colon cancer
(Submitter supplied) 5-hydroxymethylcytosine (5-mC) and gene expression profiling of T84 cell differentiation; 5-hmC profiling of colon cancer colonocyte fractions
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69333/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA285245
Series		Accession: GSE69333	ID: 200069333

4498. Assembly of methylated LSD1 and CHD1 drives AR-dependent transcription and translocation
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 17 Samples
FTP download: GEO (BED, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64530/
Series		Accession: GSE64530	ID: 200064530

4499. Assembly of methylated LSD1 and CHD1 drives AR-dependent transcription and translocation [RNA-Seq]
(Submitter supplied) The aim of the study is to identify AR target gens in LNCaP cells
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64529/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA271255
Series		Accession: GSE64529	ID: 200064529

4500. DNA repair in species with extreme lifespan differences
(Submitter supplied) We compared RNA-seq expression patterns in liver, an organ with high oxidative metabolism and abundant spontaneous DNA damage, from humans, naked mole rats, and mice, differing in maximum lifespan over a range of ~100, 30, and 3 years, respectively, for 130 genes involved in DNA repair. The results show that the longer-lived species, human and naked mole rat, share higher expression of these DNA repair genes, including core genes in several DNA repair pathways. more...
Organism:	Homo sapiens; Heterocephalus glaber; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL17021 GPL21195 9 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75606/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA304727
Series		Accession: GSE75606	ID: 200075606

4501. Gene expression profiles in NORAD knockout and PUMILIO overexpressing cells
(Submitter supplied) Purpose: PUMILIO proteins are known to repress target genes by specifically binding to PUMILIO response elements (PREs) in target mRNAs.  NORAD is a noncoding RNA that negatively regulates PUMILIO activity. The goal of this study was to determine the gene expression changes that result from knockout of NORAD or overexpression of PUMILIO and to test whether NORAD knockout causes PUMILIO hyperactivity. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 17 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75440/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA304717
Series		Accession: GSE75440	ID: 200075440

4502. RNA splicing alteration on glioblastoma and normal neural stem cells
(Submitter supplied) We identified PHF5A as a functional synthetic-lethal hit in glioblastoma stem cells compared to normal neural stem cells. We wanted to perform analysis of RNA isoforms present in glioblastoma or normal neural stem cells with or without PHF5A depletion. We performed shRNA knockdown of PHF5A or used non-silencing shRNA as a control, selected infected cells with puromycin, and isolated RNA for sequencing.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 7 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75147/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA302647
Series		Accession: GSE75147	ID: 200075147

4503. Genome-Wide Transcriptional Regulation Mediated By Biochemically Distinct Forms of SWI/SNF
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 28 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69568/
Series		Accession: GSE69568	ID: 200069568

4504. Combinatorial Regulation Mediated by Biochemically Distinct Forms of SWI/SNF [RNA-Seq]
(Submitter supplied) The precise makeup of chromatin remodeling complexes is important for determining cell type and cell function. The SWI/SNF chromatin remodeling complex is made up of multiple subunits that can be filled by mutually exclusive proteins. Inclusion or exclusion of these proteins has profound functional consequences, yet we currently understand little about the direct functional relationship between these biochemically distinct forms of remodeling complexes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 19 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69567/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA285874
Series		Accession: GSE69567	ID: 200069567

4505. Transcriptome analysis of SiHa cells
(Submitter supplied) This study assessed the transcriptional profile of SiHa cells. SiHa is a cervical cancer cell line with integrated HPV16, and was used as a model to study human gene expression in the context of integrated virus. Gene expression in SiHa, calculated by Cufflinks, was scored in windows around the locations of known viral integrations in patients or cell lines to determine if there was an association between gene expression and viral integration. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 1 Sample
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67115/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA278979
Series		Accession: GSE67115	ID: 200067115

4506. High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities
(Submitter supplied) The ability to perturb genes in human cells is crucial for elucidating gene function and holds great potential for finding therapeutic targets for diseases such as cancer. To extend the catalog of human core and context- dependent fitness genes, we have developed a high-complexity second-generation genome-scale CRISPR-Cas9 gRNA library and applied it to fitness screens in five human cell lines. Using an improved Bayesian analytical approach, we consistently discover 5-fold more fitness genes than were previously observed. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL16791 5 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75189/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA302748
Series		Accession: GSE75189	ID: 200075189

4507. Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples
(Submitter supplied) DNase I hypersensitive sites (DHSs) provide important information on the presence of transcriptional regulatory elements and the state of chromatin in mammalian cells1, 2, 3. Conventional DNase sequencing (DNase-seq) for genome-wide DHSs profiling is limited by the requirement of millions of cells4, 5. Here we report an ultrasensitive strategy, called single-cell DNase sequencing (scDNase-seq) for detection of genome-wide DHSs in single cells. more...
Organism:	Mus musculus; Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL13112 GPL11154 46 Samples
FTP download: GEO (BED, BEDGRAPH, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE61nnn/GSE61844/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA262547
Series		Accession: GSE61844	ID: 200061844

4508. Ribosomal profiling of CRISPR edited and parental CHL-1 cell line
(Submitter supplied) Ribosomal stress was evaluated in melanoma cell line CHL-1 after CRISPR editing genomic locus containing SNORD50A/B
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL16791 6 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71763/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA292020
Series		Accession: GSE71763	ID: 200071763

4509. Characterization of macrophage - cancer cell crosstalk in estrogen receptor positive and triple-negative breast cancer
(Submitter supplied) We performed whole transcriptome sequencing of human monocytes that were co-cultured with estrogen receptor positive (ER+) or triple-negative (TNBC) breast cancer cell lines and studied the biological responses related to the differential gene activation in both cell types to understand how different cancer cells educate host cells to support tumor growth
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 15 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75130/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA302603
Series		Accession: GSE75130	ID: 200075130

4510. Characterization of parental and rociletinib-resistant derived H1975 cell lines
(Submitter supplied) Through development of an in vivo orthotopic lung cancer model, we reveal an unanticipated pathway driving spontaneous metastasis that is orchestrated by the developmentally-regulated transcriptional repressor, Capicua (CIC).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74866/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA302630
Series		Accession: GSE74866	ID: 200074866

4511. Effect of CHKA knockdown on C4-2 cell transcriptome
(Submitter supplied) Analysis of C4-2 Prostate cancer cell line after 72 hours of knockdown. CHKA is overexpressed in a number of solid tumours, including prostate cancer. Results provide insight into the molecular mechanisms of CHKA in prostate carcinogenesis.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63700/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA268830
Series		Accession: GSE63700	ID: 200063700

4512. Cross-talk between PRMT1-mediated methylation and ubiquitylation on RBM15 controls RNA splicing
(Submitter supplied) RBM15, an RNA binding protein, determines cell-fate specification of many tissues including blood. We demonstrate that RBM15 is methylated by protein arginine methyltransferase 1 (PRMT1) at residue R578 leading to its degradation via ubiquitylation by an E3 ligase (CNOT4). Overexpression of PRMT1 in acute megakaryocytic leukemia cell lines blocks megakaryocyte terminal differentiation by downregulation of RBM15 protein level. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 7 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73893/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA298347
Series		Accession: GSE73893	ID: 200073893

4513. Combined ultra-low input mRNA and whole-genome sequencing from human embryonic stem cells
(Submitter supplied) Next Generation Sequencing has proven to be an exceptionally powerful tool in the field of genomics and transcriptomics. With recent development it is nowadays possible to analyze ultra-low input sample material down to single cells. Nevertheless investigating such sample material still limits the analysis to either the genome or transcriptome, hence a combined analysis of both types of nucleic acids from the same sample material is still in demand.We developed a protocol which enables the combined analysis of the genome as well as the transcriptome by Next Generation Sequencing from ultra-low input samples. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL11154 3 Samples
FTP download: GEO (TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69471/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA285681
Series		Accession: GSE69471	ID: 200069471

4514. Pervasive transcription read-through promotes aberrant expression of oncogenes and RNA chimeras in renal carcinoma
(Submitter supplied) Aberrant expression of cancer genes and non-canonical RNA species is a hallmark of cancer. However, the mechanisms driving such atypical gene expression programs are incompletely understood. Here, our transcriptional profiling of a cohort of 50 primary clear cell renal cell carcinoma (ccRCC) samples from The Cancer Genome Atlas (TCGA) reveals that transcription read-through beyond the termination site is a source of transcriptome diversity in cancer cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64451/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA271032
Series		Accession: GSE64451	ID: 200064451

4515. Ribosome profiling and RNA sequencing of MCF10A-ER-Src and fibroblast cell transformation
(Submitter supplied) We applied ribosome profiling and RNA sequencing to examine gene expression regulation during oncogenic cell transformation. One model involves normal mammary epithelial cells (MCF10A) containing ER-Src. Treatment of such cells with tamoxifen rapidly induces Src, thereby making it possible to kinetically follow the transition between normal and transformed cells. The other model consists of three isogenic cell lines derived from primary fibroblasts in a serial manner (Hahn et al., 1999). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL11154 36 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE65nnn/GSE65885/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA275305
Series		Accession: GSE65885	ID: 200065885

4516. Diverse and Targetable Kinase Alterations Drive Histiocytic Neoplasms
(Submitter supplied) Histiocytic neoplasms are clonal, hematopoietic disorders characterized by an accumulation of abnormal, monocyte-derived dendritic cells or macrophages in Langerhans Cell (LCH) and non-Langerhans (non-LCH) histiocytoses, respectively. The discovery of BRAFV600E mutations in ~50% of these patients provided the first molecular therapeutic target in histiocytosis. However, recurrent driving mutations in the majority of BRAFV600E-wildtype, non-LCH patients are unknown, and recurrent cooperating mutations in non-MAP kinase pathways are undefined for the histiocytic neoplasms. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 13 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74442/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA300424
Series		Accession: GSE74442	ID: 200074442

4517. HCT116 cells treated with the p97 inhibitior CB-5083
(Submitter supplied) The goal of this study was to analyze differential gene expression 8 hr after treatment of CB-5083, a small molecule inhibitor of p97 (VCP), in HCT116 cells grown in culture.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73588/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA297366
Series		Accession: GSE73588	ID: 200073588

4518. SOX15 governs a transcriptional program in human esophageal stratified epithelium and in a subset of esophageal adenocarcinomas
(Submitter supplied) We identified spatially restricted transcription factors and found SOX15 expression confined to stratified esophageal epithelium, with attenuation in Barrett's esophagus. SOX15 binds esophagus-specific loci and its loss in human esophageal cells affected esophagus-specific transcripts
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (BED, DIFF, FPKM_TRACKING, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62909/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA266111
Series		Accession: GSE62909	ID: 200062909

4519. Transcriptome-wide mapping of cut sites of the viral endoribonuclease SOX from Kaposi's sarcoma-associated herpesvirus (KSHV)
(Submitter supplied) Purpose: identify sites in endogenous mRNAs that are cut by KSHV SOX; Method: parallel analysis of RNA ends (PARE, following Zhai et al., 2014); Results: SOX cuts at discrete locations in mRNAs
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70373/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA288467
Series		Accession: GSE70373	ID: 200070373

4520. Messenger RNA profile analysis deciphers new Esrrb responsive genes in prostate cancer cells
(Submitter supplied) We report nuclear receptor Esrrb's responsive genes with or without Esrrb ligand DY131 in DU145 cells. Using Esrrb-null cells, we used RNA-Seq to find Esrrb responsive genes. In addition, we tested DY131-driven Esrrb-dependent genes to test the ligand dependency of Esrrb in regulating gene expression.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71208/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA290585
Series		Accession: GSE71208	ID: 200071208

4521. Next Generation Sequencing Quantitative Analysis of steroid receptor RNA activator (SRA1) Transcriptomes
(Submitter supplied) The steroid receptor RNA activator gene (SRA1) produces both a functional RNA (SRA) and a protein (SRAP), whose exact roles remain unknown. To identify cellular processes regulated by this unusual bi-faceted system, we characterized the transcriptome of two differenct cell lines upon depletion of these molecules.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16288 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74461/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA300491
Series		Accession: GSE74461	ID: 200074461

4522. The Activation-Induced Assembly of an RNA/Protein Interactome Centered on the Splicing Factor U2AF2 Regulates Gene Expression in Human CD4 T Cells [RNA-seq]
(Submitter supplied) Activation of CD4 T cells is a reaction to challenges such as microbial pathogens, cancer and toxins that defines adaptive immune responses. The roles of T cell receptor crosslinking, intracellular signaling, and transcription factor activation are well described, but the importance of post-transcriptional regulation by RNA-binding proteins (RBPs) has not been considered in depth. We describe a new model expanding and activating primary human CD4 T cells and applied this to characterizing activation-induced assembly of splicing factors centered on U2AF2. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62920/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA266296
Series		Accession: GSE62920	ID: 200062920

4523. The Activation-Induced Assembly of an RNA/Protein Interactome Centered on the Splicing Factor U2AF2 Regulates Gene Expression in Human CD4 T Cells [RIP-Seq]
(Submitter supplied) Activation of CD4 T cells is a reaction to challenges such as microbial pathogens, cancer and toxins that defines adaptive immune responses. The roles of T cell receptor crosslinking, intracellular signaling, and transcription factor activation are well described, but the importance of post-transcriptional regulation by RNA-binding proteins (RBPs) has not been considered in depth. We describe a new model expanding and activating primary human CD4 T cells and applied this to characterizing activation-induced assembly of splicing factors centered on U2AF2. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62919/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA266297
Series		Accession: GSE62919	ID: 200062919

4524. Pericentromeric satellite repeat expansions through RNA-derived DNA intermediates in cancer
(Submitter supplied) Aberrant transcription of the HSATII pericentromeric satellite repeat is present in a wide variety of epithelial cancers. We observed that HSATII expression is induced in colon cancer cells cultured as xenografts or under non-adherent conditions in vitro, but it is rapidly lost in standard 2D cultures. Unexpectedly, physiological induction of endogenous HSATII RNA, as well as introduction of synthetic HSATII transcripts, generate complementary DNA intermediates in the form of DNA:RNA hybrids. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL14761 6 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64471/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA271086
Series		Accession: GSE64471	ID: 200064471

4525. JMJD1C is required for the survival of acute myeloid leukemia by functioning as a co-activator for key transcription factors
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 17 Samples
FTP download: GEO (TDF, XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63486/
Series		Accession: GSE63486	ID: 200063486

4526. RNA expression analysis upon JMJD1C depletion
(Submitter supplied) The AML1-ETO fusion protein, a transcription factor generated by the t(8;21) translocation in acute myeloid leukaemia (AML), dictates a leukemic program by increasing self-renewal and inhibiting differentiation.  Here we demonstrate that the histone demethylase JMJD1C functions as a co-activator for AML1-ETO and is required for its transcriptional program. JMJD1C is directly recruited by AML1-ETO to its target genes and regulates their expression by maintaining low H3K9me2 levels. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TDF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63485/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA268020
Series		Accession: GSE63485	ID: 200063485

4527. Retroviral Replicating Vectors Deliver Cytosine Deaminase Leading to Targeted 5-FU-Mediated Cytotoxicity in Multiple Human Cancer Types
(Submitter supplied) Toca 511 is a modified Retroviral Replicating Vector based on Moloney g‑retrovirus with an amphotropic envelope. As an investigational cancer treatment, Toca 511 preferentially infects cancer cells without direct cell lysis and encodes an enhanced yeast cytosine deaminase that converts the antifungal drug 5‑fluorocytosine to the anticancer drug, 5-fluorouracil. A panel of established human cancers cell lines, derived from glioblastoma, colon, and breast cancer tissue was used to evaluate parameters critical for effective anticancer activity. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72955/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA295406
Series		Accession: GSE72955	ID: 200072955

4528. Identification of differentially spliced genes by wild type or S34F mutation of U2AF1
(Submitter supplied) Identification of differentially spliced genes by wild type or S34F mutation of U2AF1
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66553/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA277313
Series		Accession: GSE66553	ID: 200066553

4529. RNA-seq of tumor-educated platelets enables blood-based pan-cancer, multiclass and molecular pathway cancer diagnostics
(Submitter supplied) We report RNA-sequencing data of 283 blood platelet samples, including 228 tumor-educated platelet (TEP) samples collected from patients with six different malignant tumors (non-small cell lung cancer, colorectal cancer, pancreatic cancer, glioblastoma, breast cancer and hepatobiliary carcinomas). In addition, we report RNA-sequencing data of blood platelets isolated from 55 healthy individuals. This dataset highlights the ability of TEP RNA-based 'liquid biopsies' in patients with several types with cancer, including the ability for pan-cancer, multiclass cancer and companion diagnostics.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 285 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68086/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA281708
Series		Accession: GSE68086	ID: 200068086

4530. A MYC-driven change in mitochondrial dynamics limits stem cell properties of mammary epithelial cells (RNA-seq)
(Submitter supplied) In several developmental lineages, an increase in expression of the MYC proto-oncogene drives the transition from quiescent stem cells to transit amplifying cells. The mechanism by which MYC restricts self-renewal of adult stem cells is unknown. Here, we show that MYC activates a stereotypic transcriptional program of genes involved in protein translation and mitochondrial biogenesis in mammary epithelial cells and indirectly inhibits the YAP/TAZ co-activators that are essential for mammary stem cell self-renewal. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66250/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA276279
Series		Accession: GSE66250	ID: 200066250

4531. Transcriptomic profiling of sequential tumours from breast cancer patients provides a global view of metastatic expression changes following endocrine therapy
(Submitter supplied) We profiled primary breast cancer, nodal and liver metastatic tumours from three patients. At the time of initial diagnosis, all three patients presented with luminal breast cancer with adjacent nodal metastasis. They all received 5 years of enodrine therapy and all subsequently developed liver metastasis.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58708/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA253208
Series		Accession: GSE58708	ID: 200058708

4532. Identification of genes are regulated by AURKA at transcription level
(Submitter supplied) Purpose: AURKA plays an important role in breast cancer development. Exploring the gene expression profiles regulated by AURKA will facilitate to understand the mechanism which is responsible for AURKA induced breast cancer development.  Results: We found that 350 genes were significantly up-regulated during AURKA overexpression in MCF-10A cells, 346 genes were significantly down-regulated during AURKA overexpression in MCF-10A cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57931/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA248443
Series		Accession: GSE57931	ID: 200057931

4533. Enhancers
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL15520 20 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72002/
Series		Accession: GSE72002	ID: 200072002

4534. Identifying Glioblastoma Gene Networks Based on Hypergeometric Test Analysis
(Submitter supplied) Patient specific therapy is emerging as an important possibility for many cancer patients.  However, to identify such therapies it is essential to determine the genomic and transcriptional alterations present in one tumor relative to control samples. This presents a challenge since use of a single sample precludes many standard statistical analysis techniques.  We reasoned that one means of addressing this issue is by comparing transcriptional changes in one tumor with those observed in a large cohort of patients analyzed by The Cancer Genome Atlas (TCGA). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (BEDGRAPH, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62731/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA265085
Series		Accession: GSE62731	ID: 200062731

4535. FOXM1 Cistrome Predicts Breast Cancer Metastatic Outcome Better Than FOXM1 Expression Levels or Tumor Proliferation Index
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL11154 GPL9115 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73371/
Series		Accession: GSE73371	ID: 200073371

4536. FOXM1 Cistrome Predicts Breast Cancer Metastatic Outcome Better Than FOXM1 Expression Levels or Tumor Proliferation Index [RNA-Seq]
(Submitter supplied) FOXM1 is a key transcription factor regulating cell cycle progression, DNA damage response, and a host of other hallmark cancer features, but the role of the FOXM1 cistrome in driving estrogen receptor-positive (ER+) vs. ER- breast cancer clinical outcomes remains undefined.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73370/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA296813
Series		Accession: GSE73370	ID: 200073370

4537. RNA-seq following enhancer repression
(Submitter supplied) Using RNA-seq to identify genes regulated by dCas9-KRAB mediated enhancer repression in NCI-H2009 lung adenocarcinoma cells
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 8 Samples
FTP download: GEO (GCT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72001/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA292701
Series		Accession: GSE72001	ID: 200072001

4538. Aneuploidy-induced cellular stresses limit autophagic degradation.
(Submitter supplied) An unbalanced karyotype, a condition known as aneuploidy, has a profound impact on cellular physiology and is a hallmark of cancer. Determining how aneuploidy affects cells is thus critical to understanding tumorigenesis. Here we show that aneuploidy interferes with the degradation of autophagosomes within lysosomes. Mis-folded proteins that accumulate in aneuploid cells due to aneuploidy-induced proteomic changes overwhelm the lysosome with cargo, leading to the observed lysosomal degradation defects. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE60nnn/GSE60570/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA258554
Series		Accession: GSE60570	ID: 200060570

4539. Quadruplex ligand Tetra-Pt(bpy) Induces the Death of Human ALT Cancer Cells by Inhibiting Homologue Recombination-Mediated Telomere Elongation
(Submitter supplied) The RNA-seq results reveal Tetra-Pt(bpy) has no effect on gene expression.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74029/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA298773
Series		Accession: GSE74029	ID: 200074029

4540. Mitochondrial phosphoenolpyruvate carboxykinase (PCK2) regulates metabolic adaptation and glucose-independent tumor cell growth
(Submitter supplied) Cancer cells must adapt metabolically to survive and proliferate when nutrients are limiting. Here we used combined transcriptional-metabolomic network analysis to identify metabolic pathways that support glucose-independent tumor cell growth. We found that glucose deprivation stimulated the re-wiring of the tricarboxylic acid (TCA) cycle and co-opting early steps of gluconeogenesis to promote cell proliferation under low glucose. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66556/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA277316
Series		Accession: GSE66556	ID: 200066556

4541. Androgen receptor programming in human tissue implicates HOXB13 in prostate pathogenesis
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL15520 GPL18573 GPL11154 37 Samples
FTP download: GEO (BED, BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70079/
Series		Accession: GSE70079	ID: 200070079

4542. Deregulation of HIF-Responsive Demethylases Causes Synthetic Lethality Between the VHL Tumor Suppressor Gene and the EZH1 Histone Methyltransferase
(Submitter supplied) Comparison of ccRCC cells with high HIF or low HIF activity
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70767/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA289629
Series		Accession: GSE70767	ID: 200070767

4543. Chromatin-remodelling complex NURF is essential for differentiation of adult melanocyte stem cells
(Submitter supplied) MIcrophthalmia-associated Transcription Factor (MITF) regulates melanocyte and melanoma physiology. ShRNA-mediated silencing of the NURF subunit BPTF revealed its essential role in several melanoma cell lines and in untransformed melanocytes in vitro. Comparative RNA-seq shows that MITF and BPTF co-regulate overlapping gene expression programs in cell lines in vitro. Somatic and specific inactivation of Bptf in developing murine melanoblasts in vivo shows that Bptf regulates their proliferation, migration and morphology. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 5 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72915/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA295316
Series		Accession: GSE72915	ID: 200072915

4544. RNA-sequencing analysis of human fibrolamellar hepatocellular carcinoma and 4 maturational stages of the human hepatobiliary system
(Submitter supplied) The etiology of fibrolamellar hepatocellular carcinoma (FL-HCC), a liver cancer occurring increasingly in children to young adults, is poorly understood. We performed high-throughput sequencing on mRNA isolated from a newly developed model of FL-HCC and 4 different maturational lineages of the hepatobiliary system. Our results indicate that the transcriptome of FL-HCC is most similar to that of biliary tree stem cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73114/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA296091
Series		Accession: GSE73114	ID: 200073114

4545. Synergistic gene expression signature observed in TK6 cells upon co-exposure to UVC-irradiation and protein kinase C-activating tumor promoters
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 62 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71521/
Series		Accession: GSE71521	ID: 200071521

4546. Synergistic gene expression signature observed in TK6 cells upon co-exposure to UVC-irradiation and protein kinase C-activating tumor promoters, a dosage study (study 2/2)
(Submitter supplied) The purpose of this study, including this dosage series and another  time course series, was to establish gene expression signatures representing the interaction of pathways deregulated by tumor promoting agents and pathways induced by DNA damage.  Human lymphoblastoid TK6 cells were pretreated with the protein kinase C activating tumor promoter 12-O-tetradecanoylphorbol-13-acetate (TPA) and exposed to UVC-irradiation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 21 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71520/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA291428
Series		Accession: GSE71520	ID: 200071520

4547. Synergistic gene expression signature observed in TK6 cells upon co-exposure to UVC-irradiation and protein kinase C-activating tumor promoters, a time course study (study 1/2)
(Submitter supplied) The purpose of this study, including this time course series and another dosage series, was to establish gene expression signatures representing the interaction of pathways deregulated by tumor promoting agents and pathways induced by DNA damage.  Human lymphoblastoid TK6 cells were pretreated with the protein kinase C activating tumor promoter 12-O-tetradecanoylphorbol-13-acetate (TPA) and exposed to UVC-irradiation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 41 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71519/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA291429
Series		Accession: GSE71519	ID: 200071519

4548. Perturbations of PIP3 signaling trigger a global remodeling of mRNA landscape and reveal a transcriptional feedback loop
(Submitter supplied) PIP3 is synthesized by PI3Ks and regulates complex cell responses, such as growth and migration. Signals that drive long-term reshaping of cell phenotypes are difficult to resolve because of complex feedback networks that operate over extended times. It is clear PIP3-dependent modulation of mRNA accumulation is important in this process but is poorly understood. We have quantified the genome-wide mRNA-landscape of non-transformed, breast epithelium-derived MCF10a cells and its response to transient (EGF or PI3Ka-selective inhibitor) or chronic (isogenic cells expressing an oncomutant PI3Ka allele or lacking the PIP3-phosphatase /tumour-suppressor, PTEN) perturbations of PIP3.These results show that whilst many mRNAs are changed by long-term  genetic perturbation of PIP3 signaling (“butterfly effect”), a much smaller number change with a directional logic that aligns with different PIP3 perturbations, allowing discrimination of more directly regulated mRNAs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 75 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69822/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA286870
Series		Accession: GSE69822	ID: 200069822

4549. Comparative analysis of Rtf1- and PAF1C-regulated genes
(Submitter supplied) Paf1 and Ski8 were selected as representative subunits of the Paf1 complex (PAF1C), and RNA-seq analysis was performed in triplicate to compare the genes affected by Paf1, Ski8, and Rtf1 knockdown in HeLa cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 12 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73632/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA297458
Series		Accession: GSE73632	ID: 200073632

4550. IL-1β and SERPINA3 are markers of an aggressive Barrett’s Oesophagus phenotype identified using mRNA sequencing
(Submitter supplied) Introduction: The identification of biomarkers in Barrett’s oesophagus (BO) that stratify groups at risk of progressing to oesophageal adenocarcinoma (OAC) would allow tailored surveillance strategies. We have applied a novel high throughput RNA sequencing analysis characterizing the BO mRNA transcriptome across the metaplasia-dysplasia sequence to identify potential markers of progression in an unbiased fashion and functionally validated these at the protein level. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 21 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58963/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA253993
Series		Accession: GSE58963	ID: 200058963

4551. Illumina Human Polycystic Liver Disease and Normal Biliary Stem Cell RNAseq
(Submitter supplied) Background & aims: Polycystic liver disease (PLD) is an autosomal dominantly inherited disorder caused by mutations in genes such as PRKCSH and SEC63. It has been thought that cysts develop from biliary progenitor cells due to loss-of-heterozygosity (LOH), leading to aberrant proliferation or defects in differentiation. Cyst expansion can be suppressed by somatostatin analogues such as lanreotide. There is no human in vitro model available that truly recapitulates polycystic liver disease. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73579/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA297355
Series		Accession: GSE73579	ID: 200073579

4552. Preferential Iron Trafficking Characterizes Glioblastoma Stem-like Cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL16791 GPL17692 19 Samples
FTP download: GEO (BW, CEL, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72204/
Series		Accession: GSE72204	ID: 200072204

4553. RNA-seq Profiles in Preferential Iron Trafficking Characterizes Glioblastoma Stem-like Cells
(Submitter supplied) Glioblastomas display hierarchies with self-renewing cancer stem-like cells (CSCs). RNA sequencing and enhancer mapping revealed regulatory programs unique to CSCs causing upregulation of the iron transporter transferrin, the top differentially expressed gene compared to tissue-specific progenitors. Direct interrogation of iron uptake demonstrated CSCs potently extract iron from the microenvironment more effectively than other tumor cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72202/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA293352
Series		Accession: GSE72202	ID: 200072202

4554. Genome-wide Analysis of Human Constitutive Androstane Receptor (CAR) Transcriptome in Wild-type and CAR-knockout HepaRG cells
(Submitter supplied) The constitutive androstane receptor (CAR, NR1I3) modulates the transcription of numerous genes involving drug metabolism, energy homeostasis, and cell proliferation. Most functions of CAR however were defined from animal studies. Given the known species difference of CAR and the significant cross-talk between CAR and the pregnane X receptor (PXR), it is extremely difficult to decipher the exact role of human CAR (hCAR) in gene regulation, relying predominantly on pharmacological manipulations. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (CSV, XLS, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71446/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA291214
Series		Accession: GSE71446	ID: 200071446

4555. Chemoresistance signature generated by genome-wide analysis of methylation, microRNAs, and gene expression in chemoresistant breast cancer cells
(Submitter supplied) We used RNA-seq and RRBS sequence to characterize the transcriptomic and methylome changes in chemoresistant and sensitive breast cancer cells
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (XLS, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68815/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA283827
Series		Accession: GSE68815	ID: 200068815

4556. PTEN suppresses neoplastic transformation of human neural stem cells by transcriptional repression of Pax7
(Submitter supplied) Our data throw light upon the effect of PTEN deficiency on gene expression, epigenomic modifications(H3K4me3, H3K27me3, 5-Hydroxymethylcytosine and 5-methylcytosin).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform: GPL11154 21 Samples
FTP download: GEO (BED, BEDGRAPH, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE61nnn/GSE61794/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA262146
Series		Accession: GSE61794	ID: 200061794

4557. Mediator kinase inhibition further activates super-enhancer-associated genes in AML
(Submitter supplied) Super-enhancers (SEs), which are composed of large clusters of enhancers densely loaded with the Mediator complex, transcription factors and chromatin regulators, drive high expression of genes implicated in cell identity and disease, such as lineage-controlling transcription factors and oncogenes. BRD4 and CDK7 are positive regulators of SE-mediated transcription. By contrast, negative regulators of SE-associated genes have not been well described. more...
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
5 related Platforms 89 Samples
FTP download: GEO (CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE65nnn/GSE65161/
Series		Accession: GSE65161	ID: 200065161

4558. Genome-wide maps of PBX3-binding sites and Quantitative Analysis of PBX3-Regulated Transcriptomes
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 5 Samples
FTP download: GEO (TAR, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71262/
Series		Accession: GSE71262	ID: 200071262

4559. Next Generation Sequencing Facilitates Quantitative Analysis of PBX3 Regulated Transcriptomes
(Submitter supplied) The goals of this study are to analyze the transcriptome profiling (RNA-seq) after PBX3 overexpression in SMMC-7721 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71261/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA290723
Series		Accession: GSE71261	ID: 200071261

4560. Genome-wide maps of nuclear lamina interactions in single human cells (CEL-seq)
(Submitter supplied) Mammalian interphase chromosomes interact with the nuclear lamina (NL) through hundreds of large Lamina Associated Domains (LADs). We report a method to map NL contacts genome-wide in single human cells. Analysis of ~400 maps reveals a core architecture of gene-poor LADs that contact the NL with high cell-to-cell consistency, interspersed by LADs with more variable NL interactions. The variable contacts are more sensitive to a change in genome ploidy than the consistent contacts. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 1 Sample
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68596/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA283181
Series		Accession: GSE68596	ID: 200068596

4561. hTERT promotes cell adhesion and migration independent of telomerase activity
(Submitter supplied) We sequenced mRNA from 6 human cell lines stably over-expressed specific gene or empty vector, and searched for differently expressed genes after gene over-expression as compared to empty vector.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73277/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA296510
Series		Accession: GSE73277	ID: 200073277

4562. Select correlative genes involved in pathogenesis of idiopathic interstitial pneumonia by high-throughput sequencing analysis
(Submitter supplied) We report abonormally expressed genes of idiopathic interstitial pneumonia by RNA-seq analysis. BMP3 was found down-regulated in idiopathic intestital pneumonia patients, and it closely correlated with pathogenesis of disease. The role of BMP3 in advancement of idiopathic interstitial pneumonia was verified by a series of experiments.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73189/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA296108
Series		Accession: GSE73189	ID: 200073189

4563. Single-cell transcriptome profiling for metastatic renal cell carcinoma patient-derived cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome variation profiling by genome tiling array
Platforms: GPL16791 GPL10150 125 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73122/
Series		Accession: GSE73122	ID: 200073122

4564. Single-cell transcriptome profiling for metastatic renal cell carcinoma patient-derived cells [RNA-seq]
(Submitter supplied) Clear cell renal cell carcinoma (ccRCC) initiated from the renal epithelium is the most prevalent histological type of adult kidney cancers. Dissecting intratumoral heterogeneity (ITH) of ccRCC has leveraged to extend our knowledge on how primary tumors harboring driver mutations evolve and spread to other sites. The cellular fractions within and across the primary (pRCC) and metastatic RCC (mRCC) are heterogeneous in both their genetic and biological features determining the variability in clinical aggressiveness and sensitivity to the therapy. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 121 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73121/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA296119
Series		Accession: GSE73121	ID: 200073121

4565. Ligand-dependent genomic function of glucocorticoid receptor in triple-negative breast cancer
(Submitter supplied) Glucocorticoids (GC) have been widely used as coadjuvants in the treatment of solid tumors, but GC treatment may be associated with poor pharmacotherapeutic response and/or prognosis. The genomic action of GC in these tumors is largely unknown. Here we find that dexamethasone (Dex, a synthetic GC) regulated genes in triple-negative breast cancer (TNBC) cells are associated with drug resistance. Importantly, these GC-regulated genes are aberrantly expressed in TNBC patients and associated with unfavorable clinical outcomes. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL11154 22 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE56nnn/GSE56022/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA242236
Series		Accession: GSE56022	ID: 200056022

4566. RNA-Seq of Single Prostate CTCs Implicates Non-Canonical Wnt Signaling in Antiandrogen Resistance
(Submitter supplied) Prostate cancer is initially responsive to androgen deprivation, but the effectiveness of androgen receptor (AR) inhibitors in recurrent disease is variable. Biopsy of bone metastases is challenging, hence sampling circulating tumor cells (CTCs) may reveal drug resistance mechanisms. We established single cell RNA-sequencing profiles of 77 intact CTCs isolated from 13 patients (mean 6 CTCs/patient) using microfluidic enrichment. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16288 169 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67980/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA281419
Series		Accession: GSE67980	ID: 200067980

4567. Non-genomic and Immune Evolution in Melanoma with Acquired MAPKi Resistance
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing; Methylation profiling by genome tiling array
Platforms: GPL17692 GPL11154 GPL13534 218 Samples
FTP download: GEO (CEL, IDAT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE65nnn/GSE65186/
Series		Accession: GSE65186	ID: 200065186

4568. RNAseq changes in pre MAPKi treatment and post MAPKi resistance Melanomas
(Submitter supplied) Melanoma resistance to MAPK- or T cell checkpoint-targeted therapies represents a major clinical challenge, and treatment failures of MAPK-targeted therapies due to acquired resistance often require salvage immunotherapies. We show that genomic analysis of acquired resistance to MAPK inhibitors revealed key driver genes but failedto adequately account for clinical resistance. From a large-scale comparative analysis of temporal transcriptomes from patient-matched tumor biopsies, we discovered highly recurrent differential expression and signature outputs of c-MET, LEF1 and YAP1 as drivers of acquired MAPK inhibitor resistance. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 70 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE65nnn/GSE65185/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA273359
Series		Accession: GSE65185	ID: 200065185

4569. RNA-sequencing of mRNAs from control and CAP-D3 deficient Salmonella infected HT-29 cells
(Submitter supplied) BACKGROUND & AIMS- More frequent interaction of bacteria with the colonic epithelium is associated with ulcerative colitis (UC).  The identities of all proteins which promote bacterial clearance in colonic epithelial cells are unknown.  Previously, we discovered that dCAP-D3 (Chromosome Associated Protein-D3), regulates responses to bacterial infection.  We examined whether CAP-D3 promotes bacterial clearance in human colonic epithelium. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 16 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62520/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA264328
Series		Accession: GSE62520	ID: 200062520

4570. DNMT1-associated long non-coding RNA regulate global gene expression and DNA methylation in colon cancer
(Submitter supplied) The investigation of the association of long non-coding RNAs (lncRNAs) with DNMT1 by RIP-seq reveals that DNMT1 interacts with DACOR1. We identified the genomic occupancy sites of DACOR1 through ChIRP-seq, which we found to significantly overlap with known differentially methylated regions (DMRs) in colon tumors.  Induction of DACOR1 in colon cancer cell lines significantly reduced their ability to form colonies in vitro, suggesting a growth suppressor function. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms: GPL9115 GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58989/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA254057
Series		Accession: GSE58989	ID: 200058989

4571. TMPyP4 promotes cancer cell migration at low doses, but induces cell death at high doses
(Submitter supplied) The RNA-seq results reveal TMPyP4 and TPyP4 could promote cancer cell migration.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72983/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA295536
Series		Accession: GSE72983	ID: 200072983

4572. EGFR Mutation Promotes Glioblastoma Through Epigenome and Transcription Factor Network Remodeling
(Submitter supplied) Epidermal Growth Factor Receptor (EGFR) gene amplification and mutations are the most common oncogenic events in Glioblastoma (GBM), but the mechanisms by which they promote aggressive tumor growth are not well understood. Here, through integrated epigenome and transcriptome analyses of cell lines, genotyped clinical samples and TCGA data, we show that EGFR mutations remodel the activated enhancer landscape of GBM, promoting tumorigenesis through a SOX9 and FOXG1-dependent transcriptional regulatory network in vitro and in vivo. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platform: GPL11154 87 Samples
FTP download: GEO (BIGWIG, BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72468/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA294444
Series		Accession: GSE72468	ID: 200072468

4573. Cancer associated SF3B1 hotspot mutations induce cryptic 3' splice site selection through use of a different branch point
(Submitter supplied) Recurrent mutations in the spliceosome are observed in several human cancers but their functional and therapeutic significance remain elusive. SF3B1, the most frequently mutated component of the spliceosome in cancer, is involved in the recognition of the branch point sequence (BPS) during selection of the 3’ splice site (ss) in RNA splicing. Here, we report that common and tumor-specific splicing aberrations are induced by SF3B1 mutations and establish aberrant 3’ ss selection as the most frequent splicing defect. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL13112 72 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72790/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA295064
Series		Accession: GSE72790	ID: 200072790

4574. Transcriptional plasticity promotes primary and acquired resistance to BET bromodomain inhibition
(Submitter supplied) Following the discovery of BRD4 as a non-oncogene addiction target in acute myeloid leukemia (AML), BET inhibitors are being explored as promising therapeutic avenue in numerous cancers. While clinical trials have reported single-agent activity in advanced hematologic malignancies, mechanisms determining the response to BET inhibition remain poorly understood. To identify factors involved in primary and acquired BET resistance in leukemia, we performed a chromatin-focused shRNAmir screen in a sensitive MLL/AF9; NrasG12D‑driven AML model, and investigated dynamic transcriptional profiles in sensitive and resistant murine and human leukemias. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
6 related Platforms 103 Samples
FTP download: GEO (BED, BW, GTF, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63782/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA269063
Series		Accession: GSE63782	ID: 200063782

4575. Oncogenic MYC induces a dependency on the spliceosome in human cancer
(Submitter supplied) c-MYC (MYC) overexpression or hyperactivation is one of the most common drivers of human cancer. Despite intensive study, the MYC oncogene remains recalcitrant to therapeutic inhibition. Like other classic oncogenes, hyperactivation of MYC leads to collateral stresses onto cancer cells, suggesting that tumors harbor unique vulnerabilities arising from oncogenic activation of MYC. Herein, we discover the spliceosome as a new target of oncogenic stress in MYC-driven cancers. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 11 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66182/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA276068
Series		Accession: GSE66182	ID: 200066182

4576. Differential Gene Expression between MCF10A and MCF7 cells
(Submitter supplied) These RNA-seq data were generated to correlate with genomic interaction data in a related Hi-C analysis.  MCF10A is a normal-like mammary epithelial cell line and MCF7 is a transformed estrogen responsive breast cancer cell line derived from a metastatic site; both are commonly used in models of breast cancer progression.  Analysis revealed a set of genes related to repression of WNT signalling that were both up-regulated in MCF7 and located in genomic regions that had transitioned from closed to open structure in MCF7. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71862/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA292330
Series		Accession: GSE71862	ID: 200071862

4577. Global analysis of androgen-signaling reveals the function of miRNAs for the epigenomic regulation in prostate cancer cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Other
5 related Platforms 73 Samples
FTP download: GEO (BED, CEL, CHP) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66039/
Series		Accession: GSE66039	ID: 200066039

4578. Genome wide analysis of androgen-regulated transcripts
(Submitter supplied) Prostate cancer is the most common cancer in men and AR downstream signalings promote prostate cancer cell proliferation. To investigate the AR signaling, we performed RNA sequence analysis in AR positive prostate cancer cell line, LNCaP. In addition, we used hormone-refractory prostate cancer model cells, Bicalutamide-resistant (BicR) to explore the differences of androgen signaling in prostate cancer progression.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18723 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66036/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA275745
Series		Accession: GSE66036	ID: 200066036

4579. Estrogen Receptor Beta Impacts Hormone-Induced Alternative mRNA Splicing in Breast Cancer Cells
(Submitter supplied) Estrogens play an important role in breast cancer (BC) development and progression, where the two isoforms of the estrogen receptor (ERα and ERβ) are generally co-expressed and mediate the effects of these hormones in cancer cells. ERβ has been suggested to exert an antagonist role toward the oncogenic activities of ERα, and for this reason it is considered an oncosuppressor. As clinical evidence regarding a prognostic role for this receptor subtype in hormone-responsive BC is still limited and conflicting, more knowledge is required on the biological functions of ERβ in cancer cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64590/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA271362
Series		Accession: GSE64590	ID: 200064590

4580. Silencing RNA-binding  protein CELF1 inhibits tumor growth and alters gene expression in oral squamous cell carcinoma
(Submitter supplied) RNA-binding proteins (RBPs) are critical regulators of gene expression, but only a small fraction have been studied for their role in malignancy.  Here we report a systematic analysis of RBP CUGBP Elav-Like Family member 1 (CELF1 alias CUGBP1) roles in mRNA alternative splicing, translation and turnover in oral cancer cells. CELF1 is overexpressed in carcinogen-induced oral cancer tumorigenesis mouse model and specific inhibition of CELF1 reduces  tumor growth in vivo. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57254/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA246124
Series		Accession: GSE57254	ID: 200057254

4581. CETCh-Seq  of Mammalian Transcription Factors
(Submitter supplied) Chromatin immunoprecipitation followed by next-generation DNA sequencing (ChIP-seq) is a widely used technique for identifying transcription factor (TF) binding events throughout an entire genome. However, ChIP-seq is limited by the availability of suitable ChIP-seq grade  antibodies, and the vast majority of commercially available antibodies fail to generate usable  datasets. To ameliorate these technical obstacles, we present a robust methodological  approach for performing ChIP-seq through epitope tagging of endogenous TFs. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL16791 GPL17021 29 Samples
FTP download: GEO (BEDGRAPH, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72082/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA293987
Series		Accession: GSE72082	ID: 200072082

4582. Identification of differentially expressed mRNAs in HCSC cell lines compared with HCC cell lines
(Submitter supplied) Hep3B and Huh7 are two types of human hepatoma cell lines (HCC). In our laboratory, we cultured their stem-like cancer cells (HCSCs), Hep3B-C and Huh7-C. And we have demonstrated that these cells had enhanced stem cell properties, drug resistance, properties of EMT, and stronger tumor-initiating capabilities. To explore functionally crucial mRNAs in HCSCs, 2 samples of HCSCs and 2 samples of HCCs were sequenced by the Illumina Genome Analyzer II. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70537/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA288962
Series		Accession: GSE70537	ID: 200070537

4583. RNA-Seq experiment to identify genes regulated by ATF4
(Submitter supplied) Activating Transcription Factor 4 (ATF4) is a transcription factor induced by the integrated stress response (ISR). This experiment is a genome-wide profiling of ATF4-dependent RNA expression in human HAP-1 cells. HAP-1 is a near-haploid human cell line that was derived from KBM-7 cells isolated from a patient with Chronic Myelogenous Leukemia. We analyzed WT and ATF4 KO cells. We induced ATF4 expression by mimicking amino acid starvation with the drug histidinol.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 4 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69308/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA285117
Series		Accession: GSE69308	ID: 200069308

4584. Genome-wide expression profile of the Tet-On HCT116 inducible cell line that express either the human HNF4α2 or HNF4α8 under control of Doxycycline (DOX)
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 36 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62891/
Series		Accession: GSE62891	ID: 200062891

4585. Genome-wide expression profile of the Tet-On HCT116 inducible cell line that express either the human HNF4α2 or HNF4α8 under control of Doxycycline (DOX) [RNAseq]
(Submitter supplied) Purpose: Aim of the study is to identify functional differences between the P1 and P2-HNF4α isoforms. To do this, we generated Tet-On inducible lines that express either the human (P1) HNF4α2 or (P2) HNF4α8 under control of DOX in the HCT116 human colon cancer cells. Methods: HNF4α2 and Parental lines were induced with 0.3 μg/mL DOX, while HNF4α8 line was induced with either 0.1 or 0.3 μg/mL DOX for 24 hours. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 21 Samples
FTP download: GEO (DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62889/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA265990
Series		Accession: GSE62889	ID: 200062889

4586. Comparative whole-transcriptomic analysis between normal and AKAP-Lbc-depleted human embryonic stem cells
(Submitter supplied) Human embryonic stem cells (hESCs) have the unique property of immortality, ability to infinitely self-renew and survive in vitro. In contrast to tumor-deribed cells, their immortality are free from any genomic abberations. Instead, they depend on the AKAP-Lbc/Rho signaling cascade. To understand the downstream way, we performed RNA-seq analyses between normal and AKAP-Lbc-depleted hESCs using the doxycyclin-inducible gene silensing strategy.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 6 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67128/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA279024
Series		Accession: GSE67128	ID: 200067128

4587. RNA-Seq whole transcriptome analysis of normal human epidermal keratinocytes and cutaneous squamous cell carcinoma cell lines.
(Submitter supplied) The incidence of keratinocyte-derived skin cancer, cutaneous squamous cell carcinoma (cSCC) is increasing worldwide making it the second most common metastatic skin cancer. In this project we used SOLiD next generation sequencing to characterize gene expression profiles in normal human epidermal keratinocytes (NHEKs) and cSCC cell lines.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9442 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66412/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA276887
Series		Accession: GSE66412	ID: 200066412

4588. Physical and functional CSL-p53 interactions underlie control of cancer stromal cell evolution
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL16791 6 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE65nnn/GSE65474/
Series		Accession: GSE65474	ID: 200065474

4589. Physical and functional CSL-p53 interactions underlie control of cancer stromal cell evolution [RNA-seq]
(Submitter supplied) Senescence of stromal fibroblasts has been linked to establishment of cancer associated fibroblasts (CAF) and aging-associated increase of tumors. However, in clinically occurring carcinomas, density and proliferation of CAFs are frequently increased rather than decreased. We previously showed that genetic deletion or down-modulation of the canonical Notch effector CSL/RBP-Jκ in skin dermal fibroblasts is sufficient for CAF activation with consequent development of multifocal keratinocyte tumors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE65nnn/GSE65473/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA274128
Series		Accession: GSE65473	ID: 200065473

4590. The miR-146b-3p/PAX8/NIS Regulatory Circuit Modulates the Differentiation Phenotype and Function of Thyroid Cells During Carcinogenesis
(Submitter supplied) To comprehensively characterize microRNAs (miRNA) expression and their target genes in thyroid cancer, we performed next-generation sequencing expression analysis of this disease. Recent studies have found that only the most abundant microRNAs mediate significant target suppression. We sequenced small RNA from 8 papillary thyroid carcinomas (PTC) with paired samples of normal thyroid tissue. We found that only a small set of abundant miRNAs are differentially expressed after pair-wise comparison (12 upregulated and 8 downregulated) reaching the minimum threshold amount to repress target mRNAs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL10999 41 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63511/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA268095
Series		Accession: GSE63511	ID: 200063511

4591. Ribosome profiling reveals an important role for translational control in circadian gene expression
(Submitter supplied) Physiological and behavioral circadian rhythms are driven by a conserved transcriptional/translational negative feedback loop in mammals. Although most core clock factors are transcription factors, post-transcriptional control introduces delays that are critical for circadian oscillations. Little work has been done on circadian regulation of translation, so to address this deficit we conducted ribosome profiling experiments in a human cell model for an autonomous clock. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL11154 96 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE56nnn/GSE56924/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA244941
Series		Accession: GSE56924	ID: 200056924

4592. Genome-wide map of H3K4me3 before and after methionine restriction in HCT116 cells.
(Submitter supplied) The goals of this study were to compare the distribution of H3K4me3 before and after methionine restriction to understand how nutrient availability and alterations in methionine metabolism affect the epigenetic state and regulate gene transcription.  To do this we performed ChIP-seq with an H3K4me3 antibody and RNA-seq using PolyA+ mRNA.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (BW, CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72131/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA293125
Series		Accession: GSE72131	ID: 200072131

4593. CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function
(Submitter supplied) CTCF/cohesin play a central role in insulator function and higher-order chromatin organization of mammalian genomes. Recent studies identified a correlation between the orientation of CTCF-binding sites (CBSs) and chromatin loops. To test the functional significance of this observation, we combined CRISPR/Cas9-based genomic-DNA-fragment editing with chromosome-conformation-capture experiments to show that the location and relative orientations of CBSs determine the specificity of long-range chromatin looping in mammalian genomes, using protocadherin (Pcdh) and β-globin as model genes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71275/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA290779
Series		Accession: GSE71275	ID: 200071275

4594. Mitotic stress is an integral part of the oncogene-induced senescence program that promotes multinucleation and cell cycle arrest
(Submitter supplied) Oncogene-induced senescence (OIS) is a tumor suppression mechanism that blocks cell proliferation in response to oncogenic signalling. OIS is frequently accompanied by multinucleation; however, the origin of this is unknown. Here we show that multinucleate OIS cells originated mostly from failed mitosis. Prior to senescence, mutant RasV12 activation in primary human fibroblasts compromised mitosis, associated with abnormal expression of mitotic genes that enter M-phase. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70668/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA289328
Series		Accession: GSE70668	ID: 200070668

4595. PAF1, a molecular regulator of promoter-proximal pausing   by RNA Polymerase II
(Submitter supplied) The control of promoter-proximal pausing and the release of RNA polymerase II (RNA Pol II) is a widely used mechanism for regulating gene expression in metazoans, especially for genes that respond to environmental and developmental cues. Here, we identify Pol II associated Factor 1 (PAF1) as a major regulator of promoter-proximal pausing. Knockdown of PAF1 leads to increased release of paused Pol II into gene bodies at thousands of genes. more...
Organism:	Homo sapiens; Drosophila melanogaster
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Other
Platforms: GPL18573 GPL11154 GPL19132 61 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70408/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA288695
Series		Accession: GSE70408	ID: 200070408

4596. The Small Molecule Genistein Increases Hepcidin Expression in Human Hepatocytes
(Submitter supplied) Hepcidin, a peptide hormone that decreases intestinal iron absorption and macrophage iron release, is a potential drug target for patients with iron overload syndromes because its levels are inappropriately low in these individuals.  Endogenous stimulants of Hepcidin transcription include bone morphogenic protein 6 (BMP) and interleukin-6 (IL-6) via effects on Smad4 or Stat3, respectively.  We conducted a small-scale chemical screen in zebrafish embryos to identify small molecules that modulate hepcidin expression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 8 Samples
FTP download: GEO (PDF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE40nnn/GSE40069/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA172723
Series		Accession: GSE40069	ID: 200040069

4597. Research resource: global identification of estrogen receptor β target genes in triple negative breast cancer cells
(Submitter supplied) The goal of this work was to identify all estrogen receptor beta target genes using RNA sequencing in MDA-MB-468 triple negative breast cancer cells engineered with inducible expression of full length estrogen receptor beta.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71960/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA292572
Series		Accession: GSE71960	ID: 200071960

4598. Wnt addiction of genetically defined cancers reversed by PORCN inhibition
(Submitter supplied) Enhanced sensitivity to Wnts is an emerging hallmark of a subset of cancers, defined in part by mutations regulating the abundance of their receptors. Inhibition of Wnt secretion by blocking an essential post-translational modification, palmitoleation, provides a useful therapeutic intervention. Inhibition of PORCN in RSPO3-translocated cancers via treatment with ETC-159 causes a marked remodeling of the transcriptome, with loss of cell cycle, stem cell, and proliferation genes and an increase in differentiation markers. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69687/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA286198
Series		Accession: GSE69687	ID: 200069687

4599. Decoding breast cancer tissue-stroma interactions using species-specific sequencing
(Submitter supplied) Decoding genome-wide effects of experimental tissue-tissue or cell-cell interactions is important, for example, to better understand tumor-stroma interactions after transplantation (xenografting). Transcriptome analysis of intermixed human and mouse cells has frequently relied on the need to separate the two cell populations prior to transcriptome analysis, which introduces confounding effects on gene expression. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16512 GPL13112 GPL11154 21 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66744/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA277852
Series		Accession: GSE66744	ID: 200066744

4600. Disease-associated mutation in SRSF2 misregulates splicing by altering RNA binding affinities
(Submitter supplied) SRSF2 is an RNA binding protein that plays important roles in splicing of mRNA precursors. Mutations in SRSF2 are frequently found in patients with myelodysplastic syndromes and certain leukemias, but how they affect SRSF2 function has only begun to be examined. Here we used CRISPR/Cas9 to introduce the P95H mutation to SRSF2 in K562 leukemia cells, generating an isogenic model so that splicing alterations can be attributed solely to mutant SRSF2. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71299/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA290859
Series		Accession: GSE71299	ID: 200071299

4601. Comparison of poly(A) and capture RNA-seq: controlled degradation in vitro
(Submitter supplied) We compare the performance of two library preparation protocols (poly(A) and exome capture) in in vitro degraded RNA samples
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 40 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64113/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA270181
Series		Accession: GSE64113	ID: 200064113

4602. Generation of low passage high grade serous ovarian cancer cell lines from primary tumors
(Submitter supplied) High grade serous ovarian cancers (HGSC) are deadly malignancies that relapse despite carboplatin chemotherapy.  Many commercially ovarian cancer cell lines are not good models for HGSC. Here we demonstrate that 3 low passage cell lines derived from HGSC have similar transcriptomes to their parental bulk tumors. These cell lines recapitulated tumor characteristics of the primary cancer and had responded to therapy in the same manner as primary HGSC cells, demonstrating they are accurate models for HGSCs.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70073/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA287645
Series		Accession: GSE70073	ID: 200070073

4603. Apoptosis enhancing drugs overcome innate platinum resistance in CA125 negative tumor initiating populations of high grade serous ovarian cancer
(Submitter supplied) High grade serous ovarian cancers (HGSC) are deadly malignancies that relapse despite carboplatin chemotherapy. Here we show that 16 independent primary HGSCs contain a CA125 negative population enriched for carboplatin resistant cancer initiating cells. Transcriptome analysis reveals up-regulation of homologous recombination DNA repair and anti-apoptotic signals in this population. While treatment with carboplatin enriches for CA125 negative cells, co-treatment with carboplatin and birinapant eliminates these cells in HGSCs expressing high levels of the inhibitor of apoptosis protein cIAP in the CA125 negative population. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 20 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70072/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA287643
Series		Accession: GSE70072	ID: 200070072

4604. Effect of OVO-like 1 knockdown on global transcript expression in differentiated BeWo trophoblast cells
(Submitter supplied) We had previously discovered that the transcription factor OVO-like 1 (OVOL1) was highly induced during trophoblast differentiation. In this study, we used an lentiviral shRNA strategy to decrease OVOL1 expression in BeWo trophoblast cells. Control cells were transduced with shRNAs targeting no known mammalian transcript (shCont). Following stimulation of differentiation (48h exposure to 8-bromo-cyclic adenosine monophosphate), a RNA-seq approach was used to determine global transcript differences in OVOL1-knockdown cells compared to control cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66962/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA278477
Series		Accession: GSE66962	ID: 200066962

4605. RNA-sequencing in OS-RC-2 cells under the knockdown of Arkadia or ESRP2
(Submitter supplied) Tumor-specific alternative splicing is implicated in the progression of cancer, including clear cell renal cell carcinoma (ccRCC). Using ccRCC RNA-sequencing data from The Cancer Genome Atlas, we found that epithelial splicing regulatory protein 2 (ESRP2), one of the key regulators of alternative splicing in epithelial cells, is expressed in ccRCC. ESRP2 mRNA expression did not correlate with the overall survival rate of ccRCC patients, but the expression of some ESRP-target exons correlated with the good prognosis and with the expression of Arkadia (also known as RNF111) in ccRCC. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66741/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA277837
Series		Accession: GSE66741	ID: 200066741

4606. The Cushing's disease adipose gene expression profile reveals effects of long term glucocorticoids on adipose tissue lipid, protein and glucose metabolism
(Submitter supplied) Glucocorticoids have major effects on adipose tissue metabolism. To study tissue mRNA expression changes induced by chronic elevated endogenous glucocorticoids, we performed RNA sequencing on subcutaneous adipose tissue from patients with Cushing’s disease (n=5) compared to patients with non-functioning pituitary adenomas (n=11). We found higher expression of transcripts involved in several metabolic pathways, including lipogenesis, proteolysis and glucose oxidation as well as decreased expression of transcripts involved in inflammation and protein synthesis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66446/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA276977
Series		Accession: GSE66446	ID: 200066446

4607. Prevalent p53 gain-of-function mutants co-opt epigenetic pathways to drive cancer growth
(Submitter supplied) We investigated the genomewide binding pattern of prevalent p53 gain-of-function (GOF) mutants by ChIP-seq, in a panel of breast cancer cell lines. We assessed the genomewide changes of H3K4me3 upon GOF p53 knockdown in MDA-MB-468 breast cancer cells bearing the p53 R273H mutation.
Organism:	Homo sapiens; Mus musculus
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL19057 15 Samples
FTP download: GEO (BEDGRAPH, BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59176/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA254538
Series		Accession: GSE59176	ID: 200059176

4608. Identification and functional characterization of long noncoding RNAs in breast cancer
(Submitter supplied) In this study, we have integrated RNA-seq data from subcellular fractionated RNA (i.e., cytoplasm, nucleoplasm, and chromatin-associated) with GRO-seq data using a novel bioinformatics pipeline. This has yielded a comprehensive catalog of polyadenylated lncRNAs in MCF-7 cells, about half of which have not been annotated previously and about a quarter of which are estrogen-regulated. Knockdown of selected lncRNAs, such as lncRNA152 and lncRNA67 followed by RNA-seq suggest that these lncRNAs regulate the expression of cell cycle genes.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 25 Samples
FTP download: GEO (BW, GTF, TXT, XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63189/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA266932
Series		Accession: GSE63189	ID: 200063189

4609. Complete hematologic response of early-T-cell progenitor acute lymphoblastic leukemia to the gamma-secretase inhibitor BMS-906024: genetic and epigenetic findings in an outlier case
(Submitter supplied) Notch pathway antagonists such as gamma-secretase inhibitors (GSI) are being tested in diverse cancers, but exceptional responses have yet to be reported. We describe the case of a patient with relapsed/refractory early-T-cell progenitor acute lymphoblastic leukemia (ETP-ALL) who achieved a complete hematologic response following treatment with the GSI BMS-906024. Whole exome sequencing of leukemic blasts revealed heterozygous gain-of-function driver mutations in NOTCH1, CSF3R, and PTPN11, and a homozygous/hemizygous loss-of-function mutation in DNMT3A. more...
Organism:	Homo sapiens
Type:		Other; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (BEDGRAPH, CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71414/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA291188
Series		Accession: GSE71414	ID: 200071414

4610. LIN28A modulates splicing and gene expression programs in breast cancer cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL9052 GPL11154 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71013/
Series		Accession: GSE71013	ID: 200071013

4611. LIN28A modulates splicing and gene expression programs in breast cancer cells [RNA-Seq]
(Submitter supplied) The goals of this study were to identify LIN28 downstream gene targets in breast cancer cells. We use a subclone of the MCF-7 breast cancer cell line, MCF-7M as our model system. Methods: mRNA profiles from MCF-7M breast cancer cells treated with siRNA against non-targeting control (NT), LIN28, hnRNP A1, LIN28 and hnRNPA1 (LIN28A1) for 72 hrs were generated by deep sequencing, in duplicate, using Illumina HiSeq 2000. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71012/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA290103
Series		Accession: GSE71012	ID: 200071012

4612. LIN28A modulates splicing and gene expression programs in breast cancer cells [RIP-Seq]
(Submitter supplied) The goals of this study were to identify LIN28 downstream gene targets in breast cancer cells. We use a subclone of the MCF-7 breast cancer cell line, MCF-7M as our model system. Methods: mRNA-protein complexes (mRNP) lysates were prepared from MCF-7M cells and incubated with Protein-A Sepharose beads (Sigma-Aldrich) and either LIN28 (Abcam) or control normal rabbit serum IgG antibodies. LIN28 interacting mRNAs were identified by whole genome sequencing. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71009/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA290096
Series		Accession: GSE71009	ID: 200071009

4613. A Molecular Portrait Of High-Grade Ductal Carcinoma In Situ (DCIS)
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.  Description of samples employed for the subseries NGS analyses including age, race, ER/PR immunohistochemistry results, ITIL/STIL scores and PAM50 classification is provided in the 'Supplementary Data1_Samples data.xlsx'.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform: GPL11154 64 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69994/
Series		Accession: GSE69994	ID: 200069994

4614. A Molecular Portrait Of High-Grade Ductal Carcinoma In Situ (DCIS) [RNA-seq]
(Submitter supplied) DCIS is a non-invasive precursor lesion to invasive breast carcinoma. We still have no understanding on why only some DCIS lesions evolve to invasive cancer while others appear not to do so during the life span of the patient. Here, we performed full exome (tumor vs. matching normal), transcriptome and methylome analysis of 30 pure high-grade DCIS (HG-DCIS) and 10 normal breast epithelial samples. Sixty two percent of HG-DCIS cases displayed mutations affecting cancer driver genes or potential drivers. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 35 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69240/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA284949
Series		Accession: GSE69240	ID: 200069240

4615. Comparative analyses of CTCF and BORIS occupancies uncover two distinct classes of CTCF binding genomic regions
(Submitter supplied) CTCF and BORIS (CTCFL), two paralogous mammalian proteins sharing nearly identical DNA binding domains, are thought to function in mutually exclusive manners in DNA binding and transcriptional regulation. Here we show that these two proteins co-occupy a specific subset of regulatory elements consisting of clustered CTCF binding motifs (termed 2xCTSes). BORIS occupancy at 2xCTSes is largely invariant in BORIS-positive cancer cells, with the genomic pattern recapitulating the germline-specific BORIS binding to chromatin. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL11154 GPL13112 GPL17301 27 Samples
FTP download: GEO (BED, TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70764/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA289515
Series		Accession: GSE70764	ID: 200070764

4616. Comparative transcriptome analysis reveals that ECM-Receptor Interaction contributes to the venous metastases of hepatocellular carcinoma
(Submitter supplied) Hepatocellular carcinoma (HCC) is the most common kind of liver cancer in the world. Portal vein tumor thrombus (PVTT) is one of the most serious complications of HCC and strongly correlated to a poor prognosis for HCC patients. However, the detailed mechanisms of PVTT development still remains to be explored. In this study, we presented the large scale transcriptome analysis of 11 HCC with PVTT patients by RNA-sequencing. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 33 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69164/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA284733
Series		Accession: GSE69164	ID: 200069164

4617. The LIN28B/let-7 axis is a novel therapeutic pathway in Multiple Myeloma
(Submitter supplied) MYC is a major oncogenic driver of Multiple Myeloma (MM) and yet almost no therapeutic agents exist that target MYC in MM. Here we report that the let-7 biogenesis inhibitor LIN28B correlates with MYC expression in MM and is associated with adverse outcome. We also demonstrate that the LIN28B/let-7 axis modulates the expression of MYC, itself a let-7 target. Further, perturbation of the axis regulates the proliferation of MM cells in vivo in a xenograft tumor model. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (RPKM) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71100/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA290364
Series		Accession: GSE71100	ID: 200071100

4618. p53 in colorectal cancer cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms: GPL15456 GPL11154 6 Samples
FTP download: GEO (RPKM) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67110/
Series		Accession: GSE67110	ID: 200067110

4619. Genome-wide RNA-expression analysis after p53 activation in colorectal cancer cells.
(Submitter supplied) In order to comprehensively identify RNA-expression changes after p53-activation, total RNA was isolated and subjected to next generation seqencing (RNA-Seq) after activation of a conditional p53 allele in SW480 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (RPKM) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67109/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA278971
Series		Accession: GSE67109	ID: 200067109

4620. Analysis Of The TGFb-Induced Program In Primary Airway Epithelial Cells Shows Essential Role Of NF-kB/RelA Signaling Network In Type II Epithelial Mesenchymal Transition
(Submitter supplied) The airway epithelial cell plays a central role in coordinating pulmonary response to injury and inflammation.  Here, transforming growth factor-b (TGFb) activates gene expression programs to induce stem cell-like properties, inhibit expression of differentiated epithelial adhesion proteins and express mesenchymal contractile proteins.  This process is known as epithelial mesenchymal transition (EMT); although much is known about the role of EMT in cellular metastasis in an oncogene-transformed cell, less is known about Type II EMT, that occurring in normal epithelial cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE61nnn/GSE61220/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA260526
Series		Accession: GSE61220	ID: 200061220

4621. Treatment of prostate cancer cells with S-adenosylmethionine leads to genomewide alterations of transcription profiles
(Submitter supplied) The analysis investigates the impact of methyl donor S-adenosylmethionin on transcription and methylation profiles of prostate carcinoma cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71070/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA290227
Series		Accession: GSE71070	ID: 200071070

4622. RNA-seq profiling of lung adenocarcinoma and paired normal tissue
(Submitter supplied) To analyze transcriptome data for the mouse xenograft cells derived from a human lung adenocarcinoma patient, reference RNA-seq data were generated for the tracking of gene expression changes associated with the xeno-engraftment and culture.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70968/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA290027
Series		Accession: GSE70968	ID: 200070968

4623. Latency expression of the Epstein-Barr virus-encoded MHC class I TAP inhibitor, BNLF2a in EBV-positive gastric carcinomas
(Submitter supplied) RNA Sequencing performed on EBV positive gastric cancer biopsies and cells lines to study expression of EBV specific genes.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70513/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA288939
Series		Accession: GSE70513	ID: 200070513

4624. mRNA and small RNA associated with Crohn's disease behavior
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL16791 74 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66209/
Series		Accession: GSE66209	ID: 200066209

4625. mRNA and small RNA associated with Crohn's disease behavior [RNA-Seq]
(Submitter supplied) There is a need for reliable prognostic markers that can guide therapeutic intervention in Crohn’s disease (CD). We examined whether different behavioral phenotypes in CD can be classified based on colonic miRNA or mRNA expression and if miRNAs have prognostic utility for CD. We perform high-throughput sequencing of small RNA and mRNA isolated from colon tissue from CD patients and non-IBD (NIBD) controls. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 33 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66207/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA276116
Series		Accession: GSE66207	ID: 200066207

4626. Interphase condensins regulate ligand-depedent enhancer activation
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 47 Samples
FTP download: GEO (BIGWIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62229/
Series		Accession: GSE62229	ID: 200062229

4627. Interphase condensins regulate ligand-depedent enhancer activation (GRO-seq)
(Submitter supplied) An emerging theme of gene regulation is the involvement of architectural chromosomal molecules in transcription control. Condensins are critical regulators of mitotic chromosomes, but their interphase chromatin localization and functions remain poorly understood. Here we report that both the condensin I and condensin II complexes exhibit an unexpected, dramatic 17-?-estradiol-induced preferential recruitment to oestrogen receptor ? (ER-?)-bound active enhancers in interphase breast cancer cells, exhibiting non-canonical interaction with ER-? distinct from classic cofactors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (BIGWIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62228/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA263517
Series		Accession: GSE62228	ID: 200062228

4628. Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens
(Submitter supplied) Background: To determine differentially expressed and spliced RNA transcripts in chronic lymphocytic leukemia specimens a high throughput RNA-sequencing (HTS RNA-seq) analysis was performed. Methods:  Ten CLL specimens and five normal peripheral blood CD19+ B cells were analyzed by HTS RNA-seq. The library preparation was performed with Illumina TrueSeq RNA kit and analyzed by Illumina HiSeq 2000 sequencing system. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70830/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA289651
Series		Accession: GSE70830	ID: 200070830

4629. MYC is a major determinant of mitotic cell fate
(Submitter supplied) Purpose: To determine global gene expression changes following siRNA knockdown of Myc, Kcnk1, and Snta1 compared to non-targeting siRNAs or mock-transfected cells Methods: Total RNA was processed using the Illumina TruSeq Stranded mRNA Sample Preparation Kit according to manufacturer’s protocol. Generated cDNA libraries were sequenced using an Illumina HiSeq 2000 sequencer with four biological replicates sequenced per condition using single read, 50 cycle runs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 21 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68219/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA282044
Series		Accession: GSE68219	ID: 200068219

4630. Epoxyeicosatrienoic Acids Enhance Haematopoietic Stem and Progenitor Cell Specification and Engraftment
(Submitter supplied) Haematopoietic stem and progenitor cell (HSPC) transplant is a widely used treatment for life-threatening conditions including leukemia; however, the molecular mechanisms regulating HSPC engraftment of the recipient niche remain incompletely understood. Here, we developed a competitive HSPC transplant method in adult zebrafish, using in vivo imaging as a non-invasive readout. We used this system to conduct a chemical screen and identified epoxyeicosatrienoic acids (EET) as a family of lipids that enhance HSPC engraftment. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL9052 GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66767/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA277940
Series		Accession: GSE66767	ID: 200066767

4631. Heterogeneous effects of massive hypoxia pathway activation in kidney cancer
(Submitter supplied) General activation of hypoxia-inducible factor (HIF) pathways is classically associated with adverse prognosis in cancer and has been proposed to contribute to oncogenic drive. In clear cell renal carcinoma (CCRC) HIF pathways are upregulated by inactivation of the von-Hippel-Lindau tumour suppressor. However HIF-1a and HIF-2a have contrasting effects on experimental tumour progression. To better understand this paradox we examined pan-genomic patterns of HIF DNA binding and associated gene expression in response to manipulation of HIF-1a and HIF-2a and related the findings to CCRC prognosis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 19 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67237/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA279384
Series		Accession: GSE67237	ID: 200067237

4632. Leucegene: AML sequencing
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 285 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67040/
Series		Accession: GSE67040	ID: 200067040

4633. Leucegene: AML sequencing (part 5)
(Submitter supplied) RNA sequencing of human leukemia
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 263 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67039/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA278767
Series		Accession: GSE67039	ID: 200067039

4634. Leucegene: AML sequencing (part 4)
(Submitter supplied) RNA sequencing of human leukemia
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 22 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66917/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA278364
Series		Accession: GSE66917	ID: 200066917

4635. Leucegene: AML sequencing (part 3)
(Submitter supplied) RNA sequencing of human leukemia
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 82 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62190/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA263397
Series		Accession: GSE62190	ID: 200062190

4636. Genome-wide maps of H3K36me3 in ccRCC and RNA-seq of matched nephrectomy samples
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69198/
Series		Accession: GSE69198	ID: 200069198

4637. RNA sequencing of matched nephrectomy samples [RNA-seq]
(Submitter supplied) To address the need to study frozen clinical specimens using next-generation RNA, DNA, chromatin immunoprecipitation (ChIP) sequencing and protein analyses, we developed a biobank work flow to prospectively collect biospecimens from patients with renal cell carcinoma (RCC). We describe our standard operating procedures and work flow to annotate pathologic results and clinical outcomes. We report quality control outcomes, nucleic acid yields of our RCC submissions (N=16) to The Cancer Genome Atlas (TCGA) project, as well as newer discovery platforms by describing mass spectrometry analysis of albumin oxidation in plasma and 6 ChIP sequencing libraries generated from nephrectomy specimens after histone H3 lysine 36 trimethylation (H3K36me3) immunoprecipitation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69197/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA284822
Series		Accession: GSE69197	ID: 200069197

4638. mRNA and miRNA expression data from human osteosarcoma (OS)
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; synthetic construct
Type:		Non-coding RNA profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL16384 GPL570 12 Samples
FTP download: GEO (CEL, CHP) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70415/
Series		Accession: GSE70415	ID: 200070415

4639. Histone variant H2A.Z.2 mediates proliferation and drug sensitivity of malignant melanoma [RNA-seq]
(Submitter supplied) Here we report a novel role for H2A.Z.2 (H2AFV) as a mediator of cell proliferation and sensitivity to targeted therapies in malignant melanoma. While both H2A.Z.1 and H2A.Z.2 are highly expressed in metastatic melanoma and correlate with decreased patient survival, only H2A.Z.2 deficiency results in impaired cellular proliferation of melanoma cells, which occurs via a G1/S arrest. Integrated gene expression and ChIP-seq analyses revealed that H2A.Z.2 positively regulates E2F target genes, and that such genes acquire a distinct H2A.Z occupancy signature over the promoter and gene body in metastatic melanoma cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 3 Samples
FTP download: GEO (BIGWIG, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68221/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA282049
Series		Accession: GSE68221	ID: 200068221

4640. laryngo-pharyngeal tumor RNA-seq study for both mRNA and miRNA
(Submitter supplied) Cancers of the upper aero-digestive tracts (oral cavity, pharynx and larynx) are the sixth most common cancer worldwide. Laryngo-pharyngeal squamous cell carcinomas are one of the most common cancers in this category. Despite recent advances in the field of cancer research using high-throughput tools, the information, especially on tumors of hypopharynx, is relatively scarce. We have used next-generation sequencing and computational biology to study both the genes and miRNA from laryngo-pharyngeal tumors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL16288 28 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67994/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA281942
Series		Accession: GSE67994	ID: 200067994

4641. The MEF2B Regulatory Network - RNA-seq data
(Submitter supplied) Myocyte enhancer factor 2B (MEF2B) is a transcription factor with somatic mutation hotspots at K4, Y69 and D83 in diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL). The recurrence of these mutations indicates that they may drive lymphoma development. However, inferring the mechanisms by which they may drive lymphoma development was complicated by our limited understanding of MEF2B’s normal functions. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67447/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA279975
Series		Accession: GSE67447	ID: 200067447

4642. Optimized siRNAs with a minimal off-target effect facilitate the screening of essential genes in cancer cells
(Submitter supplied) siRNAs with dN are a promising and easy approach to characterize essential genes by minimizing the off-target effect in cancer cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62968/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA266318
Series		Accession: GSE62968	ID: 200062968

4643. Histone variant H2A.Z.2 mediates proliferation and drug sensitivity of malignant melanoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL6244 12 Samples
FTP download: GEO (CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59060/
Series		Accession: GSE59060	ID: 200059060

4644. Deep Sequencing Identifies Multiple Fusion Transcripts, Differentially Expressed Genes, and Generalized Immune Suppression in BRAF (V600E) mutant vs. BRAF wild-type Papillary Thyroid Carcinoma
(Submitter supplied) CONTEXT:  BRAF V600E mutation (BRAF-mut.) confers aggressiveness in papillary thyroid carcinoma, but unidentified genomic abnormalities may be required for full phenotypic expression.  OBJECTIVE:  To perform deep sequencing to identify genes differentially expressed between BRAF-mut. and BRAF-wild-type (BRAF-WT) tumors, and to compare to patient clinical status.  DESIGN:  BRAF-mut. and BRAF-WT tumors were identified in patients with T1N0 and with T23N1 tumors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 20 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48953/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA212391
Series		Accession: GSE48953	ID: 200048953

4645. Patient Derived Xenograft for Delivery of Precision Medicine in Castrate Resistant Prostate Cancer
(Submitter supplied) Developing animal models representating the cancer biology of advanced prostate cancer patients is challenging but essential for delivering individualized medical therapies. In an effort to develop patient derived xenograft (PDX) models, we took the metastatic site tissue from the rib lesion twice (ie, before and after enzalutamide treatment) over a twelve week period  and implanted subcutaneously and under the renal capsule in immuno-deficient mice. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70380/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA288475
Series		Accession: GSE70380	ID: 200070380

4646. Next Generation Sequencing Facilitates Quantitative Analysis of CNE1-mock, CNE1-BART1, CNE-BART3, CNE1-BART7 cells
(Submitter supplied) By using  NGS-derived retinal transcriptome profiling (RNA-seq) to compare the gene expression profiling between 4 differently treated NPC cells
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE43nnn/GSE43126/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA184667
Series		Accession: GSE43126	ID: 200043126

4647. The novel functional effects of exogenous EBV-miR-BARTs on NPC progression
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Rattus norvegicus; Macacine gammaherpesvirus 4; Homo sapiens; Mus musculus; Human gammaherpesvirus 8; Macaca mulatta polyomavirus 1
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by array
Platforms: GPL11154 GPL16414 44 Samples
FTP download: GEO (GPR, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE42nnn/GSE42945/
Series		Accession: GSE42945	ID: 200042945

4648. The RNA-binding protein Musashi1 is a central regulator of adhesion pathways in glioblastoma
(Submitter supplied) The conserved RNA-binding protein Musashi1 (MSI1) has emerged as a key oncogenic factor in numerous solid tumors, including glioblastoma. However, its mechanism of action has not yet been established comprehensively. We set out to map its impact on the transcriptome in U251 cells using RNA-seq and iCLIP.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL10999 GPL11154 9 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68800/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA283838
Series		Accession: GSE68800	ID: 200068800

4649. RNA-seq analysis reveals significant effects of EGFR signaling on mesenchymal stem cells (MSC)
(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goal of this study is to analyse the whole transcriptome of MSCs stimulated with TGFα in order to comprehensively assess the genes regulated by EGFR signalling Methods: Libraries of cDNA were obtained from poly(A)-RNA fractions from not-stimulated or TGFα-stimulated MSCs and sequenced with a SOLiD 5500xl platform. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16288 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE60nnn/GSE60560/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA258540
Series		Accession: GSE60560	ID: 200060560

4650. The DAXX co-repressor is directly recruited to active regulatory elements genome-wide to regulate autophagy programs in a model of human prostate cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68656/
Series		Accession: GSE68656	ID: 200068656

4651. The DAXX co-repressor is directly recruited to active regulatory elements genome-wide to regulate autophagy programs in a model of human prostate cancer (RNA-seq)
(Submitter supplied) This study was aimed at understanding the genome-wide binding and regulatory role of the DAXX transcriptional repressor, recently implicated in PCa. ChIP-Seq analysis of genome-wide distribution of DAXX in PC3 cells revealed over 59,000 DAXX binding sites, found at regulatory enhancers and promoters. ChIP-Seq analysis of DNA methyltransferase 1 (DNMT1), which is a key epigenetic partner for DAXX repression, revealed that DNMT1 binding was restricted to a small number of DAXX sites. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68645/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA283302
Series		Accession: GSE68645	ID: 200068645

4652. The oncofusion protein FUS-ERG targets key hematopoietic regulators and modulates the all-trans retinoic acid signaling pathway in t(16;21) acute myeloid leukemia
(Submitter supplied) Fusion proteins involving the ETS factor ERG have been associated with multiple cancers such as Ewing's sarcoma and prostate cancer. In acute myeloid leukemias harboring  t(16;21) another ERG fusion protein is expressed, FUS-ERG. Here, we found that this FUS-ERG oncofusion protein acts in the context of a heptad of proteins (ERG, FLI1, GATA2, LYL1, LNMO2, RUNX1 and TAL1) central to proper expression of genes involved in maintaining a stem cell hematopoietic phenotype. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL10999 20 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE60nnn/GSE60477/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA258377
Series		Accession: GSE60477	ID: 200060477

4653. Genetic disruption of COX-1 inhibits multiple oncogenic pathways
(Submitter supplied) We performed RNA sequencing in isogenic models of COX-1 proficient (OV3/SCR) and COX-1 deficient (OV3/COX1KD) OVCAR-3 ovarian cancer cells. COX-1 knockdown was associated with a coordinated anti-oncogenic phenotype, with growth, angiogenesis, migration/invasion, and epithelial-mesenchymal transition among the pathways down-regulated.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66173/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA276014
Series		Accession: GSE66173	ID: 200066173

4654. Mutational activation of a mechanosensitive megachannel drives metastatic cell survival.
(Submitter supplied) Next-generation sequencing has revolutionized cancer biology by accelerating the unbiased discovery of novel mutations across human cancers. Transforming such discoveries into a conceptual framework of cancer progression requires narrowing the vast number of mutations down to the driver elements, and further reducing these to mutations that govern cancer progression as opposed to tumor initiation. By integrating next-generation RNA-sequencing (RNA-seq) with in vivo selection, we devise an approach that identifies a series of novel recurrent non-synonymous amino acid mutations that are enriched in metastatic breast cancer cells and predicted to significantly alter protein function. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 8 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE45nnn/GSE45162/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA193090
Series		Accession: GSE45162	ID: 200045162

4655. Expression profiling of invasive breast carcinoma samples from Institut Curie
(Submitter supplied) Genomic hallmarks of homologous recombination deficiency in invasive breast carcinomas to appear in Internationa Journal of Cancer Transcriptome analysis of 243 (plus 12 duplicates) primary breast invasive carcinoma samples of various molecular subtypes.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16311 255 Samples
FTP download: GEO (CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69986/
Series		Accession: GSE69986	ID: 200069986

4656. renal cell carcinoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 22 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66885/
Series		Accession: GSE66885	ID: 200066885

4657. Tumor exosome integrins determine organotropic metastasis
(Submitter supplied) Stephen Paget first proposed, in 1889, that organ distribution of metastases is a non-random event, yet metastatic organotropism remains one of the greatest mysteries in cancer biology. Here, we demonstrate that exosomes released by lung-, liver- and brain-tropic tumor cells fuse preferentially with resident cells at their predicted destination, such as fibroblasts and epithelial cells in the lung, Kupffer cells in the liver, and endothelial cells in the brain. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68919/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA284109
Series		Accession: GSE68919	ID: 200068919

4658. RNA sequencing of SETD2 isogenic renal cell carcinoma cell lines
(Submitter supplied) RNA sequencing of SETD2 isogenic renal cell carcinoma cell lines.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66879/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA278161
Series		Accession: GSE66879	ID: 200066879

4659. Acute TNF-induced repression of cell identity genes is mediated by NFkB-directed redistribution of cofactors from super-enhancers
(Submitter supplied) The proinflammatory cytokine tumor necrosis factor (TNF) plays a central role in low-grade adipose tissue inflammation and development of insulin resistance during obesity. In this context, nuclear factor kappa-light-chain-enhancer of activated B cells (NFkB), is directly involved and required for the acute activation of the inflammatory gene program. Here we show that the major transactivating subunit of NF?B, v-rel avian reticuloendotheliosis viral oncogene homolog A (RELA), is also required for acute TNF-induced suppression of adipocyte genes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18460 36 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64233/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA270506
Series		Accession: GSE64233	ID: 200064233

4660. Dynamics of MBD2 deposition across methylated DNA regions during malignant transformation of human mammary epithelial cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by genome tiling array; Methylation profiling by genome tiling array
Platforms: GPL11154 GPL5082 30 Samples
FTP download: GEO (BED, BEDGRAPH, CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63237/
Series		Accession: GSE63237	ID: 200063237

4661. Characterizing the Chemoresistant Ovarian Cancer Population using the Heterogeneous PDX
(Submitter supplied) The patient-derived xenograft (PDX) model retains the heterogeneity of patient tumors, allowing a means to not only examine efficacy of a therapy across a population, but also study crucial aspects of cancer biology in response to treatment. Herein we describe the development and characterization of an ovarian-PDX model in order to study the development of chemoresistance. We demonstrate that PDX tumors are not simply composed of tumor-initiating cells, but recapitulate the original tumor’s heterogeneity, oncogene expression profiles, and clinical response to chemotherapy. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58586/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA252939
Series		Accession: GSE58586	ID: 200058586

4662. Regulating Interleukin-2 activity with engineered receptor signaling clamps
(Submitter supplied) Interleukin-2 (IL-2) is a pleiotropic cytokine that regulates lymphocyte function by signaling through heterodimerization of the IL-2Rβ and γc receptor subunits. Previously, we engineered an IL-2 “superkine” (H9) with enhanced affinity for IL-2Rβ. Here, we describe next-generation IL-2 variants that function as “receptor signaling clamps.” They retain high-affinity for IL-2Rβ, thereby inhibiting binding of endogenous IL-2, but their engagement of γc is weakened, thereby attenuating IL-2Rβ-γc heterodimerization. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 20 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64713/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA271704
Series		Accession: GSE64713	ID: 200064713

4663. Single-cell RNA-Seq transcriptome analysis of circular RNAs in mouse embryos
(Submitter supplied) We reported a new method of single-cell universal poly(A)-independent RNA sequencing (SUPeR-seq) to obtain single cell whole transcriptome analysis that covers both poly(A) plus and poly(A) minus RNA species. We built libraries of single mouse ESC , 10pg, 100pg and 1ng diluted mouse ES total RNA, single HEK293T cell and mouse early embryos before 4-cell stage. We analyzed these data using bioinformatics and find a good coverage of non-polyadenylated RNAs, circular RNA for example. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
4 related Platforms 118 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53386/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA231896
Series		Accession: GSE53386	ID: 200053386

4664. TALENs-mediated gene disruption of FLT3 in leukemia cells: Using genome-editing approach for exploring the molecular basis of gene abnormality
(Submitter supplied) Novel analytic tools are needed to elucidate the molecular basis of leukemia-relevant gene mutations in the post-genome era. We generated isogenic leukemia cell clones in which the FLT3 gene was disrupted in a single allele using TALENs. Isogenic clones with mono-allelic disrupted FLT3 were compared to an isogenic wild-type control clone and parental leukemia cells for transcriptional expression, downstream FLT3 signaling and proliferation capacity. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69678/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA286172
Series		Accession: GSE69678	ID: 200069678

4665. Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer [RNA-Seq]
(Submitter supplied) Basal-like and luminal breast tumors have distinct clinical behavior and molecular profiles, yet the underlying mechanisms are poorly defined. To interrogate processes that determine these distinct phenotypes and their inheritance pattern, we generated somatic cell fusions and performed integrated genetic and epigenetic (DNA methylation and chromatin) profiling. We found that the basal-like trait is generally dominant and it is largely defined by epigenetic repression of luminal transcription factors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 10 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69114/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA284585
Series		Accession: GSE69114	ID: 200069114

4666. Identification of transcripts regulated by CEBPA protein and its P30 isoform in K562
(Submitter supplied) To investigate the effect of CEBPA and its mutant isoform P30 on the expression of mRNAs and long non-coding RNAs (lncRNAs), we utilized the K562 AML cell line carrying a stable and Tet-on inducible CEBPA  or P30 allele.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL10999 GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE65nnn/GSE65235/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA273465
Series		Accession: GSE65235	ID: 200065235

4667. Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer [DGE]
(Submitter supplied) Basal-like and luminal breast tumors have distinct clinical behavior and molecular profiles, yet the underlying mechanisms are poorly defined. To interrogate processes that determine these distinct phenotypes and their inheritance pattern, we generated somatic cell fusions and performed integrated genetic and epigenetic (DNA methylation and chromatin) profiling. We found that the basal-like trait is generally dominant and it is largely defined by epigenetic repression of luminal transcription factors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL14761 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE38nnn/GSE38790/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA170832
Series		Accession: GSE38790	ID: 200038790

4668. Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Methylation profiling by array; Genome variation profiling by SNP array; Methylation profiling by genome tiling array
7 related Platforms 106 Samples
FTP download: GEO (BED, BW, CEL, FPKM_TRACKING, PROBSCOREISLAND, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE38nnn/GSE38548/
Series		Accession: GSE38548	ID: 200038548

4669. Single-cell RNA sequencing of lung adenocarcinoma patient-derived cells
(Submitter supplied) To address how intratumoral heterogeneity affects anti-cancer drug responses, we profiled transcriptomes of single cancer cells originating from lung adenocarcinoma patient-derived xenograft (PDX) tumors. 
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL16791 208 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69405/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA285793
Series		Accession: GSE69405	ID: 200069405

4670. Alternative splicing in genes encoding adhesion- and motility-related proteins in breast cancer
(Submitter supplied) In this study, combining 1) RNA-Sequencing on MCF-7 cell line, 2) a new computational approach to identify splice isoforms and 3) an extensive experimental validation (in vitro - on MCF-10, MCF-7 and MDA-MB-231 – and ex vivo – on human breast cancer tissues) we investigated simultaneously gene expression and alternative splicing in genes encoding for adhesion and motility-related molecules-, including Semaphorins and their receptors and co-receptors.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68228/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA282078
Series		Accession: GSE68228	ID: 200068228

4671. Human Schlafen 5 (SLFN5) is a Regulator of Motility and   Invasiveness of Renal Cell Carcinoma (RCC) Cells
(Submitter supplied) There is some emerging evidence that members of the Schlafen (SLFN) family of  proteins mediate antineoplastic responses, but the mechanisms accounting for these  effects are not known. We provide evidence that human SLFN5, an interferon (IFN)-  inducible member of the family, exhibits key roles in controlling motility and  invasiveness of renal cell carcinoma (RCC) cells. Our studies define the mechanism by  which this occurs, demonstrating that SLFN5 negatively controls expression of matrix  metalloproteinases (MMP)-1 and -13 and several other genes involved in the control of  malignant cell motility. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64399/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA270890
Series		Accession: GSE64399	ID: 200064399

4672. A Class of H3K4me1/H3K9me2 marked active GATA2 enhancers directs a GATA2-dependent transcription program underlying prostate cancer progression.
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL9115 GPL11154 6 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE38nnn/GSE38452/
Series		Accession: GSE38452	ID: 200038452

4673. Hi-seq 2000 sequencing facilitates quantitative analysis of transcriptomes in LNCaP cells with or without SiGATA2 treatment.
(Submitter supplied) We obtained 1,367 GATA2 up-regulated and 759 GATA2 down-regulated genes (p< 0.001).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE38nnn/GSE38393/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA167797
Series		Accession: GSE38393	ID: 200038393

4674. A resource of ribosomal RNA-depleted RNA-seq from different normal adult and fetal human tissues
(Submitter supplied) Gene expression is the most fundamental level at which the genotype leads to the phenotype of the organism. Enabled by ultra-high-throughput next-generation DNA sequencing, RNA-Seq involves shotgun sequencing of fragmented RNA transcripts by next-generation sequencing followed by in silico assembly, and is rapidly becoming the most popular method for gene expression analysis. Poly[A]+ RNA-Seq analyses of normal human adult tissue samples such as Illumina’s Human BodyMap 2.0 Project and the RNA-Seq atlas have provided a useful global resource and framework for comparisons with diseased tissues such as cancer. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 19 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69360/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA283012
Series		Accession: GSE69360	ID: 200069360

4675. Activation of proto-oncogenes by disruption of chromosome neighborhoods [RNA-Seq]
(Submitter supplied) Mutations such as gene fusion, translocation and focal amplification are a frequent cause of proto-oncogene activation during tumorigenesis, but such mutations do not explain all cases of proto-oncogene activation. Here we show that disruption of local chromosome conformation can also activate proto-oncogenes in human cells. We mapped chromosome structures in T-cell acute lymphoblastic leukemia (T-ALL), and found that active oncogenes and silent proto-oncogenes generally occur within insulated neighborhoods formed by the looping of two interacting CTCF sites co-occupied by cohesin. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 1 Sample
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68975/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA284252
Series		Accession: GSE68975	ID: 200068975

4676. The Landscape of Antisense Gene Expression in Human Cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 376 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66729/
Series		Accession: GSE66729	ID: 200066729

4677. The Landscape of Antisense Gene Expression in Human Cancers [II]
(Submitter supplied) High throughput RNA sequencing has revealed pervasive transcription of human genome than previously anticipated. However, the extent of natural antisense transcripts (NATs) expression, their regulation of cognate sense genes, and the role of NATs in cancer remain poorly understood. Here, we use strand-specific paired-end RNA sequencing (ssRNASeq) data from 376 cancer patients covering 9 tissue types to comprehensively characterize the landscape of antisense expression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 353 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66728/
Series		Accession: GSE66728	ID: 200066728

4678. The Landscape of Antisense Gene Expression in Human Cancers [I]
(Submitter supplied) High throughput RNA sequencing has revealed pervasive transcription of human genome than previously anticipated. However, the extent of natural antisense transcripts (NATs) expression, their regulation of cognate sense genes, and the role of NATs in cancer remain poorly understood. Here, we use strand-specific paired-end RNA sequencing (ssRNASeq) data from 376 cancer patients covering 9 tissue types to comprehensively characterize the landscape of antisense expression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 23 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66727/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA262128
Series		Accession: GSE66727	ID: 200066727

4679. Genome-Wide Specificity of DNA-Binding, Gene Regulation, and Chromatin Remodeling by TALE- and CRISPR/Cas9-Based Transcription Factors
(Submitter supplied) Synthetic DNA-binding proteins have found broad application in gene therapies and as tools for interrogating biology. Engineered proteins based on the CRISPR/Cas9 and TALE systems have been used to alter genomic DNA sequences, control transcription of endogenous genes, and modify epigenetic states. Although the activity of these proteins at their intended genomic target sites have been assessed, the genome-wide effects of their action have not been extensively characterized. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68341/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA282486
Series		Accession: GSE68341	ID: 200068341

4680. Progesterone receptor directs a distinct estrogen receptor-alpha chromatin binding profile in breast cancer to elicit good clinical outcome
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 197 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68359/
Series		Accession: GSE68359	ID: 200068359

4681. RNA-seq in two ER+ breast cancer cell lines with and without progestins
(Submitter supplied) Exploring effect of progesterone/progestin treatment on gene expression
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 48 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68358/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA282505
Series		Accession: GSE68358	ID: 200068358

4682. RNA-Seq reveals an unprecedented complexity of the neuroblastoma transcriptome and is suitable for clinical endpoint prediction [RNA-Seq]
(Submitter supplied) We generated gene expression profiles from 498 primary neuroblastomas using RNA-Seq and microarrays. We sought to systematically evaluate the capability of RNA deep-sequencing (RNA-Seq)-based classification for clinical endpoint prediction in comparison to microarray-based ones. The neuroblastoma cohort was randomly divided into training and validation sets, and 360 predictive models on six clinical endpoints were generated and evaluated. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17553 498 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE49nnn/GSE49711/
Series		Accession: GSE49711	ID: 200049711

4683. 8p Loss of Heterozygosity triggers metastasis and drug resistance
(Submitter supplied) Chromosome arm deletions are frequently observed in human cancers. Such large-scale aberrations may trigger phenotypes distinct from those that arise by loss of single genes. Using TALEN-based genomic engineering, we generated cell models with targeted 8p loss-of-heterozygosity (LOH) that mimics an 8p deletion commonly found in breast cancer patients. 8p LOH triggered up-regulation of the mevalonate pathway. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68042/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA281617
Series		Accession: GSE68042	ID: 200068042

4684. Scalable Microfluidics for Single Cell RNA Printing and Sequencing
(Submitter supplied) Single cell transcriptomics has emerged as a powerful approach to dissecting phenotypic heterogeneity in complex, unsynchronized cellular populations.  However, many important biological questions demand quantitative analysis of large numbers of individual cells. Hence, new tools are urgently needed for efficient, inexpensive, and parallel manipulation of RNA from individual cells. We report a simple microfluidic platform for trapping single cell lysates in sealed, picoliter microwells capable of “printing” RNA on glass or capturing RNA on polymer beads. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 643 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66357/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA276634
Series		Accession: GSE66357	ID: 200066357

4685. Droplet barcoding for single cell transcriptomics applied to embryonic stem cells
(Submitter supplied) Recently, RNA sequencing has achieved single cell resolution, but what is limiting is an effective way to routinely isolate and process large numbers of individual cells for in-depth sequencing, and to do so quantitatively. We have developed a droplet-microfluidic approach for parallel barcoding thousands of individual cells for subsequent RNA profiling by next-generation sequencing. This high-throughput method shows a surprisingly low noise profile and is readily adaptable to other sequencing-based assays. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
5 related Platforms 8 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE65nnn/GSE65525/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA274274
Series		Accession: GSE65525	ID: 200065525

4686. RNA-seq transcriptomic analysis of sarcomatoid (E/S), rhabdoid (E/R) and non-sarcomatoid (E*) clear cell renal cell carcinoma
(Submitter supplied) The biphasic epithelioid (E-) and sarcomatoid(S-) components of sarcomatoid RCC and epithelioid (E-) and rhabdoid (R-) components of rhabdoid RCC shared a similar transcriptomic signature, despite morphologic differences; by contrast, the transcriptome of sarcomatoid and rhabdoid RCC was sharply distinct from non-sarcomatoid RCC.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59066/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA254324
Series		Accession: GSE59066	ID: 200059066

4687. Different molecular pathways along with pathogenesis of three subtypes of Leiomyosarcoma
(Submitter supplied) Leiomyosarcoma (LMS) is a malignant neoplasm of smooth muscle and is an aggressive soft tissue tumor, have complex genetic abnormalities and could be defined as three molecular subtypes. Since that the molecular heterogeneity of LMS, the pathogenesis analysis per subtype will be highly necessary and helpful to understand the etiology of this more common sarcoma.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL10999 GPL11154 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE54nnn/GSE54511/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA236775
Series		Accession: GSE54511	ID: 200054511

4688. Undifferentiated pleomorphic sarcoma recapitulates the expressional profile of Subtype II Leiomyosarcoma
(Submitter supplied) Background: Undifferentiated pleomorphic sarcoma (UPS), used to be called malignant fibrous histiocytoma (MFH), is a malignant soft tissue tumor of uncertain origin, and is characterized by morphology. UPS often share similar morphological characters with other sarcomas, especially Leiomyosarcoma.  Leiomyosarcoma (LMS) is another malignant soft tissue sarcoma with complex genomic abnormalities, origin from smooth muscle. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53844/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA233524
Series		Accession: GSE53844	ID: 200053844

4689. Stratification of Leiomyosarcoma molecular subtypes by 3' end RNA-sequencing: Toward precision medicine
(Submitter supplied) Leiomyosarcoma (LMS) is a malignant neoplasm with smooth muscle differentiation.  Little is known about its molecular heterogeneity and no targeted therapy currently exists for LMS.  We demonstrate the existence of 3 molecular subtypes in a cohort of 99 cases and an independent cohort of 82 LMS.  Two new FFPE tissue-compatible diagnostic immunohistochemical markers are identified: LMOD1 for subtype I LMS and ARL4C for subtype II LMS. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 99 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE45nnn/GSE45510/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA194525
Series		Accession: GSE45510	ID: 200045510

4690. RNA sequencing analysis of miR-603 overexpression
(Submitter supplied) Alzheimer’s disease (AD) is a serious neurodegenerative disease in which miRNAs have been linked to its pathogenesis. miR-603 is a primate-specific miRNA. Through ADNI data analysis, we found a SNP rs11014002 in pre-miR-603 which promotes the biogenesis of mature miR-603 is associated with AD risk. We further identified that LRPAP1, a protein which antagonizes the function of LRP1 in Aβ clearance and AD susceptibility, is a target gene of miR-603. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68987/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA284262
Series		Accession: GSE68987	ID: 200068987

4691. Argonaute 2 binds directly to tRNA genes and promotes gene repression in cis
(Submitter supplied) To further our understanding of the RNAi machinery within the human nucleus, we analyzed the chromatin and RNA binding of Argonaute 2 (AGO2) within human cancer cell lines. Our data indicated that AGO2 binds directly to nascent tRNA and 5S rRNA, and to the genomic loci from which these RNAs are transcribed, in a small RNA- and DICER-independent manner. AGO2 chromatin binding was not observed at non-TFIIIC-dependent RNA polymerase (Pol) III genes or at extra-TFIIIC (ETC) sites, indicating that the interaction is specific for TFIIIC-dependent Pol III genes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL11154 GPL10999 11 Samples
FTP download: GEO (BED, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68813/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA283872
Series		Accession: GSE68813	ID: 200068813

4692. A microfluidic device for label-free, physical capture of circulating tumor cell-clusters
(Submitter supplied) Cancer cells metastasize through the bloodstream either as single migratory circulating tumor cells (CTCs) or as multicellular groupings (CTC-clusters). Existing technologies for CTC enrichment are designed primarily to isolate single CTCs, and while CTC-clusters are detectable in some cases, their true prevalence and significance remain to be determined. Here, we developed a microchip technology (Cluster-Chip) specifically designed to capture CTC-clusters independent of tumor-specific markers from unprocessed blood. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16288 17 Samples
FTP download: GEO (TXT, XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67939/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA281253
Series		Accession: GSE67939	ID: 200067939

4693. RNAi profiling of primary human AML cells identifies ROCK1 as a therapeutic target and nominates Fasudil as an anti-leukemic drug.
(Submitter supplied) Acute myeloid leukemia (AML) is characterized by a marked genetic heterogeneity, which complicates the development of novel therapeutics. The delineation of pathways essential within the patient-individual mutational background might overcome this limitation and facilitate personalized treatment. We report the results of a large-scale lentiviral loss-offunction RNA-interference-(RNAi)-screen in primary leukemic cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing; Other
Platform: GPL11154 10 Samples
FTP download: GEO (TXT, VCF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68925/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA284119
Series		Accession: GSE68925	ID: 200068925

4694. Reprogrammed myeloid cell transcriptomes in NSCLC
(Submitter supplied) Lung cancer is the leading cause of cancer related mortality worldwide, with non-small cell lung cancer (NSCLC) as the most prevalent form.  Despite advances in treatment options including minimally invasive surgery, CT-guided radiation, novel chemotherapeutic regimens, and targeted therapeutics, prognosis remains dismal. Therefore, further molecular analysis of NSCLC is necessary to identify novel molecular targets that impact prognosis and the design of new-targeted therapies. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 17 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68795/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA283843
Series		Accession: GSE68795	ID: 200068795

4695. SRSF2 mutations impair hematopoiesis and alter exon recognition
(Submitter supplied) Mutations within genes encoding spliceosomal proteins are the most common class of mutations in patients with myelodysplastic syndromes, yet it is currently not well understood how these mutations impact hematopoiesis or RNA splicing. Here we report that mutations affecting the splicing factor SRSF2 alter its normal RNA recognition activity, resulting in impaired hematopoietic differentiation and myelodysplasia. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL13112 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE65nnn/GSE65349/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA273749
Series		Accession: GSE65349	ID: 200065349

4696. Investigation about fibroblasts of different origins in culture
(Submitter supplied) The goal of this study was to determine if fibroblasts from different origin (skin, colon, tumors) were keeping their characteristic while extracted and cultured ex vivo for several passages. HUVEC was used as a control, being cells from a different background. Surprisingly, fibroblasts from different origins are losing their independant characteristic to cluster in a similar way after 5-6 passages in culture in vitro, showing an activated status.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67945/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA281358
Series		Accession: GSE67945	ID: 200067945

4697. Global Gene Expression analysis of CUTLL1 cell lines after treatment with Perhexiline
(Submitter supplied) We identify perhexiline, a small molecule inhibitor of mitochondrial carnitine palmitoyltransferase-1, as a HES1-signature antagonist drug with robust antileukemic activity against NOTCH1 induced leukemias in vitro and in vivo.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66014/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA275672
Series		Accession: GSE66014	ID: 200066014

4698. Prospective derivation of a 'Living Organoid Biobank' of colorectal cancer patients
(Submitter supplied) In Rspondin-based three-dimensional cultures, Lgr5 stem cells from multiple organs form ever-expanding epithelial organoids that retain their tissue identity. Here we report the establishment of tumor organoid cultures from 20 consecutive colorectal carcinoma (CRC) patients. For most, organoids were also generated from adjacent normal tissue. Organoids closely resemble the original tumor. The spectrum of genetic changes within the 'living biobank' agrees well with previous large-scale mutational analyses of CRC. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 108 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE65nnn/GSE65253/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA273501
Series		Accession: GSE65253	ID: 200065253

4699. Cancer Cells Hijack PRC2 to Modify Multiple Cytokine Pathways
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by genome tiling array; Expression profiling by array
4 related Platforms 83 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67766/
Series		Accession: GSE67766	ID: 200067766

4700. Study the effect of SUZ12 on the responsiveness of IFNg target genes in multiple cancer and non cancer cell lines
(Submitter supplied) We studied the effect of knocking down SUZ12 on the responsiveness of IFNg target genes
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 44 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67240/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA279312
Series		Accession: GSE67240	ID: 200067240

4701. smRNA sequencing analysis to identify p53-dependent non-coding RNA networks in Chronic Lymphocytic Leukemia
(Submitter supplied) Mutations of the tumor suppressor p53 lead to chemotherapy resistance and a dismal prognosis in chronic lymphocytic leukemia (CLL). Comparing miRNA/non-coding RNA expression profiles between p53 wild-type and p53 mutant samples in response to DNA damage, we exploit the impaired transcriptional activity of mutant p53 to map out p53 targets in primary CLL by small RNA sequencing. Focusing on miRNAs, we identify a set of p53-dependent miRNAs (miR-182-5p, miR-7-5p, miR-320c/d) in addition to the key p53 target miR-34a. more...
Organism:	Homo sapiens
Type:		Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 70 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66186/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA276078
Series		Accession: GSE66186	ID: 200066186

4702. RNA-Sequencing of human papillary thyroid carcinomas
(Submitter supplied) RNA-Sequencing analysis of 18 papillary thyroid carcinoma biopsies and of 4 healthy donors' thyroids. In this analysis we assessed differential gene expression and investigated the mutational landscape in this tumor type. Analysis of gene fusion was also performed, leading to the identification of a novel chimeric transcript, potential driver in tumor initiation.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 22 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64912/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA272493
Series		Accession: GSE64912	ID: 200064912

4703. Gene Expression Signature in Adipose Tissue of Acromegaly Patients
(Submitter supplied) OBJECTIVE: Acromegaly is a rare endocrine disorder with excess growth hormone (GH) production. This disorder has important metabolic effects in insulin resistance and lipolysis. The objective of this study was to explore transcriptional changes induced by GH in adipose tissue. METHODS: The patients underwent clinical and metabolic profiling including assessment of HOMA-IR. Explants of adipose tissue were assayed ex-vivo for lipolysis and ceramide levels. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57803/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA248131
Series		Accession: GSE57803	ID: 200057803

4704. Stem cell and neurogenic gene-expression profiles link prostate basal cells to aggressive prostate cancer
(Submitter supplied) The prostate gland mainly contains basal and luminal cells constructed as a pseudostratified epithelium. Annotation of prostate epithelial transcriptomes provides a foundation for discoveries that can impact disease understanding and treatment. Here, we describe a whole-genome transcriptome analysis of human benign prostatic basal and luminal populations by using deep RNA sequencing. Combined with comprehensive molecular and biological characterizations, we show that the differential gene expression profiles account for their distinct functional phenotypes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67070/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA278856
Series		Accession: GSE67070	ID: 200067070

4705. IL-33 activates tumor stroma to promote intestinal polyposis
(Submitter supplied) Tumor epithelial cells develop within a microenvironment consisting of extracellular matrix, growth factors, and cytokines produced by non-epithelial stromal cells. In response to paracrine signals from tumor epithelia, stromal cells modify the microenvironment to promote tumor growth and metastasis. Here, we identify interleukin (IL)-33 as an epithelial cell-derived regulator of stromal cell activation and mediator of intestinal polyposis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (GTF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62518/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA264321
Series		Accession: GSE62518	ID: 200062518

4706. Small molecule inhibition of ERK dimerization prevents tumorigenesis by Ras-ERK pathway oncogenes
(Submitter supplied) About 50% of human malignancies exhibit unregulated signalling through the Ras-ERK1/2 (ERK) pathway, as a consequence of activating mutations in members of Ras and Raf families. However, the quest for alternative Ras-ERK pathway-directed therapies is desirable. Upon phosphorylation ERK dimerize. We had previously demonstrated that dimerization is essential for ERK extranuclear but not nuclear signaling. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 10 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68230/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA282079
Series		Accession: GSE68230	ID: 200068230

4707. Circular RNAs in the mammalian brain are highly abundant, conserved, and dynamically expressed
(Submitter supplied) Circular RNAs (circRNAs) are an endogenous class of animal RNAs. Despite their abundance, their function and expression in the nervous system are unknown. Therefore, we sequenced RNA from different brain regions, primary neurons, isolated synapses, as well as during neuronal differentiation. Using these and other available data, we discovered and analyzed thousands of neuronal human and mouse circRNAs. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
4 related Platforms 25 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE65nnn/GSE65926/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA275421
Series		Accession: GSE65926	ID: 200065926

4708. Small RNA mediated DNA (cytosine-5) methyltransferase 1 inhibition leads to aberrant DNA methylation
(Submitter supplied) Mammalian cells contain copious amounts of RNA including both coding and non-coding RNA (ncRNA). Generally the ncRNAs function to regulate gene expression at the transcriptional and post-transcriptional level. Among ncRNA, the long ncRNA and small ncRNA can affect histone modification, DNA methylation targeting and gene silencing. Here we show that endogenous DNA methyltransferase 1 (DNMT1) co-purifies with inhibitory ncRNAs. more...
Organism:	Homo sapiens
Type:		Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL9115 11 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68027/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA281584
Series		Accession: GSE68027	ID: 200068027

4709. mRNA profiling reveals determinants of trastuzumab efficiency in HER2-positive breast cancer
(Submitter supplied) The intention was to detect genes that are determining trastuzumab efficiency in HER2-positive breast cancer cell lines with different resistance phenotypes. While BT474 should be sensitive to the drug treatment, HCC1954 is expected to be resistant due to a PI3K mutation. The cell line BTR50 has been derived from BT474 and was cultured to be resistant as well. Based on RNA-Seq data, we performed differential expression analyses on these breast cancer cell lines with and without trastuzumab treatment. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE55nnn/GSE55005/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA238231
Series		Accession: GSE55005	ID: 200055005

4710. Integrative Genomic Analysis Reveals Widespread Enhancer Regulation by p53 in Response to DNA Damage
(Submitter supplied) The tumor suppressor p53 has been studied extensively as a direct transcriptional activator of protein-coding genes.  Recent studies, however, have shed light on novel regulatory functions of p53 within noncoding regions of the genome.  Here, we use a systematic approach that integrates transcriptome-wide differential expression analysis, genome-wide p53 binding profiles, chromatin state maps, and additional genomic features to characterize the global regulatory roles of p53 in response to DNA damage in both human and mouse fibroblast models. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
4 related Platforms 24 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE55nnn/GSE55727/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA240784
Series		Accession: GSE55727	ID: 200055727

4711. Next-Generation Sequencing Analysis Reveals Differential Expression Profiles of miRNA-mRNA Target Pairs in KSHV-Infected Cells [mRNA-Seq]
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below. Purpose: Kaposi’s sarcoma (KS)-associated herpesvirus (KSHV) causes several lymphoproliferative disorders, including KS, a common AIDS-associated malignancy. Cellular and viral microRNAs (miRNAs) have been shown to play important roles in regulating the expression of genes in oncogenesis. Herpesviruses, including KSHV, encode for miRNAs that are involved in angiogenesis, inflammation and apoptosis. more...
Organism:	Homo sapiens; Human gammaherpesvirus 8
Type:		Expression profiling by high throughput sequencing
Platforms: GPL19367 GPL11154 6 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62829/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA265452
Series		Accession: GSE62829	ID: 200062829

4712. EZH2 inhibitor efficacy in non-Hodgkin lymphoma does not require suppression of H3K27 mono-methylation
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 10 Samples
FTP download: GEO (TDF, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62058/
Series		Accession: GSE62058	ID: 200062058

4713. EZH2 inhibitor efficacy in non-Hodgkin lymphoma does not require suppression of H3K27 mono-methylation [RNA-Seq]
(Submitter supplied) Here we report the discovery of highly potent and selective EZH2 small molecule inhibitors, their validation by a cellular thermal shift assay, their application across a large lymphoma cell panel and their efficacy in GCBDLBCL xenograft models.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TDF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62056/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA263115
Series		Accession: GSE62056	ID: 200062056

4714. AXL mediates resistance to PI3Kα inhibition by activating the EGFR/PKC/mTOR axis in head and neck and esophageal squamous cell carcinomas.
(Submitter supplied) Phosphoinositide-3-kinase (PI3K)-α inhibitors are clinically active in squamous carcinoma (SCC) of the head and neck (H&N) bearing mutations or amplification of PIK3CA. We aimed to identify potential mechanism of resistance and have observed that SCCs cells overcome the antitumor effects of the PI3Kα inhibitor BYL719 by maintaining PI3K-independent activation of the mammalian target of rapamycin (mTOR). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE61nnn/GSE61515/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA261341
Series		Accession: GSE61515	ID: 200061515

4715. Splicing function of mitotic regulators links R-loop mediated DNA damage to tumor cell killing
(Submitter supplied) We discovered that two mitotic regulators, BuGZ and Bub3, involved in splicing regulation during interphase
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 20 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67770/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA280861
Series		Accession: GSE67770	ID: 200067770

4716. The tumor virus landscape of AIDS-related lymphomas
(Submitter supplied) Immunodeficiency dramatically increases susceptibility to cancer as a result of reduced immune surveillance and enhanced opportunities for virus-mediated oncogenesis. While AIDS-related lymphomas (ARLs) are frequently associated with known oncogenic viruses, many cases contain no known transforming virus. To discover novel transforming viruses, we profiled a set of ARL samples using whole transcriptome sequencing. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 25 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67763/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA280845
Series		Accession: GSE67763	ID: 200067763

4717. Genome-wide effect of inhibition of glutamine transporter ASCT2 in PC-3 cells by BenSer or GPNA
(Submitter supplied) To determine the global effects of ASCT2 inhibition, we used next generation sequencing to determine mRNA expression changes in PC-3 cells treated with BenSer or GPNA for 48 h.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE65nnn/GSE65112/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA273014
Series		Accession: GSE65112	ID: 200065112

4718. Modeling Familial Cancer with iPSC Approaches
(Submitter supplied) In vitro modeling of human disease has recently become feasible with the adoption of induced pluripotent stem cell (iPSC) technology. Here, we established patient-derived iPSCs from an Li-Fraumeni Syndrome (LFS) family and investigated the role of mutant p53 in the development of osteosarcoma (OS). Several members of this family carried a heterozygous p53(G245D) mutation and presented with a broad spectrum of tumors including OS. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL16791 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58123/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA249062
Series		Accession: GSE58123	ID: 200058123

4719. Profile of gene expression in U87-MG xenografts expressing control vector (V0), the ubiquitin ligase KPC1 or the p50 subunit of the NF-kB transcription factor, using RNASeq analysis of transcripts mapped independently to the human and murine genomes
(Submitter supplied) Purpose: We identified KPC1 as the ubiquitin ligase that binds to the p105 precursor of NF-kB, ubiquitinates it and mediates its proteasomal processing to generate the p50 active subunit of the transcription factor. Using U87-MG human glioblastoma xenografts, we observed that overexpression of KPC1 results in strong inhibition of tumor growth mediated via excessive generation of p50.The goal of this RNASeq study was to analyze the profile of gene expression in xenografts overexpressing control (V0), KPC1 or p50 vectors, and to further understand how the altered gene expression patterns can explain the tumor suppressive effect we observed. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (FPKM_TRACKING, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE60nnn/GSE60530/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA258473
Series		Accession: GSE60530	ID: 200060530

4720. Transcriptome Sequencing (RNA-seq) of Normal Human Osteoblasts
(Submitter supplied) Three normal human osteoblast samples, acquired from PromoCell, were used as controls to compare to RNA-seq data from prepublished osteosarcoma samples (submitted to the European Bioinformatics Institute; EGAS00001000263) for the purpose of evaluating expression levels of genes identified as common insertions sites in a Sleeping Beauty screen of osteosarcomas in mice.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 3 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57925/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA248432
Series		Accession: GSE57925	ID: 200057925

4721. RNA-Seq Samples of siTFE3 in 8988T PDA Cell Line to Investigate Transcriptional Control of the Autophagy-Lysosome System
(Submitter supplied) The activation of cellular quality control pathways to maintain metabolic homeostasis and mitigate diverse cellular stresses is emerging as a critical growth and survival mechanism in many cancers. Autophagy, a highly conserved cellular self-degradative process, is a key player in the initiation and maintenance of pancreatic ductal adenocarcinoma (PDA). However, the regulatory circuits that activate autophagy, and how they enable reprogramming of PDA cell metabolism are unknown. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62077/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA263163
Series		Accession: GSE62077	ID: 200062077

4722. Immunoglobulin transcript sequence and somatic hypermutation computation from unselected RNA-seq reads in Chronic Lymphocytic Leukemia
(Submitter supplied) IGHV mutation status is a well-established prognostic factor in chronic lymphocytic leukemia, and also provides crucial insights into tumor cell biology and function. Currently, determination of IGHV transcript sequence, from which mutation status is calculated, requires a specialized laboratory procedure. RNA sequencing is a method that provides high resolution, high dynamic range transcriptome data that can be used for differential expression, isoform discovery, and variant determination. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 17 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66228/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA276143
Series		Accession: GSE66228	ID: 200066228

4723. BRG1 recruitment by transcription factors MITF and SOX10 defines a specific configuration of regulatory elements in the melanocyte lineage
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 27 Samples
FTP download: GEO (TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE61nnn/GSE61967/
Series		Accession: GSE61967	ID: 200061967

4724. BRG1 recruitment by transcription factors MITF and SOX10 defines a specific configuration of regulatory elements in the melanocyte lineage (RNA-seq)
(Submitter supplied) Microphthalmia-associated transcription factor (MITF) is the master regulator of the melanocyte lineage. By tandem affinity purification and mass spectrometry, we present a comprehensive characterisation of the MITF interactome comprising multiple novel cofactors involved in transcription, DNA replication and repair and chromatin organisation, including a BRG1 chromatin remodelling complex comprising CHD7. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 19 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE61nnn/GSE61966/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA262824
Series		Accession: GSE61966	ID: 200061966

4725. BCLAF1 and its pre-mRNA splicing regulator SRSF10 both regulate tumorigenic capacity of human colon cancer cells
(Submitter supplied) Bcl-2-accociated transcription factor 1(BCLAF1) has been shown to be involved in multiple biological processes. Transcript variants encoding different isoforms that are generated by alternative splicing have been found for this gene, but little is known about the mechanisms governing its splicing regulation and whether the misregulation is associated with cancer development. Mechanistic analysis revealed that splicing factor SRSF10 specifically interacts with exon5a and activates its inclusion, as RNAi-mediated knockdown of SRSF10 induced a dramatic skipping of exon5a. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57325/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA246274
Series		Accession: GSE57325	ID: 200057325

4726. Next Generation Sequencing Identification of HBV-MLL4 integration and its molecular basis in Chinese hepatocellular carcinoma
(Submitter supplied) Purpose: To gain molecular insights of HBV integration that may contribute to HCC tumorigenesis, we performed whole transcriptome sequencing and whole genome copy number profiling of hepatocellular carcinoma (HCC) samples from 50 Chinese patients. Results: We identified a total of 33 HBV-human integration sites in 16 of 44 HBV-positive HCC tissues, which were enriched in HBV genotype C-infected patients. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 55 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE65nnn/GSE65485/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA279878
Series		Accession: GSE65485	ID: 200065485

4727. Specific molecular signatures underlie response to decitabine in CMML
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 53 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE61nnn/GSE61163/
Series		Accession: GSE61163	ID: 200061163

4728. Specific molecular signatures underlie response to decitabine in CMML [RNA-seq]
(Submitter supplied) Myelodysplastic syndromes and chronic myelomonocytic leukemia (CMML) are characterized by mutations in epigenetic modifiers and aberrant DNA methylation. DNA methyltransferase inhibitors (DMTis) are used to treat these disorders, but response is highly variable with few means to predict which patients will benefit. To develop a molecular means of predicting response at diagnosis, we examined baseline differences in mutations, DNA methylation, and gene expression in 40 CMML patients responsive and resistant to decitabine (DAC). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE61nnn/GSE61162/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA260377
Series		Accession: GSE61162	ID: 200061162

4729. aCGH and RNA-Seq expression profiling of Chinese hepatocellular carcinoma patients
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome variation profiling by genome tiling array
Platform: GPL4091 64 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE65nnn/GSE65486/
Series		Accession: GSE65486	ID: 200065486

4730. RNA Polymerase II Pausing Can Be Retained or Acquired During Activation of Genes Involved in the Epithelial to Mesenchymal Transition
(Submitter supplied) Promoter-proximal RNA polymerase II (Pol II) pausing is implicated in the regulation of gene transcription. However, the mechanisms of pausing including its dynamics during transcriptional responses remain to be fully understood. We performed global analysis of short capped RNAs and Pol II Chromatin Immunoprecipitation sequencing in MCF-7 breast cancer cells to map Pol II pausing across the genome, and used permanganate footprinting to specifically follow pausing during transcriptional activation of several genes involved in the Epithelial to Mesenchymal Transition (EMT). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL15520 5 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67041/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA278768
Series		Accession: GSE67041	ID: 200067041

4731. Therapy induced tumour secretomes promote resistance and tumour progression
(Submitter supplied) Drug resistance invariably limits the clinical efficacy of targeted therapy with kinase inhibitors against cancer. We found that targeted therapy with BRAF, ALK, or EGFR inhibitors induces a complex network of secreted signals in drug-stressed melanoma and lung adenocarcinoma cells. This therapy-induced secretome (TIS) stimulates the outgrowth, infiltration and metastasis of drug-resistant cancer clones in the tumour. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL11154 41 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64741/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA271773
Series		Accession: GSE64741	ID: 200064741

4732. LED, a long non-coding RNA activator of enhancer RNAs, is hypermethylated in human cancers
(Submitter supplied) LED, a long non-coding RNA induced by Nutlin-3a, was found to activate enhancer RNAs, one of which was found in an intron of CDKN1A (p21).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platform: GPL11154 21 Samples
FTP download: GEO (BED, TSV, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53499/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA232137
Series		Accession: GSE53499	ID: 200053499

4733. Genomic-scale identification of host genes regulated by EBV during the lytic cycle
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL10999 GPL16791 8 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58246/
Series		Accession: GSE58246	ID: 200058246

4734. Genomic-scale identification of host genes regulated by EBV during lytic cycle [RNA-Seq]
(Submitter supplied) Infection of resting primary B-lymphocytes by Epstein Barr virus (EBV) generates a population of cells that are effectively immortal. This represents the first step in the establishment of life-long viral latency in vivo and generates precursors that can develop into the lymphoid malignancies. However, virus spread requires a switch from latency to the lytic replication cycle, a process orchestrated by the virally encoded protein Zta, an AP1-like transcription factor that interacts with a 7 base-pair DNA sequence element. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57732/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA247968
Series		Accession: GSE57732	ID: 200057732

4735. Pancreatic cancer exosomes induce pre-metastatic niche formation in the liver
(Submitter supplied) Pancreatic cancers (PCs) are highly metastatic with poor prognosis, mainly due to delayed detection. We hypothesized that intercellular communication is critical for metastatic progression. Here, we show that PC-derived exosomes induce liver pre-metastatic niche formation in naïve mice and consequently increase liver metastatic burden. Uptake of PC-derived exosomes by Kupffer cells caused transforming growth factor β secretion and upregulation of fibronectin production by hepatic stellate cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66876/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA278149
Series		Accession: GSE66876	ID: 200066876

4736. SMO variants explain the majority of drug resistance in basal cell carcinoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Other; Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL15520 107 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58377/
Series		Accession: GSE58377	ID: 200058377

4737. SMO variants explain the majority of drug resistance in basal cell carcinoma [RNA-Seq]
(Submitter supplied) Advanced basal cell carcinomas (BCCs) frequently acquire resistance to Smoothened (SMO) inhibitors through unknown mechanisms, providing a unique opportunity to study human tumor evolution. Here, we identify SMO mutations in 50% (22/44) of resistant BCCs compared with 5.6% (2/36) of untreated BCCs (p<0.0001), and show that these mutations maintain Hedgehog signaling in the presence of SMO inhibitors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 21 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58375/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA252377
Series		Accession: GSE58375	ID: 200058375

4738. Transcriptome profiling of human lung cancer cell lines.
(Submitter supplied) Purpose: The aim of this study is to compare different RNA extraction methods using a mixture design that allows the relative changes of the majority of genes profiled to be estimated. A number of samples were degraded to allow us to compare methods for dealing with more variable samples. Methods - Cell Culture: Lung adenocarcinoma cell lines NCI-H1975 and HCC827 from a range of passages (2-4) were grown on 3 separate occasions in RPMI media (Gibco) supplemented with Glutamax and 10% fetal calf serum to a 70% confluence. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 40 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64098/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA270114
Series		Accession: GSE64098	ID: 200064098

4739. Systematic Mapping of ADAR1 Binding Reveals its Regulatory Roles in Multiple RNA Processing Pathways
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE55nnn/GSE55363/
Series		Accession: GSE55363	ID: 200055363

4740. Systematic Mapping of ADAR1 Binding Reveals its Regulatory Roles in Multiple RNA Processing Pathways [CLIP-seq]
(Submitter supplied) ADARs are the primary factors underlying A-to-I editing in metazoans. We conducted the first global study of ADAR1-RNA interaction in human cells using CLIP-Seq. In contrast to the expected predominant binding of ADAR1 to Alu repeats, thousands of CLIP sites were located in non-Alu regions. This unexpectedly frequent non-Alu binding enabled discovery of transcriptome-wide functional and biophysical targets of ADAR1 in the regulation of mRNA processing including alternative 3' UTR usage and alternative splicing. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE55nnn/GSE55361/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA239413
Series		Accession: GSE55361	ID: 200055361

4741. Integrative transcriptome-wide analyses reveal critical HER2-regulated mRNAs and lincRNAs in HER2+ breast cancer
(Submitter supplied) Breast cancer is a major health problem affecting millions of women worldwide. Over 200,000 new cases are diagnosed annually in the USA, with approximately 40,000 of these cases resulting in death. HER2-positive (HER2+) breast tumors, representing 20–30 % of early-stage breast cancer diagnoses, are characterized by the amplification of the HER2 gene. However, the critical genes and pathways that become affected by HER2 amplification in humans are yet to be specifically identified. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE60nnn/GSE60182/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA257691
Series		Accession: GSE60182	ID: 200060182

4742. Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state.
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 52 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE60nnn/GSE60666/
Series		Accession: GSE60666	ID: 200060666

4743. Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state.
(Submitter supplied) Understanding the molecular processes underlying intra-tumor heterogeneity is of critical importance to improve the efficiency of therapy and overcome drug resistance. In malignant melanoma, heterogeneity is though to arise -at least partly- through epigenetic rather than genetic reprogramming of proliferating cells, leading to the appearance within the primary tumors of a phenotypically distinct invasive cell subpopulation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 17 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE60nnn/GSE60664/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA259212
Series		Accession: GSE60664	ID: 200060664

4744. TNFα Signaling Exposes Latent Estrogen Receptor Binding Sites in Breast Cancer Cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59532/
Series		Accession: GSE59532	ID: 200059532

4745. TNFα Signaling Exposes Latent Estrogen Receptor Binding Sites in Breast Cancer Cells [GRO-seq]
(Submitter supplied) The interplay between mitogenic and proinflammatory signaling pathways play key roles in determining the phenotypes and clinical outcomes of breast cancers.  We have used global nuclear run-on coupled with deep sequencing to characterize the immediate transcriptional responses of MCF-7 breast cancer cells treated with estradiol, TNFα, or both.  In addition, we have integrated these data with chromatin immunoprecipitation coupled with deep sequencing for estrogen receptor alpha (ERα), the pioneer factor FoxA1 and the p65 subunit of the NF-κB transcription factor. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59531/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA255508
Series		Accession: GSE59531	ID: 200059531

4746. Genome-wide modelling of transcription kinetics reveals patterns of RNA processing delays
(Submitter supplied) We descrive a joint model of transcriptional activation and mRNA accumulation, using estrogen receptor ERα activation in MCF-7 breast cancer cell line, which can be used for inference of transcription rate, RNA processing delay and degradation rate given data from high-throughput sequencing time course experiments.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 20 Samples
FTP download: GEO (TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62789/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA265118
Series		Accession: GSE62789	ID: 200062789

4747. DNA repair and recovery of RNA synthesis following exposure to ultraviolet light are delayed in long genes
(Submitter supplied) The kinetics of DNA repair and RNA synthesis recovery in human cells following UV-irradiation were assessed using nascent RNA Bru-seq and quantitative long PCR. It was found that UV light inhibited transcription elongation and that recovery of RNA synthesis occurred as a wave in the 5’-3’ direction with slow recovery and TC-NER at the 3’ end of long genes. RNA synthesis resumed fully at the 3’-end of genes after a 24-hour recovery in wild-type fibroblasts, but not in cells deficient in transcription-coupled nucleotide excision repair (TC-NER) or global genomic NER (GG-NER). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 20 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE65nnn/GSE65985/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA275636
Series		Accession: GSE65985	ID: 200065985

4748. Differential susceptibility of human pleural and peritoneal mesothelial cells to asbestos exposure
(Submitter supplied) We hypothesize that the observed differences in incidences of pleural and peritoneal malignant mesothelioma (MM) are the result of differences in the direct response of these cell types to asbestos rather than to differences mediated by the in vivo microenvironment. To test this hypothesis, we characterized cellular responses to asbestos in a controlled environment using high-throughput RNA sequence and other assays.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63966/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA269624
Series		Accession: GSE63966	ID: 200063966

4749. Effect of PRDM11 depletion in U2932 cells
(Submitter supplied) The PR-domain family e(PRDMs) encodes transcriptional regulators, several of which are deregulated in cancer. We found that loss of Prdm11 accelerates MYC-driven lymphomagenesis in the Eµ-Myc mouse model. Moreover, we show that patients with PRDM11-deficient diffuse large B cell lymphomas (DLBCLs) have poorer overall survival and belong to the non-Germinal Center B cell (GCB)-like subtype. Mechanistically, genome-wide mapping of PRDM11 binding sites coupled with transcriptome sequencing in human DLBCL cells evidenced that PRDM11 associates with transcriptional start sites of target genes and regulates important oncogenes such as FOS and JUN. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE56nnn/GSE56235/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA242683
Series		Accession: GSE56235	ID: 200056235

4750. Single mammalian cells compensate for differences in cellular volume and DNA copy number through independent global transcriptional mechanisms
(Submitter supplied) We performed single-cell and bulk transcriptome profiling in two different human cell lines. We performed single-cell RNA sequencing in live and fixed cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL16791 98 Samples
FTP download: GEO (TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66053/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA275801
Series		Accession: GSE66053	ID: 200066053

4751. SRSF2 is essential for hematopoiesis and its myelodysplastic syndromes-related mutations dysregulate alternative pre-mRNA splicing
(Submitter supplied) We report the biological function of Srsf2 in hematopoiesis in conditional knockout mouse models. Ablation of Srsf2 in the hematopoietic lineage caused embryonic lethality, and Srsf2-deficient fetal liver cells showed significantly enhanced apoptosis and decreased hematopoietic stem/progenitor cells. Induced ablation of Srsf2 in adult Mx1Cre/ Srsf2flox/flox mice upon polyinosinic:polycytidylic acid injection demonstrated a significant decrease in lineage-/Sca+/cKit+ cells in bone marrow. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 23 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE61nnn/GSE61052/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA260162
Series		Accession: GSE61052	ID: 200061052

4752. MiRNA23B REGULATES SELF-RENEWAL AND CHEMORESISTANCE PROPERTIES OF COLON CANCER STEM CELLS
(Submitter supplied) MiRNAs have been identfied to play an important role in cancer stem cells. MiR23b is differentially expressed in various forms of cancer including colorectal cancer as compared to their normal counterparts. MiR23b regulates various aspects of cell behaviour such as differentiation, apoptosis and motility. The goal of the study was to identify the novel role of miR23b in self-renewal property of colon cancer stem cells via regulation of its candidate target mRNAs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59290/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA254974
Series		Accession: GSE59290	ID: 200059290

4753. Gene expression profiling of patient's DCIS-IDC tandem lesions by RNA sequencing analysis
(Submitter supplied) Tandem DCIS/IDC are defined as ductal carcicnoma in situ (DCIS) lesions that have concurrent invasive ductal carcinoma (IDC) within the same breast. These are identified radiologically by an area of clustered microcalcifications adjacent to (contiguous with) an invasive mass. Our radiologist (Dr. William P. Smith) has provided us with biopsy cores from each region. One core from each region (DCIS and IDC) has bas been collected and subjected to RNA sequencing for our studies to compare changes from DCIS to IDC in each individual patient.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66301/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA276455
Series		Accession: GSE66301	ID: 200066301

4754. TWIST1-induced microRNA-424 drives an intermediate epithelial-to-mesenchymal transition that opposes metastasis
(Submitter supplied) Epithelial-to-mesenchymal transition (EMT) is a dynamic process that relies on cellular plasticity; an EMT/MET axis is critical for metastatic colonization of carcinomas. Unlike epithelial programming, regulation of mesenchymal programming is not well understood in EMT. Here we describe the first microRNA that enhances exclusively mesenchymal programming. We demonstrate that microRNA-424 is up-regulated early during a TWIST1/SNAI1-induced EMT, and that it causes cells to express mesenchymal genes without affecting epithelial genes, resulting in a mixed/intermediate EMT. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE54nnn/GSE54505/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA236738
Series		Accession: GSE54505	ID: 200054505

4755. Transcriptome analysis in chronic lymphocytic leukemia cells using RNA sequencing (RNA-seq)
(Submitter supplied) Chronic lymphocytic leukemia (CLL) is a biologically and clinically heterogeneous disease. The somatic hypermutation status of the immunoglobulin heavy chain variable (IGHV) genes has been identified as one of the most robust prognostic markers in CLL. Patients with unmutated IGHV status (U-CLL) typically experience an inferior outcome compared to those whose clones express mutated IGHV genes (M-CLL). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 52 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66117/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA276003
Series		Accession: GSE66117	ID: 200066117

4756. Transcriptome analysis and Genome-wide DNA methylation maps in chronic lymphocytic leukemia cells determined by next-generation sequencing
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms: GPL10999 GPL11154 111 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66167/
Series		Accession: GSE66167	ID: 200066167

4757. Transriptional profiling upon heat shock and recovery in cells deficient for FBXW7 and their wild type counterpart.
(Submitter supplied) FBXW7 modulates stress response by post-translational modification of HSF1 HSF1 orchestrates the heat-shock response upon exposure to heat stress and activates a transcriptional program vital for cancer cells. Genes positively regulated by HSF1 show increeased expression during heat shock while their expression is reduced during recovery. Genes negatively regulated by HSF1 show the opposite pattern. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57397/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA246391
Series		Accession: GSE57397	ID: 200057397

4758. Identification of active transcriptional regulatory elements with GRO-seq
(Submitter supplied) Transcriptional regulatory elements (TREs), including enhancers and promoters, determine the transcription levels of associated genes.  We have recently shown that global run-on and sequencing (GRO-seq) with enrichment for 5'-capped RNAs reveals active TREs with high accuracy.  Here, we demonstrate that active TREs can be identified by applying sensitive machine-learning methods to standard GRO-seq data. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Third-party reanalysis
Platform: GPL11154 2 Samples
FTP download: GEO (BED, BIGWIG, BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66031/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA275737
Series		Accession: GSE66031	ID: 200066031

4759. Integrin αvβ3 acting as membrane receptor for thyroid hormones mediates angiogenesis in malignant T cells
(Submitter supplied) We have found that thyroid hormones (THs), acting as soluble integrin αvβ3 ligands, activate growth-related signaling pathways in T-cell lymphomas (TCL). Specifically, TH-activated αvβ3 integrin signaling promotes TCL proliferation and angiogenesis, in part, via the up-regulation of VEGF.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63122/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA266733
Series		Accession: GSE63122	ID: 200063122

4760. FBXW7 modulates stress response by post-translational modification of HSF1
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 21 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57399/
Series		Accession: GSE57399	ID: 200057399

4761. ALS-causative mutations in FUS/TLS confer gain- and loss-of-function by altered association with SMN and U1-snRNP
(Submitter supplied) The RNA-binding protein FUS/TLS, mutation in which is causative of the fatal motor neuron disease ALS, is demonstrated to directly bind to the U1-snRNP and SMN complexes. ALS-causative mutations in FUS/TLS are shown to abnormally enhance their interaction with SMN and reduce interaction with U1-snRNP. Correspondingly, global RNA analysis reveals a mutant-dependent loss of splicing activity, with ALS-linked mutants failing to reverse changes caused by loss of wild-type FUS/TLS. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 49 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64078/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA270070
Series		Accession: GSE64078	ID: 200064078

4762. Whole Transcriptome RNA-seq Analysis: the Tumorigenesis and Metastasis of Melanoma
(Submitter supplied) To better understand the tumorigenesis and metastasis of human metastatic melanoma(MM) , we analyzed the transcriptomes of three cell lines that represent the three distinct stages of MM pathogenesis: the normal stage (HEMn), the onset of MM (A375), and the metastasis stage (A2085). Using the next generation sequencing (NGS) technology, we detected unsymmetrical expression of genes particularly in Chr9, 12, and 14 among three cell lines, an indication of the involvement of these genes in the tumorigenesis and metastasis of MM. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9442 3 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE35nnn/GSE35704/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA152041
Series		Accession: GSE35704	ID: 200035704

4763. Discovery of cis-spliced chimeric RNAs between adjacent genes in human prostate cells
(Submitter supplied) Total RNA extracted from prostate cancer LNCaP cells transfected with siRNA against CTCF(siCTCF), or negative control siRNA (si-)were processed, and sequenced by two different companies using Illumina Hi-seq 2000 platform to generate RNA sequencing with two output sequences: paired-end 50bp and 101bp in read length. Nearly 100 million and 50 million raw reads were yielded from each sample respectively. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (FPKM_TRACKING, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63487/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA268024
Series		Accession: GSE63487	ID: 200063487

4764. Orphan nuclear receptor TR4 uses non-equivalent binding sites to regulate gene targets from proximal and distal transcriptional regulatory elements during human definitive erythropoiesis
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL9115 9 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE54nnn/GSE54761/
Series		Accession: GSE54761	ID: 200054761

4765. Orphan nuclear receptor TR4 uses non-equivalent binding sites to regulate gene targets from proximal and distal transcriptional regulatory elements during human definitive erythropoiesis [RNA-seq]
(Submitter supplied) We knocked down TR4 expression by 2 lentiviral mediated vectors at day 11 of erythroid differentiation in order to identify TR4 downstream targets.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE54nnn/GSE54760/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA237565
Series		Accession: GSE54760	ID: 200054760

4766. Pluripotent cell models of Fanconi anemia identify the early pathological defect in human hemoangiogenic progenitors
(Submitter supplied) Fanconi anemia (FA) is a disorder of genomic instability characterized by progressive bone marrow failure (BMF), developmental abnormalities and an increased susceptibility to cancer. Although various consequences in hematopoietic stem/progenitor cells have been attributed to FA-BMF, the quest to identify the initial pathological event is still ongoing. To address this issue, we established induced pluripotent stem cells (iPSCs) from fibroblasts of six FA patients with FANCA mutations. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE65nnn/GSE65507/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA274249
Series		Accession: GSE65507	ID: 200065507

4767. Genetic and drug perturbation of components in the NFkB signaling pathway in 11-18 cells
(Submitter supplied) Through the study of EGFR-mutant lung adenocarcinoma we show that NFkB signaling is rapidly engaged by EGFR oncogene inhibition to promote tumor cell persistence and therapy resistance. Unexpectedly, we found that EGFR oncogene inhibition induced an EGFR-TRAF2-RIP1-IKK complex that stimulated an NFkB-mediated transcriptional survival program. We identified a direct pharmacologic NFkB inhibitor, PBS-1086, that suppressed this adaptive survival program and increased both the magnitude and duration of initial EGFR TKI response in cellular and in vivo tumor models, including a novel patient-derived NSCLC xenograft. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 29 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE65nnn/GSE65420/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA273960
Series		Accession: GSE65420	ID: 200065420

4768. Gata6
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL11002 GPL10999 10 Samples
FTP download: GEO (TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE47nnn/GSE47537/
Series		Accession: GSE47537	ID: 200047537

4769. HITS-CLIP analysis uncovers a link between the Kaposi's sarcoma associated herpesvirus ORF57 protein and host pre-mRNA metabolism
(Submitter supplied) The Kaposi's sarcoma associated herpesvirus (KSHV) is an oncogenic virus that causes Kaposi's sarcoma, primary effusion lymphoma (PEL), and some forms of multicentric Castleman's disease. The KSHV ORF57 protein is a conserved posttranscriptional regulator of gene expression that is essential for virus replication. ORF57 is multifunctional, but most of its activities are directly linked to its ability to bind RNA. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64413/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA270976
Series		Accession: GSE64413	ID: 200064413

4770. Alternatively processed  and compiled RNA-Sequencing and clinical data for thousands of samples from The Cancer Genome Atlas
(Submitter supplied) We reprocessed RNA-Seq data for 9264 tumor samples and 741 normal samples across 24 cancer types from The Cancer Genome Atlas with "Rsubread". Rsubread is an open source R package that has shown high concordance with other existing methods of alignment and summarization, but is simple to use and takes significantly less time to process data. Additionally, we provide clinical variables publicly available as of May 20, 2015 for the tumor samples where the TCGA ids are matched.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62944/
Series		Accession: GSE62944	ID: 200062944

4771. High throughput sequencing identifies alternative splicing events regulated by PRMT9
(Submitter supplied) The human genome encodes a family of nine protein arginine methyltransferases (PRMT1-9). Different members of this enzyme family catalyze different types of protein methylation at the terminal nitrogen atoms of arginine residues, forming monomethylated arginine (MMA), asymmetrically dimethylated arginine (ADMA) and symmetrically dimethylated arginine (SDMA). The last member of this family, PRMT9, is characterized in detail here. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63953/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA269603
Series		Accession: GSE63953	ID: 200063953

4772. Massive parallel sequencing uncovers actionable FGFR2-PPHLN1 fusion and ARAF mutations in intrahepatic cholangiocarcinoma
(Submitter supplied) Intrahepatic cholangiocarcinoma (iCCA) is a fatal bile duct cancer with dismal prognosis and limited therapeutic options. By performing RNA- and exome sequencing analyses we have discovered a novel fusion event, FGFR2-PPHLN1 (16%), and damaging mutations in the ARAF oncogene (11%).
Organism:	Homo sapiens
Type:		Genome variation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL16791 30 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63420/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA267702
Series		Accession: GSE63420	ID: 200063420

4773. Ligand-Dependent Enhancer Activation Regulated by Topoisomerase-I Activity
(Submitter supplied) The discovery that enhancers are regulated transcription units, encoding eRNAs, has raised new questions about the mechanisms of their activation. Here, we report an unexpected molecular mechanism that underlies ligand-dependent enhancer activation, based on DNA nicking to relieve torsional stress from eRNA synthesis. Using dihydrotestosterone (DHT)-induced binding of androgen receptor (AR) to prostate cancer cell enhancers as a model, we show rapid recruitment, within minutes, of DNA topoisomerase I (TOP1) to a large cohort of AR-regulated enhancers. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platform: GPL11154 26 Samples
FTP download: GEO (BED, BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63202/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA266983
Series		Accession: GSE63202	ID: 200063202

4774. Analysis of allele specific expression and its chromatin state to identify genes that are escaping X chromosome inactivation
(Submitter supplied) Disappearance of the Barr body has long been considered a hallmark of cancer, although whether this corresponds to epigenetic instability and transcriptional reactivation, or to genetic loss, has remained unclear. Here we show that in breast cancer cell lines as well as primary breast tumors, the inactive X chromosome frequently displays a highly abnormal 3D nuclear organization, with global perturbations in its characteristic heterochromatic state, including apparent gain of euchromatic marks and lessening of repressive marks such as H3K27me3 and promoter DNA methylation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms: GPL11154 GPL16791 29 Samples
FTP download: GEO (BEDGRAPH, FPKM_TRACKING, TXT, XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62966/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA266312
Series		Accession: GSE62966	ID: 200062966

4775. Knock-in of PIK3CA-H1047R into MCF-10A
(Submitter supplied) We have compared the proteome, transcriptome and metabolome of two isogenic cell lines: MCF-10A, derived from human breast epithelium, and the mutant MCF-10A-H1047R. These cell lines differ by a single amino acid substitution (H1047R) caused by single nucleotide change in one allele of the PIK3CA gene which encodes the catalytic subunit p110α of phosphatidylinositol 3-kinase (PI3K). The H1047R mutation of PIK3CA is one of the most frequently encountered somatic cancer-specific mutations. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 25 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63452/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA267827
Series		Accession: GSE63452	ID: 200063452

4776. The inactive X chromosome is epigenetically unstable and transcriptionally labile in breast cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other; Genome variation profiling by SNP array; SNP genotyping by SNP array
Platforms: GPL11154 GPL16791 GPL6801 39 Samples
FTP download: GEO (BEDGRAPH, CEL, FPKM_TRACKING, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62907/
Series		Accession: GSE62907	ID: 200062907

4777. Aberrant splicing of U12-type introns is the hallmark of ZRSR2 mutant myelodysplastic syndrome
(Submitter supplied) Somatic mutations in the spliceosome gene ZRSR2— located on the X chromosome — are associated with myelodysplastic syndrome (MDS). ZRSR2 is involved in the recognition of 3΄ splice site during the early stages of spliceosome assembly; however, its precise role in RNA splicing has remained unclear. Here, we characterize ZRSR2 as an essential component of the minor spliceosome (U12-dependent) assembly. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 22 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63816/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA269142
Series		Accession: GSE63816	ID: 200063816

4778. Enhancer Sequence Variants and Transcription Factor Deregulation Synergize to Construct Pathogenic Regulatory Circuits in B Cell Lymphoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL19251 GPL11154 GPL10739 137 Samples
FTP download: GEO (BW, CEL, CHP) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62246/
Series		Accession: GSE62246	ID: 200062246

4779. Enhancer Sequence Variants and Transcription Factor Deregulation Synergize to Construct Pathogenic Regulatory Circuits in B Cell Lymphoma (RNA-Seq)
(Submitter supplied) Most B cell lymphomas arise in the germinal center (GC), where humoral immune responses evolve from potentially oncogenic cycles of mutation, proliferation, and clonal selection. Although lymphoma gene expression diverges significantly from GC-B cells, underlying mechanisms that alter the activities of corresponding regulatory elements (REs) remain elusive. Here we define the complete pathogenic circuitry of human follicular lymphoma (FL), which activates or decommissions transcriptional circuits from normal GC-B cells and commandeers enhancers from other lineages. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 14 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62241/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA263567
Series		Accession: GSE62241	ID: 200062241

4780. Mutation independent activation of the Notch pathway is associated with Lapatinib resistance in Her2+ breast cancer cell lines
(Submitter supplied) We compared untreated HCC1419 cells with Lapatinib resistant HCC1419 cells that were either treated with Lapatinib for only 9 days before harvesting (drug tolerant persisters, DTPs) or were growing in the presence of Lapatinib (>70 days) (drug tolerant expanded persisters, DTEPs). We show that the Notch pathway is significantly over-expressed in DTEPs when compared to untreated cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 7 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62074/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA263155
Series		Accession: GSE62074	ID: 200062074

4781. Type I interferon regulates the expression of long non-coding RNAs
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL13607 GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64796/
Series		Accession: GSE64796	ID: 200064796

4782. Type I interferon regulates the expression of long non-coding RNAs [RNA-seq]
(Submitter supplied) Interferons (IFNs) are key players in the antiviral response. IFN sensing by the cell activates transcription of IFN-stimulated genes (ISGs) able to induce an antiviral state by affecting viral replication and release. IFN also induces the expression of ISGs that function as negative regulators to limit the strength and duration of IFN response. The ISGs identified so far belong to coding genes. However, only a small proportion of the transcriptome corresponds to coding transcripts and it has been estimated that there could be as many coding as long non-coding RNAs (lncRNAs). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64795/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA271890
Series		Accession: GSE64795	ID: 200064795

4783. Altering cancer transcriptomes using epigenomic inhibitors
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL10904 18 Samples
FTP download: GEO (IDAT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64039/
Series		Accession: GSE64039	ID: 200064039

4784. Altering cancer transcriptomes using epigenomic inhibitors [RNA-Seq]
(Submitter supplied) We have compared the genome-wide effects on the transcriptome after treatment with ICG-001 (the specific CBP inhibitor) versus C646, a compound that competes with acetyl-coA for the Lys-coA binding pocket of both CBP and p300. We found that both drugs cause large-scale changes in the transcriptome of HCT116 colon cancer cells and PANC1 pancreatic cancer cells, and reverse some tumor-specific changes in gene expression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63776/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA269148
Series		Accession: GSE63776	ID: 200063776

4785. Next Generation Sequencing identifying the dosage compensation state in human endometrial carcinoma and adjacent tissues
(Submitter supplied) Mammals have evolved an XY sex chromosome system, resulting in dosage imbalance not only between sexes, but also between X-chromosome and autosome.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE56nnn/GSE56087/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA242387
Series		Accession: GSE56087	ID: 200056087

4786. Stably-paused genes revealed through inhibition of transcription initiation by the TFIIH inhibitor Triptolide
(Submitter supplied) Transcription by RNA Polymerase II (Pol II) in metazoan is regulated in several steps, including  preinitiation complex (PIC) formation, initiation, Pol II escape, productive elongation, cotranscriptional  RNA-processing and termination. Genome-wide studies have demonstrated that  the phenomenon of promoter-bound Pol II pausing is widespread, especially for genes involved  in developmental and stimulus-responsive pathways. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 23 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63314/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA267258
Series		Accession: GSE63314	ID: 200063314

4787. Promoter hypermethylation of TERT is associated with hepatocellular carcinoma in the Han Chinese population
(Submitter supplied) A recent study by Castelo-Branco, P., et al. Methylation of the TERT promoter and risk stratification of childhood brain tumours: an integrative genomic and molecular study. Lancet Oncol 2013;14:534-542 found upstream of the transcription start site (UTSS) hypermethylation of TERT is associated with tumor progression and poor prognosis in paediatric brain tumours. They interpreted that the UTSS region of telomerase reverse transcriptase (TERT) gene is a potentially accessible biomarker for various cancers. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63863/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA269281
Series		Accession: GSE63863	ID: 200063863

4788. Expression and Prognostic impact of LncRNAs in Acute Myeloid Leukemia
(Submitter supplied) Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides located within the intergenic stretches or overlapping antisense transcripts of protein coding genes. LncRNAs are involved in numerous biological roles including imprinting, epigenetic regulation, apoptosis and cell-cycle. To determine whether lncRNAs are associated with clinical features and recurrent mutations in older patients (aged ≥60 years) with cytogenetically normal (CN) acute myeloid leukemia (AML), we evaluated lncRNA expression in 148 untreated older CN-AML cases using a custom microarray platform.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 71 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63646/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA268523
Series		Accession: GSE63646	ID: 200063646

4789. ALDH2, CCNE1 and SMAD3 are Potential Prognostic Markers for Upper Tract Urothelial Carcinoma Revealed by Massively Parallel Sequencing.
(Submitter supplied) Purpose: upper tract urothelial carcinoma (UTUC) is the predominant subtype of the renal pelvis carcinoma but current knowledge about the molecular properties and prognostic markers is sparse. In this study, we examined the genome-wide mRNA expression spectrum of UTUC aiming to characterize the molecular basis of this cancer, and identify potential prognostic markers and thus facilitate the clinical practices. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 20 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE47nnn/GSE47702/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA207338
Series		Accession: GSE47702	ID: 200047702

4790. Redefinition of Human Androgen Responsive Elements
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL10999 GPL11154 40 Samples
FTP download: GEO (BED, BW, TAGALIGN) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE43nnn/GSE43791/
Series		Accession: GSE43791	ID: 200043791

4791. Redefinition of Human Androgen Responsive Elements [ChIP-Seq, RNA-Seq]
(Submitter supplied) The androgen receptor (AR) mediates the action of androgens by binding to androgen-responsive elements (AREs) and subsequently regulating target genes involved in prostate carcinogenesis. The precise locations, true nature, and functional roles of AREs in human prostate cancer are still unknown. Here we redefine AREs by motif-resolution AR chromatin immunoprecipitation-exonuclease (ChIP-exo) assay in human prostate cancer cells and tumors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 20 Samples
FTP download: GEO (BED, TAGALIGN, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE43nnn/GSE43785/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA187482
Series		Accession: GSE43785	ID: 200043785

4792. Gene expression profiling of TGF-B/PDGF-induced CAF
(Submitter supplied) We have found aerobic glycolysis is increased in cancer-associated fibroblasts (CAF). To explore the mechanism by which glucolysis was switched from oxidative phosphorylation, two in vitro CAF models were successfully established. To screen genes potentially regulate aerobic glysolysis, we analyzed gene expression profiling of CAF, and compared with control fibroblasts.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE61nnn/GSE61797/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA262158
Series		Accession: GSE61797	ID: 200061797

4793. The Sweden Canceromics Analysis Network - Breast (SCAN-B) Initiative: a large-scale multicenter infrastructure towards implementation of breast cancer genomic analyses in the clinical routine
(Submitter supplied) This SuperSeries is composed of the SCANB SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Expression profiling by array
Platforms: GPL11154 GPL10558 110 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE60nnn/GSE60789/
Series		Accession: GSE60789	ID: 200060789

4794. The Sweden Canceromics Analysis Network - Breast (SCAN-B) Initiative: a large-scale multicenter infrastructure towards implementation of breast cancer genomic analyses in the clinical routine [RNA-Seq]
(Submitter supplied) Breast cancer exhibits significant molecular, pathological, and clinical heterogeneity. Current clinicopathological evaluation is imperfect for predicting outcome, which results in overtreatment for many patients, and for others, leads to death from recurrent disease. Therefore, additional criteria are needed to better personalize care and maximize treatment effectiveness and survival. To address these challenges, the Sweden Cancerome Analysis Network - Breast (SCAN-B) consortium was initiated in 2010 as a multicenter prospective study with longsighted aims to 1) analyze breast cancers with next-generation genomic technologies for translational research in a population-based manner and integrated with healthcare; 2) decipher fundamental tumor biology from these analyses; 3) utilize genomic data to develop and validate new clinically-actionable biomarker assays; and 4) build the infrastructure for real-time clinical implementation of molecular diagnostic, prognostic, and predictive tests. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 55 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE60nnn/GSE60788/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA259546
Series		Accession: GSE60788	ID: 200060788

4795. Flexible multiplatform RNA profiling at the single cell level applied to enriched cancer initiating cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing; Expression profiling by RT-PCR
Platforms: GPL17989 GPL570 GPL16288 64 Samples
FTP download: GEO (CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE52nnn/GSE52717/
Series		Accession: GSE52717	ID: 200052717

4796. Flexible multiplatform RNA profiling at the single cell level applied to enriched cancer initiating cells: RNA-Seq MCF7 and MCF10A single cell data
(Submitter supplied) Accurate profiling of RNA expression of single cells is a valuable approach for broadening our understanding of cancer biology and mechanisms of dissemination, but requires the development of reliable methods for their molecular characterization. Here we evaluate a single cell methodology which generates microgram amounts of cDNA suitable for next generation sequencing (RNA-Seq), high throughput RT-qPCR and Affymetrix array analysis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16288 10 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE52nnn/GSE52716/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA229892
Series		Accession: GSE52716	ID: 200052716

4797. Flexible multiplatform RNA profiling at the single cell level applied to enriched cancer initiating cells: RNA-Seq CIC data
(Submitter supplied) Accurate profiling of RNA expression of single cells is a valuable approach for broadening our understanding of cancer biology and mechanisms of dissemination, but requires the development of reliable methods for their molecular characterization. Here we evaluate a single cell methodology which generates microgram amounts of cDNA suitable for next generation sequencing (RNA-Seq), high throughput RT-qPCR and Affymetrix array analysis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16288 12 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE52nnn/GSE52715/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA230351
Series		Accession: GSE52715	ID: 200052715

4798. shRNA knockdown of YAP1 in HCC364 cells, various drug conditions
(Submitter supplied) Through a genetic screen in BRAF mutant tumor cells, we show that the Hippo pathway effector YAP acts as a parallel survival input to promote resistance to RAF-MEK inhibitor therapy. Our data uncover YAP as a novel mechanism of resistance to RAF-MEK targeted therapy. The findings unveil the synthetic lethality of YAP and RAF-MEK co-suppression as a promising strategy to enhance response and patient survival.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64550/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA271287
Series		Accession: GSE64550	ID: 200064550

4799. SOX17 Is a Critical Specifier of Human Primordial Germ Cell Fate
(Submitter supplied) Specification of primordial germ cells (PGCs) marks the beginning of the totipotent state. However, without a tractable experimental model, the mechanism of human PGC (hPGC) specification remains unclear. Here, we demonstrate specification of hPGC-like cells (hPGCLCs) from germline competent pluripotent stem cells. The characteristics of hPGCLCs are consistent with the embryonic hPGCs and a germline seminoma that share a CD38 cell-surface marker, which collectively defines likely progression of the early human germline. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL11154 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE60nnn/GSE60138/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA257553
Series		Accession: GSE60138	ID: 200060138

4800. GIST cell cycle dysregulation is required for progression to high-risk disease but not for resistance to kinase inhibitors
(Submitter supplied) Background: To understand the transcriptional consequences of a TP53 modulation in the GIST cell context, we treated GIST430 with increasing doses of the MDM2-inhibitor nutlin-3 (racemate).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59841/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA256344
Series		Accession: GSE59841	ID: 200059841

4801. Distinct gene expression profiles between overt GIST and miniGIST
(Submitter supplied) In contrast to the paucity of clinic GIST (Gastrointestinal stromal tumor; 0.0014 % happening rate), there is a more than twenty thousand times higher rate for miniGISTs, about ~30% of human population could be identified to have miniGISTs. Exploring the molecular differences between miniGISTs and overt GISTs will help us to understand the transformation mechanisms along with GIST progression, but C-kit and PDGFRA mutations analysis failed to identify the differences between these two groups. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 13 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE52nnn/GSE52666/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA229762
Series		Accession: GSE52666	ID: 200052666

4802. Ets homologous factor regulates pathways controlling response to injury in Calu-3 airway epithelial cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platform: GPL11154 40 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63400/
Series		Accession: GSE63400	ID: 200063400

4803. Ets homologous factor regulates pathways controlling response to injury in Calu-3 airway epithelial cells [RNA-seq]
(Submitter supplied) Ets homologous factor (EHF) is an Ets family transcription factor expressed in many epithelial cell types including those lining the respiratory system. Disruption of the airway epithelium is central to many lung diseases, and a network of transcription factors coordinates its normal function. EHF can act as a transcriptional activator or a repressor, though its targets in lung epithelial cells are largely uncharacterized. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 33 Samples
FTP download: GEO (DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63397/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA267666
Series		Accession: GSE63397	ID: 200063397

4804. Genomewide analysis of the human p53 transcriptional network unveils a lncRNA tumor suppressor signature (RNA-seq)
(Submitter supplied) We report the application of high-throughput sequencing to performed the p53 regulated trancriptome in HCT116 colon cancer cells treated with the DNA damage 5FU. To study the direct targets of p53 we performed ChIP-seq to deterrmined the p53 biding sites and associated with the expression levels. With this study we identified the new genomic regions regulated by p53 and with special attention in those regions that are non coding and are differentially expressed by the DNA damage drug.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58507/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA252833
Series		Accession: GSE58507	ID: 200058507

4805. Genomewide analysis of the human p53 transcriptional network unveils a lncRNA tumor suppressor signature
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL9052 GPL17586 GPL11154 15 Samples
FTP download: GEO (CEL, TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58528/
Series		Accession: GSE58528	ID: 200058528

4806. Gene expression profiling of melanoma cell lines by high throughput sequencing
(Submitter supplied) A panel of 29 melanoma cell lines were gene expression profiled by RNA-Seq.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 29 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62526/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA264334
Series		Accession: GSE62526	ID: 200062526

4807. MYC-negative BL frequent in posttransplant patients (expression)
(Submitter supplied) We performed genomic and transcriptomic analysis of seven cases of molecular Burkitt lymphoma (mBL) developed in immunosuppressed patients who underwent solid organ transplantation. Interestingly, three cases (43%) were MYC-translocation-negative and revealed the 11q-gain/loss aberration recently identified in 3% of mBL developed in immunocompetent hosts.1 Based on array CGH data, minimal gain and loss regions of 11q (MGR/~4Mb and MLR/~13.5Mb, respectively) were defined and integrative genomic and transcriptomic analysis identified 35 differentially expressed genes, when compared with classic BL. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL570 12 Samples
FTP download: GEO (CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64085/
Series		Accession: GSE64085	ID: 200064085

4808. Lysine-Specific Demethylase 1 Has Dual Functions as a Major Regulator of Androgen Receptor Transcriptional Activity
(Submitter supplied) Lysine Specific Demethylase 1 (LSD1, KDM1A) functions as a transcriptional corepressor through demethylation of histone 3 lysine 4 (H3K4), but has coactivator function on some genes through unclear mechanisms. We show that LSD1, interacting with CoREST, associates with and coactivates androgen receptor (AR) on a large fraction of androgen-stimulated genes. A subset of these AR/LSD1-associated enhancer sites have histone 3 threonine 6 phosphorylation (H3T6ph), and these sites are further enriched for androgen-stimulated genes. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL15433 5 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE52nnn/GSE52201/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA230632
Series		Accession: GSE52201	ID: 200052201

4809. Integrated genome and transcriptome sequencing from the same cell
(Submitter supplied) Single-cell genomics and single-cell transcriptomics have recently emerged as powerful tools to study the biology of single cells at a genome-wide scale. Here we describe a method that allows the integration of genomic DNA and mRNA sequencing from the same cell. We use this method to correlate DNA copy number variation to transcriptome variability among individual cells.
Organism:	Homo sapiens; Mus musculus
Type:		Genome variation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL17021 20 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62952/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA266282
Series		Accession: GSE62952	ID: 200062952

4810. RNA-seq of autistic and control cortex
(Submitter supplied) Purpose: The goal of this study was to assess the status of splicing changes in microexons in the cortex of individuals with autism. Methods: We performed RiboZero Gold (rRNA depleted) 50bp PE RNA-seq in a larger set of case and control samples to define 12 autism and 12 control samples showing the greatest global differential gene expression change. These samples, which show differential expression of the splicing regulator SRRM4, were used to evaluate global splicing changes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 24 Samples
FTP download: GEO (R, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64018/
Series		Accession: GSE64018	ID: 200064018

4811. Convergent Sense/Antisense Transcription At Intragenic Super-Enhancers Targets AID-initiated Genomic Instability
(Submitter supplied) Activation-induced cytidine deaminase (AID) initiates both somatic hypermutation (SHM) for antibody affinity maturation and DNA breakage for antibody class switch recombination (CSR) via transcription-dependent cytidine deamination of single stranded DNA targets. While largely specific for immunglobulin genes, AID also acts on a limited set of off-targets, generating oncogenic translocations and mutations that contribute to B cell lymphoma. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms: GPL17021 GPL16791 GPL13112 9 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62296/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA263795
Series		Accession: GSE62296	ID: 200062296

4812. B cell super-enhancers and regulatory clusters recruit AID tumorigenic activity
(Submitter supplied) The antibody gene mutator AID promiscuously damages oncogenes and B cell identity genes leading to chromosomal translocations and tumorigenesis. Why non-immunoglobulin loci are susceptible to AID activity is unknown. Here we study AID-mediated lesions in the context of nuclear architecture and the B cell regulome. We show that AID targets are not randomly distributed across the genome, but are predominantly clustered within super-enhancers. more...
Organism:	Homo sapiens; Mus musculus
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other
4 related Platforms 76 Samples
FTP download: GEO (BED, BW, TAB, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62063/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA263144
Series		Accession: GSE62063	ID: 200062063

4813. Uridylation by TUT4 and TUT7 marks mRNA for degradation
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL15520 GPL16791 30 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59628/
Series		Accession: GSE59628	ID: 200059628

4814. Uridylation by TUT4 and TUT7 marks mRNA for degradation [RNA-Seq]
(Submitter supplied) Uridylation occurs pervasively on mRNAs in mammals, yet its mechanism and significance remain unknown. Here we identify TUT4 and TUT7 (also known as ZCCHC11 and ZCCHC6, respectively) as the enzymes that uridylate mRNAs. Uridylation readily occurs on deadenylated mRNAs that are not associated with poly(A) binding protein (PABPC1) in cells. Consistently, purified TUT4 and TUT7 (TUT4/7) selectively uridylate RNAs with short A tails (< ~25 nt) while PABPC1 antagonizes uridylation of polyadenylated mRNAs in vitro. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 16 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59626/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA255776
Series		Accession: GSE59626	ID: 200059626

4815. A common cell state in Triple Negative Breast Cancers represents a druggable vulnerability
(Submitter supplied) A basal (MDAMB468) and luminal (ZR75-1) cell line were treated with DMSO or PKC412 for 6h
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 10 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63721/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA268911
Series		Accession: GSE63721	ID: 200063721

4816. The effect of REST and its alternatively spliced transcript, REST-003, on breast cancer invasiveness
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 10 Samples
FTP download: GEO (FPKM_TRACKING, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63610/
Series		Accession: GSE63610	ID: 200063610

4817. Effect of REST-003 downregulation on cancer invasiveness in MDA-MB-231 cells using RNA-sequencing (RNA-seq) analysis .
(Submitter supplied) Fifty six genes from DESeq were differentially expressed in the treated versus control samples.  More than 20% were related to immune, defense, wounding and inflammatory responses
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63609/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA268447
Series		Accession: GSE63609	ID: 200063609

4818. Effect of REST on cancer invasiveness in MCF-7 and MDA-MB-231 cells using RNA-sequencing (RNA-seq) analysis .
(Submitter supplied) We report a negative correlation of invasiveness with REST expression. In addition, one alternatively spliced product (ASP) of REST, REST-003, shows a positive correlation with invasiveness. REST has a well-established role in regulating transcription of genes important for neuronal development.  Its role in cancer, though significant, is less well understood.  We would like to investigate the effect of REST on invasive phenotype. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (FPKM_TRACKING, PDF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63608/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA268448
Series		Accession: GSE63608	ID: 200063608

4819. PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration
(Submitter supplied) An increasing amount of studies integrate mRNA sequencing data into MS-based proteomics to complement the translation product search space. We present the generation of a protein synthesis-based database from deep sequencing of ribosome-protected mRNA fragments. This approach increases the overall protein identification rates with 3% and 11% (improved and new identifications) for human and mouse respectively and enables proteome-wide detection of 5’-extended proteoforms, uORF translation and near-cognate translation start sites.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58207/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA251587
Series		Accession: GSE58207	ID: 200058207

4820. Genome-wide analysis of transcriptome and translatome following eIF4A1 knockdown in MCF7 cells [RNA-Seq]
(Submitter supplied) To identify which genes were regulated by mRNA helicase activity, the effect of eIF4A1 knockdown on the MCF7 cell transcriptome and translatome was determined. eIF4A1-dependent mRNAs were highly enriched for several classes of genes with oncogenic potential, which leads to a model whereby dysregulation of mRNA unwinding contribues to the malignant phenotype in breast cancer cells via preferential translation of a subset of genes.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58111/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA251350
Series		Accession: GSE58111	ID: 200058111

4821. Characterization of human CDK12 and CDK13 in the regulation of RNA processing
(Submitter supplied) We report the total RNA-seq results after CDK9, CDK12 and CDK13 depletion in human HCT116 cells for three days. RNA-seq was performed in cells using two non-targeting replicates and two different shRNAs for each CDK knockdown.  For each CDK knockdown, most of the differentially expressed genes were down-regulated with a very small subset of genes upregulated. Different CDK proteins control distinct subsets of genes in vivo, with CDK12 and CDK13 sharing more overlap in function compared to CDK9. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58107/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA248918
Series		Accession: GSE58107	ID: 200058107

4822. InFusion: advancing discovery of fusion genes and chimeric transcripts from RNA-seq data
(Submitter supplied) Gene fusions and chimeric transcripts occur frequently in cancers and in some cases drive the development of the disease. An accurate detection of these events is crucial for cancer research and in a long-term perspective could be applied for personalized therapy. RNA-seq technology has been established as an efficient approach to investigate transcriptomes and search for gene fusions and chimeric transcripts on a genome-wide scale. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE56nnn/GSE56512/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA243568
Series		Accession: GSE56512	ID: 200056512

4823. Identification of mRNAs and lincRNAs associated with lung cancer progression using next-generation RNA sequencing from laser micro-dissected archival FFPE tissue specimens
(Submitter supplied) Adenocarcinoma in situ (AIS) is considered an intermediate step in the progression of normal lung tissue to invasive adenocarcinoma.  However, the molecular mechanisms underlying this progression remain to be fully elucidated due to difficulties in obtaining and preserving clinical samples for downstream analyses.  Formalin fixation and paraffin embedding (FFPE) is a tissue preservation system that is widely used as a means for long-term storage. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE52nnn/GSE52248/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA227275
Series		Accession: GSE52248	ID: 200052248

4824. The Estrogen receptor alpha regulated NEAT1 long non-coding RNA promotes prostate cancer progression
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
4 related Platforms 9 Samples
FTP download: GEO (BED, CSV, RPKM) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE43nnn/GSE43988/
Series		Accession: GSE43988	ID: 200043988

4825. The Estrogen receptor alpha regulated NEAT1 long non-coding RNA promotes prostate cancer progression [RNA-Seq]
(Submitter supplied) Prostate glands predominantly exhibit androgen dependence, but increasing evidence suggests that estrogen receptor signaling is involved in its development and pathogenesis. By integrating ChIP sequencing for estrogen receptor alpha (ERα) with transcriptome sequencing data from prostate cancer samples, we found ERα to significantly influence the noncoding transcriptome in prostate cancer. We identified one such long noncoding RNA, NEAT1, to play an important role in prostate cancer progression through direct regulation of transcription of its target genes. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL10999 GPL13112 4 Samples
FTP download: GEO (CSV, RPKM) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE43nnn/GSE43986/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA188303
Series		Accession: GSE43986	ID: 200043986

4826. Characterization of a network of tumor suppressor microRNA's in T Cell acute lymphoblastic leukemia
(Submitter supplied) Purpose: The purpose of this study is to identify functionally inter-connected group of miRNAs whose reduced expression promotes leukemia development in vivo. We searched for relevant target genes of these miRNAs that are upregulated in T-ALL relative to controls. Methods: In order to examine the global gene expression, we generated 9 T-ALL patients and 4 normal controls by deep sequencing using Illumina Hi-Seq sequencer. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL9052 13 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63602/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA268382
Series		Accession: GSE63602	ID: 200063602

4827. Transcriptome profiling of a mouse model of alveolar soft part sarcoma
(Submitter supplied) In order to dtermine how well a mouse genetic model of alveolar soft part sarcoma (ASPS) mimics the human disease, five human ASPS tumor samples and three normal skeletal muscle samples were profiled by RNAseq and compared to samples from five mouse tumors induced by expression of ASPSCR1-TFE3 and three normal mouse skeletal muscle samples, also profiled by RNAseq.
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL13112 GPL11154 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE54nnn/GSE54729/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA237513
Series		Accession: GSE54729	ID: 200054729

4828. NOTCH1 activation in breast cancer confers sensitivity to inhibition of SUMOylation
(Submitter supplied) Breast cancer is genetically heterogeneous, and recent studies have underlined a prominent contribution of epigenetics to the   development of this disease. To uncover new synthetic lethalities with known breast cancer oncogenes, we screened an  epigenome-focused short hairpin RNA library on a panel of engineered breast epithelial cell lines. Here we report a selective  interaction between the NOTCH1 signaling pathway and the SUMOylation cascade. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE61nnn/GSE61727/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA261961
Series		Accession: GSE61727	ID: 200061727

4829. The conserved organization of the human and mouse transcriptomes
(Submitter supplied) We characterized by RNA-seq the transcriptional profiles of a large and heterogeneous collection of mouse tissues, augmenting the mouse transcriptome with thousands of novel transcript candidates. Comparison with transcriptome profiles obtained in human cell lines reveals substantial conservation of transcriptional programs, and uncovers a distinct class of genes with levels of expression across cell types and species, that have been constrained early in vertebrate evolution. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
4 related Platforms 64 Samples
FTP download: GEO (BAM, BEDRNAELEMENTS, BIGWIG, GFF, GTF, PDF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE49nnn/GSE49417/
Series		Accession: GSE49417	ID: 200049417

4830. The permanent reduction of TIA proteins molds expression transcriptome in HeLa cells
(Submitter supplied) This study provides, for the first time, TIA1 and TIAR linked-transcriptomic analysis by using RNA-Seq next-generation sequencing technology. Illumina RNA-Seq was used to survey transcriptome profiles from permanent TIA1- and TIAR-(shRNA-mediated) deficient HeLa cells. Analysis of the transcriptomes with the Cufflinks tool revealed that differentially expressed genes, isoforms produced by alternative splicing and/or promoter usage as well as microRNAs generated a great transcriptomic heterogeneity which might reflect the complexity linked to these cell phenotypes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE46nnn/GSE46516/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA200710
Series		Accession: GSE46516	ID: 200046516

4831. The genomic landscape of nasopharyngeal carcinoma
(Submitter supplied) Nasopharyngeal carcinoma (NPC) has extremely skewed ethnic and geographic distributions, is poorly understood at the genetic level and is in need of effective therapeutic approaches. Here we determined the mutational landscape of 128 cases with NPC using whole-exome and targeted deep sequencing, as well as SNP array analysis. These approaches revealed a distinct mutational signature and nine significantly mutated genes, many of which have not been implicated previously in NPC. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63381/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA267603
Series		Accession: GSE63381	ID: 200063381

4832. HNF4α is a therapeutic target that links AMPK to WNT signaling in early-stage gastric cancer
(Submitter supplied) Background Worldwide, gastric cancer is the fourth most common malignancy and the most common cancer in East Asia. Development of targeted therapies for this disease has focused on a few known oncogenes but has had limited effects. Objective To determine oncogenic mechanisms and novel therapeutic targets specific for gastric cancer by identifying commonly dys-regulated genes from the tumors of both Asian-Pacific and Caucasian patients. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL13393 44 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63288/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA267201
Series		Accession: GSE63288	ID: 200063288

4833. Transcriptome-wide modulation of splicing by the exon junction complex
(Submitter supplied) We report that knockdown of EJC core proteins, eIF4A3, Y14, Magoh, causes a transcript-wide changes in alternative splicing, as well as some transcriptional changes. These changes are specific to EJC core proteins, and KD of UPF1 protein caused different sets of alterantive splicing changes. These changes are linked to the rate of transcription.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 10 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63091/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA266584
Series		Accession: GSE63091	ID: 200063091

4834. Establishment of Highly Tumorigenic Human Colorectal Cancer Cell Line (CR4) with Properties of Putative Cancer Stem Cells
(Submitter supplied) Colorectal cancer (CRC) has the third highest incidence and mortality rates among the US population. According to the most recent concept of carcinogenesis, human tumors are organized hierarchically, and the top of this hierarchy is occupied by malignant stem cells, or cancer stem cells (CSCs), which possess unlimited self-renewal and tumor-initiating capacities and high resistance to conventional anticancer therapies. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE56nnn/GSE56660/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA244239
Series		Accession: GSE56660	ID: 200056660

4835. TET1 is a tumour suppressor that inhibits colon cancer growth by derepressing inhibitors of the WNT pathway
(Submitter supplied) Ten eleven translocation (TET) enzymes catalyse the oxidative reactions of 5-methylcytosine (5mC) to promote the demethylation process. The reaction intermediate 5-hydroxymethylcytosine (5hmC) has been shown to be abundant in embryonic stem cells and tissues, but strongly depleted in human cancers. Genetic mutations of TET2 gene were associated with lleukemia, whereas TET1 downregulation has been shown to promote malignancy in breast cancer. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15456 2 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53172/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA231040
Series		Accession: GSE53172	ID: 200053172

4836. GATA2 shRNA Expression in Castration Resistant Prostate Cancer Cell Lines
(Submitter supplied) The transcription factor GATA2 regulates chemotherapy resistance in prostate cancer. We report a novel GATA2 transcriptional program that has implications for chemotherapy resistance disease and aggressiveness in castration resistant prostate cancer.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 27 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58966/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA254050
Series		Accession: GSE58966	ID: 200058966

4837. Integrative AUF1 PAR-CLIP analysis uncovers AUF1 roles in translation and genome integrity
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Other
Platform: GPL9115 20 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE52nnn/GSE52977/
Series		Accession: GSE52977	ID: 200052977

4838. EWS-Fli and LNC regulated genes in comparison to GFP samples
(Submitter supplied) RNA from A673 cells with shRNA-mediated knockdown of GFP (4 libraries),  EWS-FLI1 (4 libraries), or lnc277 (7 libraries) was isolated with TRIzol (Invitrogen).  Each sample was DNase treated and further purified on an RNeasy  Mini column (Qiagen) before quality analysis on an Agilent 2100 Bioanalyzer.  For each sample, 100-150ng of RNA was synthesized into cDNA, sheared on  a Covaris ultrasonicator, and amplified using the NuGen Encore Complete kit  (NuGen) to produce strand-specific and rRNA-depleted libraries. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE60nnn/GSE60949/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA259885
Series		Accession: GSE60949	ID: 200060949

4839. The long non-coding RNA lnc277 mediates a repressive gene signature in Ewing's sarcoma and is required for oncogenesis
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL9115 10 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE60nnn/GSE60891/
Series		Accession: GSE60891	ID: 200060891

4840. hnRNPK knock down in Ewing cell line
(Submitter supplied) Ewing sarcoma is a highly aggressive tumor characterized by a translocation between members of the FET family of RNA binding proteins and one of several ETS transcription factors, with the most common translocation being EWS-FLI1. EWS-FLI1 leads to changes in gene expression through mechanisms that are not completely understood. We performed RNA sequencing analysis on primary pediatric human mesenchymal progenitor cells (pMPCs) expressing EWS-FLI1 in order to identify novel target genes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE60nnn/GSE60890/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA259752
Series		Accession: GSE60890	ID: 200060890

4841. pMPC EF vs control 3seq
(Submitter supplied) Ewing sarcoma is a highly aggressive tumor characterized by a translocation between members of the FET family of RNA binding proteins and one of several ETS transcription factors, with the most common translocation being EWS-FLI1. EWS-FLI1 leads to changes in gene expression through mechanisms that are not completely understood. We performed RNA sequencing analysis on primary pediatric human mesenchymal progenitor cells (pMPCs) expressing EWS-FLI1 in order to identify novel target genes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE60nnn/GSE60889/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA259751
Series		Accession: GSE60889	ID: 200060889

4842. Overexpression of ERG in cord blood progenitors promotes expansion and recapitulates molecular signatures of high ERG leukemias
(Submitter supplied) High expression of the ETS family transcription factor ERG is associated with poor clinical outcome in acute myeloid leukemia (AML) and acute T-cell lymphoblastic leukemia (T-ALL). In murine models, high ERG expression induces both T-ALL and AML. However, no study to date has defined the effect of high ERG expression on primary human hematopoietic cells. In the present study, human CD34+ cells were transduced with retroviral vectors to elevate ERG gene expression to levels detected in high ERG AML. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53665/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA232601
Series		Accession: GSE53665	ID: 200053665

4843. Genome-wide chromatin analysis of Ewing sarcoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL11154 70 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE61nnn/GSE61953/
Series		Accession: GSE61953	ID: 200061953

4844. Genome-wide chromatin analysis of Ewing sarcoma (RNA-seq)
(Submitter supplied) We show that EWS-FLI1, an aberrant transcription factor responsible for the pathogenesis of Ewing sarcoma, reprograms gene regulatory circuits by directly inducing or directly repressing enhancers. At GGAA repeats, which lack regulatory potential in other cell types and are not evolutionarily conserved, EWS- FLI1 multimers potently induce chromatin opening, recruit p300 and WDR5, and create de novo enhancers. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE61nnn/GSE61950/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA262778
Series		Accession: GSE61950	ID: 200061950

4845. DECIDUALIZATION INDUCES A SECRETOME SWITCH IN THE PERIVASCULAR NICHE CELLS OF THE HUMAN ENDOMETRIUM
(Submitter supplied) The endometrial perivascular microenvironment is rich in mesenchymal stem-like cells that express type 1 integral membrane protein Sushi domain containing 2 (SUSD2) but the role of these cells in the decidual transformation of this tissue in pregnancy is unknown. We used an antibody directed against SUSD2 (W5C5) to isolate perivascular (W5C5+) and non-perivascular (W5C5-) fibroblasts from mid-luteal biopsies. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57182/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA245857
Series		Accession: GSE57182	ID: 200057182

4846. The Notch driven long non-coding RNA repertoire in T-cell acute lymphoblastic leukemia
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL19197 144 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62006/
Series		Accession: GSE62006	ID: 200062006

4847. RNA-sequencing of CD34+ thymocytes that were cultured on an OP9-GFP or OP9-DLL1 feeder layer.
(Submitter supplied) Genetic studies in T-cell acute lymphoblastic leukemia have uncovered a remarkable complexity of oncogenic and loss-of-function mutations. Amongst this plethora of genetic changes, NOTCH1 activating mutations stand out as the most frequently occurring genetic defect, identified in more than 50% of T-cell acute lymphoblastic leukemias, supporting an essential driver role for this gene in T-cell acute lymphoblastic leukemia oncogenesis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62000/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA262922
Series		Accession: GSE62000	ID: 200062000

4848. RNA-sequencing of the GSI treatment of the CUTLL1 cell line
(Submitter supplied) Genetic studies in T-cell acute lymphoblastic leukemia have uncovered a remarkable complexity of oncogenic and loss-of-function mutations. Amongst this plethora of genetic changes, NOTCH1 activating mutations stand out as the most frequently occurring genetic defect, identified in more than 50% of T-cell acute lymphoblastic leukemias, supporting an essential driver role for this gene in T-cell acute lymphoblastic leukemia oncogenesis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE61nnn/GSE61999/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA262921
Series		Accession: GSE61999	ID: 200061999

4849. Transcriptomic profiling of bone marrow cells from healthy individuals
(Submitter supplied) We performed whole-genome transcriptomic profiling of RNA from mononuclear cells from bone marrow aspirates taken from healthy individuals. This study complements GSE58335: transcriptomic profiling of peripheral blood mononuclear cells from healthy individuals.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE61nnn/GSE61410/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA261023
Series		Accession: GSE61410	ID: 200061410

4850. Global Transcriptome Analysis and Enhancer Landscape of Human Primary T Follicular Helper and T Effector Lymphocytes (RNA-Seq)
(Submitter supplied) T follicular helper (Tfh) cells are a subset of CD4+ T helper (Th) cells that migrate into germinal centers and promote B cell maturation into memory B and plasma cells. Tfh cells are necessary for promotion of protective humoral immunity following pathogen challenge, but when aberrantly regulated, drive pathogenic antibody formation in autoimmunity and undergo neoplastic transformation in angioimmunoblastic T-cell lymphoma and other primary cutaneous T-cell lymphomas. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58596/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA252962
Series		Accession: GSE58596	ID: 200058596

4851. Transcriptomic profiling of peripheral blood mononuclear cells from healthy individuals
(Submitter supplied) Substantial effort is currently devoted to identifying cancer-associated alterations using genomics. Here, we show that standard blood collection procedures rapidly change the transcriptional and post-transcriptional landscapes of hematopoietic cells, resulting in biased activation of specific biological pathways, up-regulation of pseudogenes, antisense RNAs, and unannotated coding isoforms, and RNA surveillance inhibition. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58335/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA252189
Series		Accession: GSE58335	ID: 200058335

4852. Exosome Transfer from Stromal to Breast Cancer Cells Regulates Therapy Resistance Pathways
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing; Other
Platforms: GPL6244 GPL15520 51 Samples
FTP download: GEO (CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE60nnn/GSE60998/
Series		Accession: GSE60998	ID: 200060998

4853. Analysis of exosome RNA from co-culture of cancer cell and stroma cell
(Submitter supplied) How stroma communicates with cancer to influence treatment response is poorly understood. We show that stromal fibroblasts protect breast cancer (BrCa) against radiation and chemotherapy through an exosome-mediated anti-viral pathway and NOTCH3. Stroma increases RAB27B and transfers exosomes to BrCa. RNA within exosomes, comprised largely of non-coding transcripts and transposable elements, stimulates the pattern recognition receptor RIG-I through a 5’-triphosphate motif to activate STAT1. more...
Organism:	Homo sapiens
Type:		Other; Expression profiling by high throughput sequencing
Platform: GPL15520 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE60nnn/GSE60997/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA260061
Series		Accession: GSE60997	ID: 200060997

4854. RNA-seq data from MCF-7 cells (breast cancer model) treated with soy extracts
(Submitter supplied) The MCF-7 were infected with either control adenovirus expressing B-galactosidase (Ad) or adenovirus expressing ERB (AdERbeta) for 72 h.  For knockdown of the endogenous ERa in MCF-7 cells, cells were treated with siRNA for 24h (AdERbeta+SiERalpha).  Then cells were treated with Veh (0.1% EtOH), 10 nM E2 or 1 uM BEs (botanical extracts) for 24h.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 30 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE56nnn/GSE56066/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA242333
Series		Accession: GSE56066	ID: 200056066

4855. ERK signaling regulates opposing functions of JUN family transcription factors in prostate cancer cell migration
(Submitter supplied) Knockdowns of c-JUN and JUND had opposite effects on PC3 prostate cell migration. We predicted that c-JUN and JUND control the same set of cell migration genes, but in opposite directions. To test this hypothesis, mRNA with expression changes in c-JUN and JUND knockdown PC3 cell lines were compared to mRNA levels in control (luciferase knockdown) PC3 cells by RNA-seq.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53470/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA232070
Series		Accession: GSE53470	ID: 200053470

4856. An Investigation of Biomarkers Derived from Legacy Microarray Data for Their Utility in the RNA-Seq Era
(Submitter supplied) Gene expression microarray has been the primary biomarker platform ubiquitously applied in biomedical research, resulting in enormous data, predictive models and biomarkers accrued. Recently, RNA-seq has looked likely to replace microarrays, but there will be a period where both technologies coexist. This raises two important questions: can microarray-based models and biomarkers be directly applied to RNA-Seq data? Can future RNA-Seq-based predictive models and biomarkers be applied to microarray data to leverage past investment? We systematically evaluated the transferability of predictive models and signature genes between microarray and RNA-seq using two large clinical data sets. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 498 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62564/
Series		Accession: GSE62564	ID: 200062564

4857. Tumor cell-specific inhibition of MYC function using small molecule inhibitors of the HUWE1 ubiquitin ligase
(Submitter supplied) Deregulated expression of MYC is a driver of colorectal carcinogenesis, necessitating novel strategies to inhibit MYC function. The ubiquitin ligase HUWE1 (HECTH9, ARFBP1,  MULE) associates with both MYC and the MYC-associated protein MIZ1. We show here that HUWE1 is required for growth of colorectal cancer cells in culture and in orthotopic xenograft models. Using high throughput screening, we identify small  molecule inhibitors of HUWE1, which inhibit MYC-dependent transactivation in colorectal cancer cells, but not in stem and normal colon epithelial cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL10999 22 Samples
FTP download: GEO (TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59223/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA254756
Series		Accession: GSE59223	ID: 200059223

4858. Transcriptome-wide ribonuclease footprinting to identify RNA-protein interaction sites
(Submitter supplied) RNA-binding proteins (RBPs) are intimately involved in all aspects of RNA processing and regulation and are linked to neurodegenerative diseases and cancer. Therefore, understanding the relationship between RBPs and their RNA targets is critical for a broader understanding of post-transcriptional regulation in normal and disease processes.  The majority of approaches to study RNA-protein interactions focus on single RBPs, however there are many hundreds RBPs encoded in the human genome, and each cell type expresses a different catalog of these regulatory molecules, greatly limiting the ability of these single RBP approaches to capture the global landscape of RNA-protein interactions. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57881/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA248315
Series		Accession: GSE57881	ID: 200057881

4859. A Novel Population of Human Cardiac Resident Mesenchymal Stem Cells
(Submitter supplied) We describe a novel population of human adult cardiac resident stem cells (CRSCs), which are positive for W8B2 antigen, originating from human adult atrial appendages. W8B2+ CRSCs exhibit a spindle-shaped morphology, are clonogenic and able to self-renew. W8B2+ CRSCs show high expression of mesenchymal but not hematopoietic nor endothelial markers. W8B2+ CRSCs expressed GATA4, HAND2, and TBX5, but not C-KIT, SCA-1, NKX2.5, PDGFRα, ISL1 or Wilm’s tumor gene-1 (WT1). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (GTF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62288/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA263766
Series		Accession: GSE62288	ID: 200062288

4860. Transcriptome sequencing for cancer stem cell properties in MCF-7 cells with knocked down CD24
(Submitter supplied) CD24 is the one of cell surface protein that anchored via glycosyl phosphatidylinositol that links to cell surface and modulates growth and differentiation signal many of cell types. A small population of cells, namely ‘Cancer Stem Cells (CSCs)’, charges highly aggressive and metastatic character of cancer cells and shows conformational change of ‘epithelial to mesenchymal transition (EMT). To understand the role of CD24 in CSC and EMT, CD24 was knocked down using siRNA in the MCF7 cell line (MCF-7 hCD24 KD) and analyzed transcriptome profiles by mRNA-sequencing. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE61nnn/GSE61917/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA262675
Series		Accession: GSE61917	ID: 200061917

4861. Identifying genes regulated by Kruppel-like factor-9 by RNA-seq in human glioblastoma stem cells.
(Submitter supplied) Kruppel-like factor-9 (KLF9), a member of the large KLF transcription factor family, has emerged as a regulator of oncogenesis, cell differentiation and neural development; however, the molecular basis for KLF9’s diverse contextual functions remains unclear. This study focuses on the functions of KLF9 in human glioblastoma stem-like cells. We establish for the first time a genome-wide map of KLF9-regulated targets in human glioblastoma stem-like cells, and show that KLF9 functions as a transcriptional repressor and thereby regulates multiple signaling pathways involved in oncogenesis and stem cell regulation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62212/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA263480
Series		Accession: GSE62212	ID: 200062212

4862. Enhancer Activation Requires Trans-Recruitment of a Mega Transcription Factor Complex
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.  Enhancers provide critical information directing cell-type specific transcriptional programs, regulated by binding of signal-dependent transcription factors and their associated cofactors. Here we report that the most strongly activated estrogen (E2)-responsive enhancers are characterized by trans-recruitment and in situ assembly of a large 1-2MDa complex of diverse DNA-binding transcription factors by ERα at ERE-containing enhancers. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL11154 GPL10999 62 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE60nnn/GSE60272/
Series		Accession: GSE60272	ID: 200060272

4863. Enhancer Activation Requires Trans-Recruitment of a Mega Transcription Factor Complex (Gro-seq)
(Submitter supplied) Enhancers provide critical information directing cell-type specific transcriptional programs, regulated by binding of signal-dependent transcription factors and their associated cofactors. Here we report that the most strongly activated estrogen (E2)-responsive enhancers are characterized by trans-recruitment and in situ assembly of a large 1-2MDa complex of diverse DNA-binding transcription factors by ERα at ERE-containing enhancers. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 14 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE60nnn/GSE60271/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA257922
Series		Accession: GSE60271	ID: 200060271

4864. Charaterization of genetic alterations and gene expression signatures found in BCR-ABL inhibitor-resistant KCL-22 subpopulations and single clones
(Submitter supplied) KCL-22 is a chronic myeloid leukemia (CML) cell line derived from a patient in blast crisis phase and harbors the BCR-ABL translocation. The catalytic (ATP-competitive) BCR-ABL inhibitors imatinib and nilotinib have dramatically improved CML patient outcome, but the development of resistance remains a clinical challenge. The recent identification of allosteric BCR-ABL inhibitors, such as GNF-2, which target the enzyme by binding to the myristoyl pocket rather than catalytic site of ABL1, may provide a strategy to broadly overcome resistance to the class of ABL1 ATP competitive inhibitors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62121/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA263248
Series		Accession: GSE62121	ID: 200062121

4865. Charaterization of genetic alterations and gene expression signatures found in erlotinib-resistant and erlotinib/crizotinib dual-resistant HCC827 subpopulations
(Submitter supplied) The non-small cell lung cancer (NSCLC) cell line HCC827 harbors an activating EGFR mutation (exon 19 deletion) that confers sensitivity to the FDA-approved EGFR inhibitor erlotinib. By applying the ClonTracer barcoding system, we were able to show the presence of pre-existing sub-populations in HCC827 that contribute to erlotinib resistance. Prior studies implicated that MET amplification confers resistance to erlotinib in this cell line. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62118/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA263242
Series		Accession: GSE62118	ID: 200062118

4866. CHD8 regulates neurodevelopmental pathways associated with autism spectrum disorder in neural progenitors [RNA-Seq]
(Submitter supplied) Truncating mutations of CHD8, encoding a chromodomain helicase, and of many other genes with diverse functions, are strong-effect risk factors for autism spectrum disorder (ASD), suggesting multiple mechanisms of pathogenesis. We explored the transcriptional networks that CHD8 regulates in neural progenitor cells (NPCs) by reducing its expression and then integrating transcriptome sequencing (RNA-seq) with genome-wide CHD8 binding (ChIP-seq). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 22 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE61nnn/GSE61491/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA261297
Series		Accession: GSE61491	ID: 200061491

4867. ETS1 is a genome-wide effector of RAS/ERK signaling in epithelial cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 17 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59022/
Series		Accession: GSE59022	ID: 200059022

4868. ETS1 is a genome-wide effector of RAS/ERK signaling in epithelial cells (RNA-Seq)
(Submitter supplied) ETS1 and RAS/ERK regulate a common gene expression program in establishing enviroment suitable for prostate cancer cell migration.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59020/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA254145
Series		Accession: GSE59020	ID: 200059020

4869. Distinct structural transitions of chromatin topological domains coordinate hormone-induced gene regulation
(Submitter supplied) The three-dimensional (3D) organization of the genome within the cell nucleus contributes to cell-specific gene expression in different cell types1. High-throughput 3C–derived methods have revealed that the genome is segmented into contiguous topologically associating domains (TADs), which help to orchestrate gene expression changes during differentiation and development2-5. Using ChIP-Seq, Hi-C and 3D modelling techniques, we reveal that TADs regulate the rapid gene expression changes induced by progestin in T47D breast cancer cells. more...
Organism:	Homo sapiens
Type:		Other; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53463/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA232055
Series		Accession: GSE53463	ID: 200053463

4870. Vitamin d receptor-mediated stromal reprogramming suppresses pancreatitis and enhances pancreatic cancer therapy
(Submitter supplied) The poor clinical outcome in pancreatic ductal adenocarcinoma (PDA) has been attributed to intrinsic resistance to chemotherapy and a growth-permissive tumor microenvironment.  Quiescent pancreatic stellate cells (PSCs) are neuroendocrine, nestin-positive, lipid-accumulating cells whose homologues in the liver are the principal repository of Vitamin A esters.  Upon activation, lipid droplets are lost and via transdifferentiation they become the key cell type responsible for driving the severe desmoplasia that characterizes PDA. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL13112 17 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE43nnn/GSE43770/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA187388
Series		Accession: GSE43770	ID: 200043770

4871. Genome-wide characterizaion of H3K27me3 levels upon inhibition of JMJD3 histone demethylase using a small molecule inhibitor in T cell leukamia
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL13112 GPL11154 47 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE56nnn/GSE56696/
Series		Accession: GSE56696	ID: 200056696

4872. Characterizing the contrasting roles of JMJD3 and UTX histone demethylases in T cell acute lymphoblastic leukemia [GSKJ4_RNA-seq]
(Submitter supplied) T-cell acute lymphoblastic leukemia (T-ALL) is an immature hematopoietic malignancy driven mainly by oncogenic activation of NOTCH1 signaling. In this study we chemically inhibited the H3K27me3 demethylase JMJD3 using the GSKJ4 inhibitor and assayed for genome-wide changes in H3K27me3 and JMJD3 enrichment. This piece of data was further integrated to expression changes using RNA sequencing as well as ChIP-Sequencing analysis of H3K27me3 upon genomic knock-down of JMJD3 and UTX. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE56nnn/GSE56691/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA244340
Series		Accession: GSE56691	ID: 200056691

4873. Characterizing the contrasting roles of JMJD3 and UTX histone demethylases in T cell acute lymphoblastic leukemia [short_hairpins_RNA-seq]
(Submitter supplied) T-cell acute lymphoblastic leukemia (T-ALL) is an immature hematopoietic malignancy driven mainly by oncogenic activation of NOTCH1 signaling. In this study we abrogated the expression of JMJD3 (KDM6B) and UTX (KDM6A) H3K27me3 demethylases in human T-ALL lines and assayed for genome-wide expression changes using RNA sequencing. This piece of data was further integrated to ChIP-Sequencing analysis of H3K27me3 from the same treatment as well as H3K27me3 and JMJD3 genome-wide analysis from treatment of T-ALL lines with the GSKJ4 inhibitor. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE56nnn/GSE56689/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA244342
Series		Accession: GSE56689	ID: 200056689

4874. Genome-wide discovery of human splicing branchpoints
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 11 Samples
FTP download: GEO (BIGWIG, BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53328/
Series		Accession: GSE53328	ID: 200053328

4875. Genome-wide discovery of human splicing branchpoints [RNAse]
(Submitter supplied) Gene splicing requires three basal genetic elements; the 3’ and 5’ splice sites and the branchpoint to which the 5’ intron termini is ligated to form a closed lariat during the splicing reaction. The 5’ and 3’ splice sites that define exon boundaries have been widely identified, revealing pervasive transcription and splicing of human genes. However, the locations of the third requisite element, the branchpoint, are still largely unknown. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53327/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA231724
Series		Accession: GSE53327	ID: 200053327

4876. Genome-wide discovery of human splicing branchpoints [BPCapture]
(Submitter supplied) Gene splicing requires three basal genetic elements; the 3’ and 5’ splice sites and the branchpoint to which the 5’ intron termini is ligated to form a closed lariat during the splicing reaction. The 5’ and 3’ splice sites that define exon boundaries have been widely identified, revealing pervasive transcription and splicing of human genes. However, the locations of the third requisite element, the branchpoint, are still largely unknown. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 3 Samples
FTP download: GEO (BED, BIGWIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53326/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA231723
Series		Accession: GSE53326	ID: 200053326

4877. Functional Annotation of Colon Cancer Risk SNPs
(Submitter supplied) To understand the funtion of Colorectal cancer GWAS results, we perform a comprehensive analysis using biofeatures of HCT116 colon cancer cell line and got a list of risk-asscociated SNP. Risk-associated SNP are likely exerting their effects through promoters or enhancer. In order to understand the importance of the genes with risk-associated SNP in their promoters and enhancers' putatively targeted genes,  we did a comparison of these genes between HCT116 colon cancer cell and normal colon and try to understand their function
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE52nnn/GSE52429/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA228915
Series		Accession: GSE52429	ID: 200052429

4878. 16q22-24 DNA amplification specifically predicts and mediates, through MAF gene, breast cancer bone metastasis.
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by genome tiling array
Platforms: GPL14965 GPL570 14 Samples
FTP download: GEO (CEL, PAIR, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE51nnn/GSE51238/
Series		Accession: GSE51238	ID: 200051238

4879. Identification of a dynamic core transcriptional network in t(8;21) AML regulating differentiation block and self-renewal
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL10999 GPL11154 20 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE60nnn/GSE60131/
Series		Accession: GSE60131	ID: 200060131

4880. U2AF1 mutations alter splice site recognition in hematological malignancies
(Submitter supplied) Whole-exome sequencing studies have identified common mutations affecting genes encoding components of the RNA splicing machinery in hematological malignancies. Here, we sought to determine how mutations affecting the 3' splice site recognition factor U2AF1 altered its normal role in RNA splicing. We find that U2AF1 mutations influence the similarity of splicing programs in leukemias, but do not give rise to widespread splicing failure. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 7 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58871/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA253774
Series		Accession: GSE58871	ID: 200058871

4881. Human Pancreatic CTCs Express the ECM Protein SPARC
(Submitter supplied) Circulating Tumor Cells (CTCs) are shed from primary tumors into the bloodstream, mediating the hematogenous spread of cancer to distant organs. To determine the relevance of ECM protein expression to human disease, CTCs were isolated from the blood of metastatic PDAC patients and subjected to single cell RNA-sequencing.  Analysis of 7 pancreatic CTCs from 3 patients revealed that the majority expressed keratins defining their epithelial origin. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16288 7 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE60nnn/GSE60407/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA258196
Series		Accession: GSE60407	ID: 200060407

4882. The histone H3.3K27M mutation in pediatric glioma reprograms H3K27 methylation and gene expression
(Submitter supplied) Recent studies have identified a Lys 27-to-methionine (K27M) mutation at one allele of H3F3A, one of the two genes encoding histone H3 variant H3.3, in 60% of high-grade pediatric glioma cases. The median survival of this group of patients after diagnosis is ∼1 yr. Here we show that the levels of H3K27 di- and trimethylation (H3K27me2 and H3K27me3) are reduced globally in H3.3K27M patient samples due to the expression of the H3.3K27M mutant allele. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 16 Samples
FTP download: GEO (BED, BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE61nnn/GSE61586/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA261535
Series		Accession: GSE61586	ID: 200061586

4883. Low MITF/AXL ratio predicts early resistance to multiple targeted drugs in melanoma
(Submitter supplied) Increased MITF expression contributes to melanoma progression and resistance to BRAF pathway inhibition. We show that, unexpectedly, lack of MITF is associated with more severe resistance to a range of inhibitors. Indeed, the presence of endogenous MITF was essential for robust drug responses. Both in primary and acquired resistance, MITF levels inversely correlated with expression of several activated receptor tyrosine kinases, most commonly AXL. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE61nnn/GSE61544/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA261431
Series		Accession: GSE61544	ID: 200061544

4884. The splicing factor RBM4 controls apoptosis, proliferation, and migration to suppress tumor progression
(Submitter supplied) Gene expression and splicing switches upon RBM4 overexpression
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58594/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA252956
Series		Accession: GSE58594	ID: 200058594

4885. Next generation sequencing of advanced non-castrate prostate cancer treated with docetaxel chemotherapy
(Submitter supplied) Early chemotherapy for advanced/metastatic non-castration resistant prostate cancer (PCa) may improve overall patient survival.  We studied the safety, tolerability and early efficacy of up-front docetaxel chemotherapy and androgen deprivation therapy (ADT) versus ADT alone for patients with newly-diagnosed advanced/metastatic PCa.  As proof of concept, we undertook in vivo gene expression profiling by next generation RNA sequencing (RNA-Seq).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE51nnn/GSE51005/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA219507
Series		Accession: GSE51005	ID: 200051005

4886. RNA-seq from control and macroH2A1-depleted IMR90 primary human lung fibroblasts
(Submitter supplied) The histone variant macroH2A1 and the poly(ADP-ribose) polymerase PARP-1 both regulate gene transcription by modulating chromatin structure and function. Of the two macroH2A1 splice variants, macroH2A1.1 and macroH2A1.2, the former is often suppressed in cancer and has the unique ability to interact with poly(ADP-ribose). Using ChIP-seq in primary lung fibroblasts, we demonstrate that macroH2A1 is incorporated into either of two spatially and functionally distinct types of chromatin; the first is marked by H3 K27 trimethylation, while the second contains a set of nine histone acetylations. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE54nnn/GSE54846/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA237809
Series		Accession: GSE54846	ID: 200054846

4887. Ribosome profiling upon inhibition of eIF4A
(Submitter supplied) Ribosome profiling of MDA-MB-231 cells treated with Silvestrol to monitor transcriptome wide, eIF4A-dependent changes in translation efficiency
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 13 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE61nnn/GSE61375/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA260909
Series		Accession: GSE61375	ID: 200061375

4888. Global loss of DNA methylation uncovers intronic enhancers in genes
(Submitter supplied) We used HCT116 colorectal cancer cells with and without mutations in DNA methyltransferases (resulting in a 95% reduction in global DNA methylation levels) to study the relationship between DNA methylation, histone modifications, and gene expression. (The double knockout cell line is called DKO1)
Organism:	Homo sapiens
Type:		Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 11 Samples
FTP download: GEO (BED, BW, GFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE60nnn/GSE60106/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA257496
Series		Accession: GSE60106	ID: 200060106

4889. Whole Transcriptomic Sequencing of Metastatic Castration Resistant Prostate Cancer Samples
(Submitter supplied) We report the gene expression profile of 8 metastatic castration resisistant prostate cancer samples analyzed by paired-end RNA-seq. We found evidence of extensive abnormal splicing as well as several novel fusion genes. Finally, we also observed several recurrent high-confidence somatic mutations.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL10999 8 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE50nnn/GSE50630/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA218119
Series		Accession: GSE50630	ID: 200050630

4890. Transcriptome wide identification of retained introns upon depletion of the splicing factors SNW1 or PRPF8
(Submitter supplied) We identified which mRNAs are dependent on the splicing factors SNW1 or PRPF8. These factors were depleted in HeLa cells by RNAi, and the levels of intronic reads in mRNAs was compared to control RNAi.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE61nnn/GSE61071/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA260186
Series		Accession: GSE61071	ID: 200061071

4891. RNA-Seq analysis of prostate tumors with or without androgen receptor splice variant
(Submitter supplied) Background.  Androgen receptor splice variant-7 (AR-V7) is a truncated form of the androgen receptor protein which lacks the ligand-binding domain, the target of enzalutamide and abiraterone, but remains constitutively active as a transcription factor. We hypothesized that detection of AR-V7 in circulating tumor cells (CTCs) from men with advanced prostate cancer would be associated with resistance to enzalutamide and abiraterone. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE56nnn/GSE56701/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA244326
Series		Accession: GSE56701	ID: 200056701

4892. Transcriptome of EBV-infected gastric cancer cell lines
(Submitter supplied) To understand epigenic dysregulation of host and viral genes upon EBV infection in human gastric cancer, genome wide transcripts by RNAseq were undertaken for total RNAs of 3 EBVnGC, their isogenic cell lines converted by in vitro EBV-infection and 3 EBV-naturally infected GC cell lines.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE60nnn/GSE60873/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA259709
Series		Accession: GSE60873	ID: 200060873

4893. Treatment of multiple myeloma cells with EZH2 small molecule inhibitor
(Submitter supplied) We investigated differential gene expression in response to treatment of multiple myeloma cells with EZH2 inhibitor
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57478/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA246529
Series		Accession: GSE57478	ID: 200057478

4894. Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome variation profiling by SNP array; SNP genotyping by SNP array; Expression profiling by high throughput sequencing
Platforms: GPL16288 GPL18544 40 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE56nnn/GSE56781/
Series		Accession: GSE56781	ID: 200056781

4895. Small molecule inhibitor of BCL2 in combination with RCHOP is effective in CD20 negative lymphoma
(Submitter supplied) Rituximab alone or in combination with chemotherapeutics is the first-line therapy for variety of lymphoproliferative disorders including low- and high grade non-Hodgkin’s lymphomas (NHL). Although the complete response rate is quite impressive, vast majority of patient presents recurrent disease. The association between CD20 expression and clinical outcome in patients strongly suggests that reduced CD20 expression leads to inferior response to RCHOP (rituximab, cyclophosphamide, vincristine, doxorubicin and prednisone). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE54nnn/GSE54201/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA235876
Series		Accession: GSE54201	ID: 200054201

4896. A histone H3.3 Lysine 36 Trimethylation Reader Connects Chromatin to Regulated Pre-mRNA Processing
(Submitter supplied) BS69 (aka ZMYND11) was initially discovered as a direct target of adenoviral E1A oncoprotein1. Subsequent studies implicated BS69 as a tumor suppressor and a transcriptional regulator2. But exactly how BS69 regulates gene expression has remained elusive. BS69 contains tandemly arranged PHD, BROMO and PWWP domains, which are known to function as chromatin recognition modalities. Here we show that BS69 selectively recognizes histone variant H3.3 lysine 36 trimethylation (H3.3K36me3) via these chromatin recognition modules. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE51nnn/GSE51261/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA222299
Series		Accession: GSE51261	ID: 200051261

4897. Chronic Myeloid Leukemia (CML), induced pluripotent stem cell (iPSC)-derived lin-CD34+CD45+ (iCD34) cell population
(Submitter supplied) Analysis of lin-CD34+CD45+ (iCD34+) cell population from two normal bone marrow-derived (BM1K and BM9) iPSCs  and two CML (CML15 and CML17) iPSCs . CML iCD34+ cells have characteristics similar to primary CML leukemia stem cell in patients. Results provide insight into molecular profile characterized CML iCD34 and mechanism of its maintenance and drug resistance.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE60nnn/GSE60065/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA257403
Series		Accession: GSE60065	ID: 200060065

4898. Gene expression profiling study by RNA-seq in colorectal cancer
(Submitter supplied) The objective of this study is to identify a prognostic signature in colorectal cancer (CRC) patients with diverse progression and heterogeneity of CRCs. We generated RNA-seq data of 54 samples (normal colon, primary CRC, and liver metastasis) from 18 CRC patients and, from the RNA-seq data, identified significant genes associated with aggressiveness of CRC. Through diverse statistical methods including generalized linear model likelihood ratio test, two significantly activated regulators were identified. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 54 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE50nnn/GSE50760/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA218851
Series		Accession: GSE50760	ID: 200050760

4899. Potent antitumor activity of Cabozantinib, a c-MET and VEGFR2 Inhibitor, in a Colorectal Cancer Patient-derived Tumor Explant Model
(Submitter supplied) Anti-angiogenic therapy is commonly used for the treatment of CRC. Although patients derive some clinical benefit, treatment resistance inevitably occurs. The MET signaling pathway has been proposed to be a major contributor of resistance to anti-angiogenic therapy. MET is upregulated in response to VEGF pathway inhibition and plays an essential role in tumorigenesis and progression of tumors. In this study we set out to determine the efficacy of cabozantinib in a preclinical CRC PDTX model. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE60nnn/GSE60939/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA259866
Series		Accession: GSE60939	ID: 200060939

4900. P493-6 treated with KJ-Pyr-9 and/or Doxycycline
(Submitter supplied) In a fluorescence polarization screen for MYC-MAX interaction, we have identified a novel small molecule inhibitor of MYC, KJ-Pyr-9, from a Kröhnke pyridine library. The Kd of KJ-Pyr-9 for MYC in vitro is 6.5 ± 1.0 nM as determined by backscattering interferometry; KJ-Pyr-9 also interferes with MYC-MAX complex formation in the cell as shown in a protein fragment complementation assay. KJ-Pyr-9 specifically inhibits MYC-induced oncogenic transformation in cell culture; it has no or only weak effects on the oncogenic activity of several unrelated oncoproteins. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58168/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA251417
Series		Accession: GSE58168	ID: 200058168

4901. Cell type-specific ribosome profiling in vivo.
(Submitter supplied) We report cell-type specific ribosome profiling in a mouse glioma model.
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL13112 25 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE51nnn/GSE51424/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA223060
Series		Accession: GSE51424	ID: 200051424

4902. Ras-induced epigenetic inactivation of RRAD promotes glucose uptake in a human ovarian cancer model
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms: GPL11154 GPL10999 6 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE55nnn/GSE55568/
Series		Accession: GSE55568	ID: 200055568

4903. Ras-induced epigenetic inactivation of RRAD promotes glucose uptake in a human ovarian cancer model [DGE-Seq]
(Submitter supplied) Ras-related associated with diabetes (RRAD) is a small Ras-related GTPase that is frequently inactivated by DNA methylation of the CpG island in its promoter region in cancer tissues. However, the role of the methylation-induced RRAD inactivation in tumorigenesis remains unclear. In this study, the Ras regulated-transcriptome and epigenome were profiled by comparing T29H (a RasV12-transformed human ovarian epithelial cell line) with T29 (an immortalized but non-transformed cell line) through Reduced representation bisulfite sequencing (RRBS-seq) and Digital gene expression (DGE) . more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE55nnn/GSE55567/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA240061
Series		Accession: GSE55567	ID: 200055567

4904. Comparison of Poly(A) capture versus Ribosomal RNA depletion methods for RNA-seq
(Submitter supplied) Methods: RNA-sequencing was performed on matched samples obtained across several different gene expression measurement methods including: (a) fresh-frozen (FF) RNA samples by mRNA-seq, Ribo-zero and DSN and (b) FFPE samples by Ribo-zero and DSN. We also assayed the matched samples with Agilent microarray. RNA-seq data was compared on the rRNA-removal efficiency, genome profile, library complexity, coverage uniformity and quantitative cosinstency across protocols and with microarray data. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Expression profiling by array
Platforms: GPL8269 GPL11154 59 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE51nnn/GSE51783/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA226742
Series		Accession: GSE51783	ID: 200051783

4905. RNA-seq of poly(A)-/ribo- or poly(A)+ RNAs from human and mouse ES cells
(Submitter supplied) We have used RNA-seq to examine circular RNAs from poly(A)-/ribo- RNAs in human and mouse embryonic stem cells, and from from RNase R treated poly(A)-/ribo- RNAs in mouse embryonic stem cells. 
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL13112 GPL11154 5 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE60nnn/GSE60467/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA258364
Series		Accession: GSE60467	ID: 200060467

4906. Transcriptome profiling in human T-ALL
(Submitter supplied) Genome-wide mapping and characterization of novel Notch-regulated long non-coding RNAs in acute leukemia
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 31 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57982/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA248647
Series		Accession: GSE57982	ID: 200057982

4907. Analysis of the RNA-Seq data of castration resistant prostate cancer (CRPCa)
(Submitter supplied) Prostate cancer is the second leading cancer that causes the death of American men. In this study, we  perform an integrative analysis of the whole-transcriptome of metastatic prostate cancer clinical samples. Specifically, we prepare our samples using an innovative protocol NuGEN, which captures the profile of the total RNA, rather than only the mRNA as the popular polyA selection protocol does. Unexpectedly high intronic expressions are observed including the gene AR (Androgen Receptor) and KLK3/PSA, a marker of prostate cancer. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 8 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE31nnn/GSE31528/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA145521
Series		Accession: GSE31528	ID: 200031528

4908. Adenovirus Small E1A Employs the Lysine Acetylases p300/CBP and Tumor Suppressor Rb to Repress Select Host Genes and Promote Productive Virus Infection
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.  Oncogenic transformation by adenovirus small e1a depends on simultaneous interactions with the host lysine acetylases p300/CBP and the tumor suppressor RB. How these interactions influence cellular gene expression remains unclear. We find that e1a displaces RBs from E2F transcription factors and promotes p300 acetylation of RB1 K873/K874 to lock it into a repressing conformation that interacts with repressive chromatin-modifying enzymes. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 31 Samples
FTP download: GEO (BED, BEDGRAPH, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59693/
Series		Accession: GSE59693	ID: 200059693

4909. Adenovirus Small E1A Employs the Lysine Acetylases p300/CBP and Tumor Suppressor Rb to Repress Select Host Genes and Promote Productive Virus Infection [RNA-seq]
(Submitter supplied) Oncogenic transformation by adenovirus small e1a depends on simultaneous interactions with the host lysine acetylases p300/CBP and the tumor suppressor RB. How these interactions influence cellular gene expression remains unclear. We find that e1a displaces RBs from E2F transcription factors and promotes p300 acetylation of RB1 K873/K874 to lock it into a repressing conformation that interacts with repressive chromatin-modifying enzymes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 11 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59688/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA256004
Series		Accession: GSE59688	ID: 200059688

4910. Suppression of the FOXM1 transcriptional program via novel small molecule inhibition
(Submitter supplied) The transcription factor FOXM1 binds to sequence-specific motifs on DNA (C/TAAACA) through its DNA binding domain (DBD), and activates proliferation- and differentiation-associated genes. Aberrant overexpression of FOXM1 is a key feature in oncogenesis and progression of many human cancers. Herein we identify novel inhibitors of FOXM1 that block DNA binding from a high-throughput screen applied to a library of 54,211 small molecules. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58626/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA253038
Series		Accession: GSE58626	ID: 200058626

4911. Transcriptomic characterization of Hepatocellular Carcinoma with CTNNB1 mutation
(Submitter supplied) we report transcritomic characterization of changes in CTNNB1 mutation positive HCCs in comparison to paratumoral tissues
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE55nnn/GSE55048/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA238330
Series		Accession: GSE55048	ID: 200055048

4912. Discovery of biomarkers predictive of GSI response in triple negative breast cancer and adenoid cystic carcinoma
(Submitter supplied) Next generation sequencing was used to identify Notch mutations in a large collection of diverse solid tumors. NOTCH1 and NOTCH2 rearrangements leading to constitutive receptor activation were confined to triple negative breast cancers (TNBC, 6 of 66 tumors). TNBC cell lines with NOTCH1 rearrangements associated with high levels of activated NOTCH1 (N1-ICD) were sensitive to the gamma-secretase inhibitor (GSI) MRK-003, both alone and in combination with pacitaxel, in vitro and in vivo, whereas cell lines with NOTCH2 rearrangements were resistant to GSI. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 27 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59810/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA256302
Series		Accession: GSE59810	ID: 200059810

4913. A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequence Quality Control consortium
(Submitter supplied) We present primary results from the Sequencing Quality Control (SEQC) project, coordinated by the United States Food and Drug Administration. Examining Illumina HiSeq, Life Technologies SOLiD and Roche 454 platforms at multiple laboratory sites using reference RNA samples with built-in controls, we assess RNA sequencing (RNA-seq) performance for sequence discovery and differential expression profiling and compare it to microarray and quantitative PCR (qPCR) data using complementary metrics. more...
Organism:	Homo sapiens; synthetic construct
Type:		Expression profiling by high throughput sequencing
5 related Platforms 3396 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE47nnn/GSE47774/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA208369
Series		Accession: GSE47774	ID: 200047774

4914. High resolution ChIP sequencing reveals novel bindings targets and prognostic role for SOX11 in Mantle cell lymphoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL9052 GPL11154 10 Samples
FTP download: GEO (BIGBED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE52nnn/GSE52149/
Series		Accession: GSE52149	ID: 200052149

4915. High resolution ChIP sequencing reveals novel bindings targets and prognostic role for SOX11 in Mantle cell lymphoma (RNA-Seq)
(Submitter supplied) SOX11 (Sex determining region Y-box 11) expression is specific for MCL as compared to other Non-Hodgkin’s lymphomas. However, the function and direct binding targets of SOX11 in MCL are largely unknown. We used high-resolution ChIP-Seq to identify the direct target genes of SOX11 in a genome-wide, unbiased manner and elucidate its functional significance. Pathway analysis identified WNT, PKA and TGF-beta signaling pathways as significantly enriched by SOX11 target genes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE52nnn/GSE52148/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA227025
Series		Accession: GSE52148	ID: 200052148

4916. UBL5 is essential for pre-mRNA splicing and sister chromatid cohesion in human cells
(Submitter supplied) UBL5 is an atypical ubiquitin-like protein, whose function in metazoans remains largely unexplored. We show that UBL5 is required for sister chromatid cohesion maintenance in human cells. UBL5 primarily associates with spliceosomal proteins, and UBL5 depletion decreases pre-mRNA splicing efficiency, leading to globally enhanced intron retention. Defective sister chromatid cohesion is a general consequence of dysfunctional pre-mRNA splicing, resulting from the selective downregulation of the cohesion protection factor Sororin. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 10 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59376/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA255215
Series		Accession: GSE59376	ID: 200059376

4917. RNA-sequencing analysis of glucose and acetate regulated transcripts in glioblastoma cells
(Submitter supplied) Our studies indicate that glucose and acetate can regulate histone acetylation by altering the acetyl-CoA concentrations in the cell. The purpose of this study was to to determine whether specific gene sets correlated with acetyl-CoA availability. We conclude that 10% of glucose-regulated genes are acetyl-CoA regulated genes (genes suppressed or induced by low glucose and reversed by acetate). Acetate usually regulated gene expression in the same direction as glucose, suggesting that acetyl-CoA is a key mediator of glucose-dependent gene expression.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57488/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA246544
Series		Accession: GSE57488	ID: 200057488

4918. A long noncoding RNA protects the heart from pathological hypertrophy
(Submitter supplied) The role of long noncoding RNA (lncRNA) in adult hearts is unknown; also unclear is how lncRNA modulates nucleosome remodelling. An estimated 70% of mouse genes undergo antisense transcription1, including myosin heavy chain 7 (Myh7), which encodes molecular motor proteins for heart contraction2. Here we identify a cluster of lncRNA transcripts from Myh7 loci and demonstrate a new lncRNA–chromatin mechanism for heart failure. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 2 Samples
FTP download: GEO (BW, FPKM_TRACKING, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE49nnn/GSE49716/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA214890
Series		Accession: GSE49716	ID: 200049716

4919. Modulation of the TNF-induced macrophage response by synovial fibroblasts
(Submitter supplied) Here we explored how the human macrophage response to tumor necrosis factor (TNF) is regulated by human synovial fibroblasts, the representative stromal cell type in the synovial lining of joints that become activated during inflammatory arthritis. Genome-wide transcriptome analysis (RNAseq) showed that co-cultured synovial fibroblasts modulate the expression of approximately one third of TNF-inducible genes in macrophages, including expression of target genes in pathways important for macrophage survival and polarization towards an alternatively activated phenotype. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57723/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA247937
Series		Accession: GSE57723	ID: 200057723

4920. TET1 regulates hypoxia-induced epithelial-mesenchymal transition through DNA demethylation
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL11154 8 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59990/
Series		Accession: GSE59990	ID: 200059990

4921. TET1 regulates hypoxia-induced epithelial-mesenchymal transition through DNA demethylation (RNA-Seq)
(Submitter supplied) In order to explore the status of DNA methylation in hypoxia response, we show that TET1, a DNA dioxygenase converting 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), regulates hypoxia-responsive gene expression. Hypoxia/HIF-2α regulates the expression of TET1. Knockdown of TET1 mitigated hypoxia-induced EMT. RNA sequencing and 5hmC sequencing identified the set of TET1-regulated genes.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59987/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA257213
Series		Accession: GSE59987	ID: 200059987

4922. Analysis of an artificial zinc finger epigenetic modulator: widespread binding but limited regulation
(Submitter supplied) Artificial transcription factors (ATFs) and genomic nucleases based on a DNA binding platform consist- ing of multiple zinc finger domains are currently be- ing developed for clinical applications. However, no genome-wide investigations into their binding speci- ficity have been performed. We have created six- finger ATFs to target two different 18 nt regions of the human SOX2 promoter; each ATF is constructed such that it contains or lacks a super KRAB do- main (SKD) that interacts with a complex contain- ing repressive histone methyltransferases. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 25 Samples
FTP download: GEO (BED, GFF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59980/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA257209
Series		Accession: GSE59980	ID: 200059980

4923. Gene expression changes as a result of E-cadherin loss in an isogenic non-malignant MCF10A and MCF10A CDH1-/- breast cells
(Submitter supplied) Background: E-cadherin is an adherens junction protein that forms homophilic intercellular contacts in epithelial cells while also interacting with the intracellular cytoskeletal networks. It has roles including establishment and maintenance of cell polarity, differentiation, migration and signalling in cell proliferation pathways. Its downregulation is commonly observed in epithelial tumours and is a hallmark of the epithelial to mesenchymal transition (EMT). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59317/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA255049
Series		Accession: GSE59317	ID: 200059317

4924. Widespread genetic epistasis among cancer genes.
(Submitter supplied) We performed NGS-based transcript profiling (RNA-seq) to profile transcripts that are expressed in MCF10A cells.  12,332 genes with FPKM>1 were considered as expressed in MCF10A cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 1 Sample
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58834/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA253627
Series		Accession: GSE58834	ID: 200058834

4925. NSD3-NUT Fusion Oncoprotein in NUT Midline Carcinoma identified in 1221 patient-derived cell line by RNA-seq
(Submitter supplied) Discarded live tumor tissue from a metastatic focus in the patient’s lung was collected under institutional review board approval through the NUT midline carcinoma registry (www.NMCRegistry.org). From this tissue the first known NUT-variant cell line, 1221, was established. To determine the putative partner gene to NUT, we performed comprehensive RNA-sequencing on RNA purified from 1221. We identified an in-frame transcript fusing the 5’ coding sequence of NSD3 (exons 1-7) to exons 2-7 of NUT. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 1 Sample
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57222/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA245923
Series		Accession: GSE57222	ID: 200057222

4926. Gene expression profiling associated with knockdown of LKB1 in human intrahepatic cholangiocarcinoma
(Submitter supplied) The experiment was designed to display differential gene expression profiling in three human intrahepatic cholangiocarcinoma (ICC) cells upon knockdow of LKB1 tumor suppressor, by using RNAseq technology.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59855/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA256469
Series		Accession: GSE59855	ID: 200059855

4927. RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer
(Submitter supplied) The translational control of oncoprotein expression is implicated in many cancers. Here we report an eIF4A/DDX2 RNA helicase-dependent mechanism of translational control that contributes to oncogenesis and underlies the anticancer effects of Silvestrol and related compounds. For example, eIF4A promotes T-ALL development in vivo and is required for leukaemia maintenance. Accordingly, inhibition of eIF4A with Silvestrol has powerful therapeutic effects in vitro and in vivo. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE56nnn/GSE56887/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA244865
Series		Accession: GSE56887	ID: 200056887

4928. Effect of TTF-1/NKX2-1 expression on TGF-beta induced gene expression in A549 lung cancer cell line.
(Submitter supplied) TTF-1/NKX2-1 was expressed by adenoviral vector and changes in gene expression were determined by RNA-sequencing.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE56nnn/GSE56356/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA243027
Series		Accession: GSE56356	ID: 200056356

4929. Role of TTF-1/NKX2-1, Smad3 and Smad4 on lung cancer cell lines
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL570 GPL10999 GPL17303 20 Samples
FTP download: GEO (BED, CEL, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE51nnn/GSE51510/
Series		Accession: GSE51510	ID: 200051510

4930. MRI-localized biopsies reveal subtype-specific differences in molecular and cellular composition at the margins of glioblastoma
(Submitter supplied) We obtained radiographically-localized biopsies during glioma resection surgeries to sample the tumor core and margins from multiple glioma patients. We also procured fresh, non-neoplastic brain tissue specimens from multiple patients having procedures to relieve epilespy symptoms or to place shunts to treat normal pressure hydrocephalus.  We then used RNA-Seq to compare expression patterns between geographically distinct regions of gliomas and computational deconvolution to estimate cell type-specific expression patterns in different disease subtypes.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 92 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59612/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA255754
Series		Accession: GSE59612	ID: 200059612

4931. Whole transcriptome sequencing in 274 glioma patients reveals gene fusion profiling and novel candidate fusion genes
(Submitter supplied) We detected fusion genes in 274 fresh surgical samples of gliomas using whole transcriptome sequencing. Using this approach we screened a panel of glioma samples and identified a number of activating novel fusion transcripts.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 274 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48865/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA212047
Series		Accession: GSE48865	ID: 200048865

4932. Identification of gene regulation patterns underlying both E2- and tamoxifen-stimulated cell growth through global gene expression profiling in breast cancer cells [MCF-7]
(Submitter supplied) A c-Src inhibitor blocks estrogen (E2)-induced stress and converts E2 responses from inducing apoptosis to growth stimulation in E2-deprived breast cancer cells. A reprogrammed cell line, MCF-7:PF, results with features of functional estrogen receptor (ER) and over-expression of insulin-like growth factor-1 receptor beta (IGF-1Rβ). We addressed the question of whether the selective ER modulator 4-hydroxytamoxifen (4-OHT) could target ER to prevent E2-stimulated growth in MCF-7:PF cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59536/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA255514
Series		Accession: GSE59536	ID: 200059536

4933. c-Src Modulates Estrogen-Induced Stress and Apoptosis in Estrogen-Deprived Breast Cancer Cells [MCF-7:5C]
(Submitter supplied) The emergence of anti-estrogen resistance in breast cancer is an important clinical phenomenon affecting long-term survival in this disease. Identifying factors that convey cell survival in this setting may guide improvements in treatment. Estrogen (E2) can induce apoptosis in breast cancer cells that have been selected for survival after E2 deprivation for long periods (MCF-7:5C cells), but the mechanisms underlying E2-induced stress in this setting have not been elucidated. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59535/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA255515
Series		Accession: GSE59535	ID: 200059535

4934. Derivation of endothelial colony forming cells from human pluripotent stem cells
(Submitter supplied) Human induced pluripotent stem (hiPS) cells and human embryonic stem (hES) cells differentiate into cells of the endothelial lineage, but derivation of cells with human umbilical cord blood endothelial colony forming cell (ECFC)-like properties has not been reported. Here we describe a novel serum- and stromal cell-free ECFC differentiation protocol for the derivation of clinically relevant numbers of ECFCs (> 108) from hiPS and hES cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 5 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE49nnn/GSE49074/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA212913
Series		Accession: GSE49074	ID: 200049074

4935. Metastasis-suppressor transcript destabilization through TARBP2 binding of mRNA hairpins
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing; Expression profiling by array
Platforms: GPL10558 GPL6885 GPL11154 78 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE49nnn/GSE49649/
Series		Accession: GSE49649	ID: 200049649

4936. RNA-Seq of ex vivo culture of circulating breast tumor cells
(Submitter supplied) Analyses of circulating tumor cells (CTC) cultured from blood of patients with cancer may allow individualized testing for susceptibility to therapeutic regimens.  We established ex vivo cultures of CTCs from six patients with metastatic estrogen receptor-positive breast cancer and performed RNA-Seq on those cultures.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16288 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE55nnn/GSE55807/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA241032
Series		Accession: GSE55807	ID: 200055807

4937. Circulating Tumor Cell Clusters are Oligoclonal Precursors of Breast Cancer Metastasis
(Submitter supplied) Clusters of circulating tumor cells (CTC-clusters) are present in the blood of patients with cancer but their contribution to metastasis is not well defined. Here, we first use mouse models to demonstrate that breast cancer cells injected intravascularly as clusters are more prone to survive and colonize the lungs than single cells. Primary mammary tumors comprised of tagged cells give rise to oligoclonal CTC-clusters, with 50-fold increased metastatic potential, compared with single CTCs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16288 29 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE51nnn/GSE51827/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA225522
Series		Accession: GSE51827	ID: 200051827

4938. Genome-wide transcriptome analysis of the dietary chemopreventive phytochemical sulforaphane on normal and prostate cancer cells.
(Submitter supplied) Epidemiological studies provide strong evidence that consumption of cruciferous vegetables, such as broccoli, can significantly reduce the risk of developing cancers. Sulforaphane (SFN), a phytochemical derived from cruciferous vegetables, induces anti-proliferative and pro-apoptotic responses in prostate cancer cells, but not in normal prostate cells. The mechanisms responsible for these specific chemopreventive properties remain unclear. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 36 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48812/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA211827
Series		Accession: GSE48812	ID: 200048812

4939. RNA-sequencing experiment: Treatment of MCF-7 breast cancer cells with the novel small molecule ZNA
(Submitter supplied) MCF-7 cells were treated with either ZNA (30 uM) or a vehice control for 3 or 12 hours.  Following RNA sequencing, the control-normalized data was used to analyze genes altered by ZNA treatment. Following RNA sequencing, the control-normalized data was used to analyze genes altered by ZNA treatment.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59251/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA254807
Series		Accession: GSE59251	ID: 200059251

4940. Bromodomain protein BRD4 is required for estrogen receptor-dependent transcription and enhancer activation
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL16791 GPL11154 38 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE55nnn/GSE55923/
Series		Accession: GSE55923	ID: 200055923

4941. Bromodomain protein BRD4 is required for estrogen receptor-dependent transcription and enhancer activation [RNA-Seq]
(Submitter supplied) The estrogen receptor-α (ERα) is a transcription factor which plays a critical role in controlling cell proliferation and tumorigenesis by recruiting various cofactors to estrogen response elements (EREs) to induce or repress gene transcription. A deeper understanding of these transcriptional mechanisms may uncover novel therapeutic targets for ERα-dependent cancers. Here we show for the first time that BRD4 regulates ERα−induced gene expression by affecting elongation-associated phosphorylation of RNA Polymerase II (RNAPII P-Ser2) and histone H2B monoubiquitination (H2Bub1). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE55nnn/GSE55922/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA241317
Series		Accession: GSE55922	ID: 200055922

4942. Activation and repression by oncogenic Myc shapes tumour-specific gene expression profiles
(Submitter supplied) In mammalian cells, the Myc oncoprotein binds to thousands of promoters. During mitogenic stimulation of primary lymphocytes, Myc promotes an increase in expression of virtually all genes. In contrast, Myc-driven tumour cells differ from normal cells in expression of specific sets of up- and downregulated genes that have significant prognostic value. To understand this discrepancy, we studied the consequences of inducible expression and depletion of Myc in human cells and murine tumour models. more...
Organism:	Mus musculus; Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL10999 GPL11002 66 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE44nnn/GSE44672/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA190879
Series		Accession: GSE44672	ID: 200044672

4943. RNA-seq analysis of vorinostat-resistant HCT116 cells following gene knockdown of potential vorinostat-resistance candidate genes
(Submitter supplied) Potential vorinostat-resistance candidate genes were identified using RNA interference screening in vorinostat-resistant HCT116 cells (HCT116-VR) using a synthetic lethal approach.  In order to understand the mechanisms by which these genes contributed to vorinostat response, transcriptomic analysis was conducted on HCT116-VR cells and those with siRNA-mediated knockdown of each of the vorinostat resistance candidate genes.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 45 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE56nnn/GSE56788/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA244587
Series		Accession: GSE56788	ID: 200056788

4944. Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis
(Submitter supplied) The c-myc proto-oncogene product, Myc, is a transcription factor that binds thousands of genomic loci. Recent work suggested that rather than up- and down-regulating selected groups of genes, Myc targets all active promoters and enhancers in the genome (a phenomenon termed "invasion") and acts as a general amplifier of transcription. However, the available data did not readily discriminate between direct and indirect effects of Myc on RNA biogenesis. more...
Organism:	Homo sapiens; Mus musculus
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL9250 GPL13112 94 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE51nnn/GSE51011/
Series		Accession: GSE51011	ID: 200051011

4945. SUMOylation modulates the transcriptional activity of androgen receptor in a target gene and pathway selective manner.
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL6947 GPL11154 GPL10558 38 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE54nnn/GSE54202/
Series		Accession: GSE54202	ID: 200054202

4946. Profiling premalignant lesions in lung squamous cell carcinomas identifies mechanisms involved in stepwise carcinogenesis
(Submitter supplied) Lung squamous cell carcinoma (SCC) is thought to arise from premalignant lesions in the airway epithelium, therefore studying these lesions is critical for understanding lung carcinogenesis. We performed RNA sequencing on laser-microdissected representative cell populations along the SCC pathological continuum of patient-matched normal basal cells, premalignant lesions, and tumor cells. We discovered transcriptomic changes and identified genomic pathways altered with initiation and progression of SCC within individual patients. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL10999 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE49nnn/GSE49155/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA213155
Series		Accession: GSE49155	ID: 200049155

4947. Chromosome as oncogenic organizer: functional consequences of structural mutations in breast cancer (RNA-Seq)
(Submitter supplied) Chromosomal structural mutations play an important role in determining the transcriptional landscape of human breast cancers. To assess the nature of these structural mutations, we analyzed a representative sampling of the major types of breast tumor samples for detailed structural mutations using paired-end tag sequencing of long-insert genomic DNA (DNA-PET) with matched transcriptome ascertainment by RNA-seq. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL13393 GPL18723 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57914/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA248408
Series		Accession: GSE57914	ID: 200057914

4948. "Drug-seq": An Approach to Identify the Genomic Targets of Chemicals Identified by Functional Phenotypic Screens
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE55nnn/GSE55904/
Series		Accession: GSE55904	ID: 200055904

4949. "Drug-seq": An Approach to Identify the Genomic Targets of Chemicals Identified by Functional Phenotypic Screens [GRO-seq]
(Submitter supplied) Here we report an approach that has permitted us to uncover the sites and mechanisms of action of a drug, referred to as SD70, initially identified by phenotypic screening for inhibitors of ligand and genotoxic stress-induced translocations in prostate cancer cells. Based on synthesis of a derivatized form of SD70 that permits its application for a ChIP-seq-like approach, referred to as Drug-seq, we were next able to efficiently map the genome-wide binding locations of this small molecule, revealing that it largely co-localized with androgen receptor (AR) on regulatory enhancers. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE55nnn/GSE55903/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA241279
Series		Accession: GSE55903	ID: 200055903

4950. Promoter methylome and integrative transcriptome profiling identify key epigenetics-regulated genes in human HCCs
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL9052 32 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE55nnn/GSE55759/
Series		Accession: GSE55759	ID: 200055759

4951. Promoter methylome and integrative transcriptome profiling identify key epigenetics-regulated genes in human HCCs [expression]
(Submitter supplied) Hepatocellular carcinoma (HCC) is one of the most common and lethal cancers worldwide and has a poor prognosis. Promoters represent an essential regulatory element of gene transcription in human genome. In order to understand the promoter methylation in relation with gene transcription in HCCs, We applied a liquid hybridization capture-based bisulfite sequencing (LHC-BS) approach to examine the promoter methylome of HCCs, for which we customized 150,407 capture probes and enabled coverage of 91.8% of the RefSeq gene promoters within human genome. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE55nnn/GSE55758/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA240900
Series		Accession: GSE55758	ID: 200055758

4952. An atlas of TNF-α-responsive promoters and enhancers in the intestinal epithelial cell model Caco-2
(Submitter supplied) Sequencing of 5'ends of RNA molecules from Caco-2 cells +/- TNFa stimulation
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE54nnn/GSE54074/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA234528
Series		Accession: GSE54074	ID: 200054074

4953. Direct ChIP-bisulfite sequencing reveals a role of H3K27me3 mediating aberrant hypermethylation of promoter CpG islands in cancer cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform: GPL11154 16 Samples
FTP download: GEO (BED, TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE43nnn/GSE43096/
Series		Accession: GSE43096	ID: 200043096

4954. Direct ChIP-bisulfite sequencing reveals a role of H3K27me3 mediating aberrant hypermethylation of promoter CpG islands in cancer cells (RNA-seq)
(Submitter supplied) Aberrant DNA hypermethylation of CpG island (CGI) promoters are associated with transcriptional repression of many tumor suppressor genes and lead to tumor progression in many cancers. Most recently, one research group observed that aberrantly hypermethylated genes in multiple cancers are already repressed, but their promoters are maintained in a hypomethylated state in pre-cancerous tissues.Their studies didn't provide a clue to explain by what mechanisms those genes were repressed in pre-cancerous tissues. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 3 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE43nnn/GSE43093/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA184402
Series		Accession: GSE43093	ID: 200043093

4955. c-Jun promotes cell migration and drives expression of the motility factor ENPP2 in soft tissue sarcomas
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL5175 GPL11154 22 Samples
FTP download: GEO (CEL, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57531/
Series		Accession: GSE57531	ID: 200057531

4956. c-Jun promotes cell migration and drives expression of the motility factor ENPP2 in soft tissue sarcomas [RNA-Seq]
(Submitter supplied) We assayed the effect of c-Jun overexpression on gene expression in the three DDLPS cell lines using RNA-Seq (Illumina).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57530/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA246600
Series		Accession: GSE57530	ID: 200057530

4957. Gene expression profiling of breast cancer cells with knockdown of PTEN
(Submitter supplied) Activation of the PI3K pathway in estrogen receptor α (ER)-positive (+) breast cancer is associated with reduced ER expression and activity, luminal B subtype, and poor outcome.  PTEN is a negative regulator of the PI3K pathway typically lost in ER-negative (-) breast cancer.  To clarify the effect of PTEN down-regulation on the response of ER+/HER2- breast cancer to endocrine therapy, we established reduced PTEN cell models using inducible knockdown. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 2 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53300/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA231626
Series		Accession: GSE53300	ID: 200053300

4958. Expression of three hepatocellular carcinoma cell lines with different organ-tropism
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE39nnn/GSE39053/
Series		Accession: GSE39053	ID: 200039053

4959. Gene expression of three hepatocellular carcinoma cell lines with different organ-tropism.
(Submitter supplied) In this study we investigated the gene expression profiling in three HCC cell lines with different organ-tropism.The parent cell line has low metastasis ability in nude mice model. Subclone 1 has higher metastasis ability specific to lung, and subclone 2 has dual metastasis ability to lung and celiac lymph node. We aimed to explore differentially expressed genes involved in process of HCC metastasis and organ-specific metastasis, and identify their biological functions.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE38nnn/GSE38945/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA169359
Series		Accession: GSE38945	ID: 200038945

4960. A specific missense mutation in GTF2I occurs at high frequency in thymic epithelial tumors
(Submitter supplied) Next generation sequencing of 28 thymic epithelial tumors (TETs) revealed a high frequency of GTF2I missense mutation (chr7:74146970T/A) in A thymomas, a  relatively indolent subtype. The GTF2I mutation was confirmed in 82% of A and 74% of AB thymomas in a series of 274 TETs but was rare in aggressive subtypes, where recurrent mutations of known cancer genes were identified. Therefore, GTF2I mutation correlated with a better survival. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL9115 GPL11154 25 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57892/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA248372
Series		Accession: GSE57892	ID: 200057892

4961. RNA-seq analysis reveals endogenous aryl hydrocarbon receptor regulation is highly associated with eicosanoid synthesis and tumor necrosis factor activity in MCF-7 cancer cells
(Submitter supplied) Background: The Aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that is activated by xenobiotic chemicals that function as AHR ligands.  The response to xenobiotic AHR ligands is toxicity and the induction of drug metabolizing enzymes. The impact of AHR knockdown on gene expression and pathways in human breast cancer cells in absence of xenobiotic AHR ligands has not been investigated on a genome-wide scale. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 11 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE52nnn/GSE52036/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA226275
Series		Accession: GSE52036	ID: 200052036

4962. Inducible PAX5 expression in a human B lymphoblastic leukemia cell line
(Submitter supplied) Hypomorphic mutations of the transcription factor PAX5 occur in one third of B-progenitor acute lymphoblastic leukemias (B-ALLs). To identify PAX5-regulated genes in B-ALL, here we employ inducible expression of PAX5 in a human B-ALL cell line (REH) that harbors a loss-of-function mutation in PAX5. In this model, inducing PAX5 expression is associated with competitive disadvantage.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57480/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA246532
Series		Accession: GSE57480	ID: 200057480

4963. SEQC Project
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Rattus norvegicus; synthetic construct
Type:		Expression profiling by array; Expression profiling by high throughput sequencing
15 related Platforms 4521 Samples
FTP download: GEO (CEL, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE47nnn/GSE47792/
Series		Accession: GSE47792	ID: 200047792

4964. Gene expression and genome-wide location analysis of breast cancer cell-lines
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Methylation profiling by genome tiling array
Platforms: GPL13534 GPL11154 41 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE46nnn/GSE46073/
Series		Accession: GSE46073	ID: 200046073

4965. Gene expression analysis of breast cancer cell-lines
(Submitter supplied) Recurrent mutations in histone modifying enzymes in multiple cancer types imply key roles in tumorigenesis. However, the functional relevance of these mutations remains unknown. Here we show that the JARID1B histone H3 lysine 4 demethylase is frequently amplified and overexpressed in luminal breast tumors and a somatic point mutation of JARID1B leads to the gain of luminal-specific gene expression programs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE45nnn/GSE45732/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA197199
Series		Accession: GSE45732	ID: 200045732

4966. Global analysis of ZNF217 chromatin occupancy in the breast cancer cell genome reveals an association with Eralpha
(Submitter supplied) Background: The ZNF217 gene, encoding a C2H2 zinc finger protein, is located at 20q13 and found amplified and overexpressed in greater than 20% of breast tumors. Current studies indicate ZNF217 drives tumorigenesis, yet the regulatory mechanisms of ZNF217 are largely unknown. Because ZNF217 associates with chromatin modifying enzymes, we postulate that ZNF217 functions to regulate specific gene signaling networks. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58326/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA251998
Series		Accession: GSE58326	ID: 200058326

4967. Rapid isolation of extracellular vesicles from cell culture and biological fluids using a synthetic peptide with specific affinity for heat shock proteins
(Submitter supplied) Background: Exosomes and extracellular vesicles (EVs) are increasingly recognized as important sources of biomarkers for disease study and diagnosis. Results: A synthetic peptide, Vn96, allows for capture of EVs from biological fluids using basic laboratory equipment. Conclusion: The Vn96-captured EVs are qualitatively equivalent or superior to exosomes isolated by ultracentrifugation. Significance: The Vn96 peptide provides an effective affinity-capture method for the isolation of EVs from biological fluids.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 5 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58464/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA252722
Series		Accession: GSE58464	ID: 200058464

4968. Single cell RNA-seq of primary human glioblastomas
(Submitter supplied) We report transcriptomes from 430 single glioblastoma cells isolated from 5 individual tumors and 102 single cells from gliomasphere cells lines generated using SMART-seq. In addition, we report population RNA-seq from the five tumors as well as RNA-seq from cell lines derived from 3 tumors (MGH26, MGH28, MGH31) cultured under serum free (GSC) and differentiated (DGC) conditions. This dataset highlights intratumoral heterogeneity with regards to the expression of de novo derived transcriptional modules and established subtype classifiers.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 875 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57872/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA248302
Series		Accession: GSE57872	ID: 200057872

4969. The identification of RBM47 binding sites and RBM47-dependent alternative splicing events in brain metastatic breast cancer cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL11154 8 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58381/
Series		Accession: GSE58381	ID: 200058381

4970. Identification of alternatively spliced transcripts in brain metastatic derivatives of MDA-MB-231 breast cancer cells in response to RBM47 expression
(Submitter supplied) Changes in alternative splicing in breast cancer cells expressing control, empty vector or Flag-tagged wild type RBM47 were analyzed using paired-end, 100bp RNAseq. Related data published together with these data are found in GSE53779
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58379/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA252383
Series		Accession: GSE58379	ID: 200058379

4971. Breast Cancer RNA-seq
(Submitter supplied) RNA-seq was performed on breast cancer cell lines and primary tumors
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 168 Samples
FTP download: GEO (BEDPE, FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58135/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA251383
Series		Accession: GSE58135	ID: 200058135

4972. The RNA-binding protein RBM47 suppresses metastatic breast cancer progression
(Submitter supplied) Through integrative analysis of clinical breast cancer gene expression datasets, cell line models of breast cancer progression, and mutation data from cancer genome resequencing studies, we have identified RNA binding motif protein 47 (RBM47) as a candidate suppressor of breast cancer metastasis. RBM47 inhibited breast cancer progression in experimental models. Transcriptome-wide analysis of RBM47 localization by HITS-CLIP revealed widespread binding to mRNAs, preferentially at the 3' UTRs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53779/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA232857
Series		Accession: GSE53779	ID: 200053779

4973. miRNA profiling of pediatric T cell lymphoblastic lymphoma
(Submitter supplied) miRNA profiling has been performed on primary tumor samples collected at diagnosis from pediatric patients affected by T-cell lymphoblastic lymphoma.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL8227 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE55nnn/GSE55846/
Series		Accession: GSE55846	ID: 200055846

4974. Transcriptomic profiling reveals new aspects of progestin signaling in breast cancer
(Submitter supplied) We have identified differentially PR-regulated genes in T47D cells and mapped PR-binding sites by using next generation sequencing
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL9052 4 Samples
FTP download: GEO (TAB, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE51nnn/GSE51428/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA223155
Series		Accession: GSE51428	ID: 200051428

4975. Cell-type restricted activity of hnRNPM promotes breast cancer metastasis via regulating alternative splicing
(Submitter supplied) Tumor metastasis remains the major cause of cancer-related death, but its molecular basis is still not well understood. Here we uncovered a splicing-mediated pathway that is essential for breast cancer metastasis. We show that the RNA-binding protein hnRNPM promotes breast cancer metastasis by activating the switch of alternative splicing that occurs during epithelial-mesenchymal transition (EMT). Genome-wide deep sequencing analysis suggests that hnRNPM potentiates TGFb signaling and identifies CD44 as a key downstream target of hnRNPM. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57243/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA247397
Series		Accession: GSE57243	ID: 200057243

4976. Targeting c-MYC by antagonizing PP2A inhibitors in breast cancer
(Submitter supplied) Inhibition of SET by siRNA or SET antagonist and CIP2A by siRNA can downregulate c-MYC and c-MYC target genes.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 5 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58008/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA248685
Series		Accession: GSE58008	ID: 200058008

4977. A novel post-translational mechanism controlling the oncogenic activity of c-Myc is enhanced in poor outcome breast cancer
(Submitter supplied) Examination of Pin1-regulated Myc target genes in a human breast epithelial cell line.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 2 Samples
FTP download: GEO (BOWTIE) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE33nnn/GSE33776/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA148595
Series		Accession: GSE33776	ID: 200033776

4978. Discovery of the p53 targetome in MCF7 cells from RNA-seq and ChIP-seq data
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 7 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE47nnn/GSE47043/
Series		Accession: GSE47043	ID: 200047043

4979. Discovery of the p53 targetome in MCF7 cells from RNA-seq data
(Submitter supplied) RNA-seq and ChIP-seq on MCF-7 breast cancer cell line upon activation of p53 by the non-genotoxic small molecule Nutlin-3a
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE47nnn/GSE47042/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA203359
Series		Accession: GSE47042	ID: 200047042

4980. Hepatosplenic T cell lymphoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing; Genome variation profiling by SNP array; Genome variation profiling by genome tiling array
4 related Platforms 24 Samples
FTP download: GEO (CEL, CYCHP, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57944/
Series		Accession: GSE57944	ID: 200057944

4981. Myelodysplastic syndromes are propagated by rare and distinct human cancer stem cells in vivo
(Submitter supplied) Gene expression analysis of purified hematopoietic stem and progenitor cells isolated from low to intermediate risk MDS patients and age-matched normal healthy controls.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 73 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE55nnn/GSE55689/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA240555
Series		Accession: GSE55689	ID: 200055689

4982. Regulation of FAS Exon Definition and Apoptosis by the Ewing Sarcoma Protein
(Submitter supplied) The Ewing’s sarcoma protein EWS belongs to the TET family (FUS/TLS, EWS, TAF15) of RNA and DNA binding proteins, implicated in DNA transcription, pre-mRNA splicing and maintenance of genomic integrity. Translocations of these genes are characteristic of particular neoplasias, including Ewing’s sarcoma. To identify physiological RNA targets of EWS, we performed in vivo cross-linking and immunoprecipitation followed by high-throughput RNA sequencing (HITS-CLIP/CLIP-Seq) in HeLa cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 3 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48065/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA208844
Series		Accession: GSE48065	ID: 200048065

4983. A Large-Scale RNAi-Based Mouse Tumorigenesis Screen Identifies    New Lung Cancer Tumor Suppressors that Repress FGFR Signaling
(Submitter supplied) We sequenced mRNA from SA cells with SFRS9 knocking down or    non-silencing control.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE47nnn/GSE47095/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA203548
Series		Accession: GSE47095	ID: 200047095

4984. TET1-mediated hydroxymethylation facilitates hypoxic gene induction in neuroblastoma
(Submitter supplied) Analysis of 5-hydroxymethylcytosine changes in hypoxia in neuroblastoma cells
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Other
Platform: GPL16791 14 Samples
FTP download: GEO (TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE55nnn/GSE55391/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA239458
Series		Accession: GSE55391	ID: 200055391

4985. CFIm25 links alternative polyadenylation to glioblastoma tumour suppression
(Submitter supplied) Purpose: To identify all of the APA targets of CFIm25 on a global scale and develop an algorithm that can idenitify APA events from standard RNA-seq data  Methods: RNA from HeLa cells treated with control siRNA and CFIm25 siRNA were subject to RNA-Seq. Using a custom-designed algorithm to mine RNA-seq data for novel APA events regulated by CFIm25.  Results: We identified over 1,400 genes with shortened 3’UTRs after CFIm25 knockdown. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE42nnn/GSE42420/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA182153
Series		Accession: GSE42420	ID: 200042420

4986. The ABRF Next-Generation Sequencing Study (ABRF-NGS): Multi-platform and cross-methodological reproducibility of transcriptome profiling by RNA-seq [Illumina HiSeq 2500]
(Submitter supplied) Next-generation sequencing (NGS) technology applications like RNA-sequencing (RNA-seq) have dramatically expanded the potential for novel genomics discoveries, but the proliferation of various platforms and protocols for RNA-seq has created a need for reference data sets to help gauge the performance characteristics of these disparate methods.  Here we describe the results of the ABRF-NGS Study on RNA-seq, which leverages replicate experiments across multiple sites using two reference RNA standards tested with four protocols (polyA selected, ribo-depleted, size selected, and degraded RNA), and examined across five NGS platforms (Illumina’s HiSeqs, Life Technologies’ Personal Genome Machine and Proton, Roche 454 GS FLX, and Pacific Biosciences RS). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 62 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48035/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA208732
Series		Accession: GSE48035	ID: 200048035

4987. The ABRF Next-Generation Sequencing Study (ABRF-NGS): Multi-platform and cross-methodological reproducibility of transcriptome profiling by RNA-seq [Ion Torrent Proton]
(Submitter supplied) Next-generation sequencing (NGS) technology applications like RNA-sequencing (RNA-seq) have dramatically expanded the potential for novel genomics discoveries, but the proliferation of various platforms and protocols for RNA-seq has created a need for reference data sets to help gauge the performance characteristics of these disparate methods.  Here we describe the results of the ABRF-NGS Study on RNA-seq, which leverages replicate experiments across multiple sites using two reference RNA standards tested with four protocols (polyA selected, ribo-depleted, size selected, and degraded RNA), and examined across five NGS platforms (Illumina’s HiSeqs, Life Technologies’ Personal Genome Machine and Proton, Roche 454 GS FLX, and Pacific Biosciences RS). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48034/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA208733
Series		Accession: GSE48034	ID: 200048034

4988. The ABRF Next-Generation Sequencing Study (ABRF-NGS): Multi-platform and cross-methodological reproducibility of transcriptome profiling by RNA-seq [Ion Torrent PGM]
(Submitter supplied) Next-generation sequencing (NGS) technology applications like RNA-sequencing (RNA-seq) have dramatically expanded the potential for novel genomics discoveries, but the proliferation of various platforms and protocols for RNA-seq has created a need for reference data sets to help gauge the performance characteristics of these disparate methods.  Here we describe the results of the ABRF-NGS Study on RNA-seq, which leverages replicate experiments across multiple sites using two reference RNA standards tested with four protocols (polyA selected, ribo-depleted, size selected, and degraded RNA), and examined across five NGS platforms (Illumina’s HiSeqs, Life Technologies’ Personal Genome Machine and Proton, Roche 454 GS FLX, and Pacific Biosciences RS). more...
Organism:	synthetic construct; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL17301 GPL17302 21 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48033/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA208735
Series		Accession: GSE48033	ID: 200048033

4989. The ABRF Next-Generation Sequencing Study (ABRF-NGS): Multi-platform and cross-methodological reproducibility of transcriptome profiling by RNA-seq [454 GS FLX Titanium]
(Submitter supplied) Next-generation sequencing (NGS) technology applications like RNA-sequencing (RNA-seq) have dramatically expanded the potential for novel genomics discoveries, but the proliferation of various platforms and protocols for RNA-seq has created a need for reference data sets to help gauge the performance characteristics of these disparate methods.  Here we describe the results of the ABRF-NGS Study on RNA-seq, which leverages replicate experiments across multiple sites using two reference RNA standards tested with four protocols (polyA selected, ribo-depleted, size selected, and degraded RNA), and examined across five NGS platforms (Illumina’s HiSeqs, Life Technologies’ Personal Genome Machine and Proton, Roche 454 GS FLX, and Pacific Biosciences RS). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL14603 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48032/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA208734
Series		Accession: GSE48032	ID: 200048032

4990. The ABRF Next-Generation Sequencing Study (ABRF-NGS): Multi-platform and cross-methodological reproducibility of transcriptome profiling by RNA-seq.
(Submitter supplied) Next-generation sequencing (NGS) technology applications like RNA-sequencing (RNA-seq) have dramatically expanded the potential for novel genomics discoveries, but the proliferation of various platforms and protocols for RNA-seq has created a need for reference data sets to help gauge the performance characteristics of these disparate methods.  Here we describe the results of the ABRF-NGS Study on RNA-seq, which leverages replicate experiments across multiple sites using two reference RNA standards tested with four protocols (polyA selected, ribo-depleted, size selected, and degraded RNA), and examined across five NGS platforms (Illumina’s HiSeqs, Life Technologies’ Personal Genome Machine and Proton, Roche 454 GS FLX, and Pacific Biosciences RS). more...
Organism:	Homo sapiens; synthetic construct
Type:		Expression profiling by high throughput sequencing
5 related Platforms 105 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE46nnn/GSE46876/
Series		Accession: GSE46876	ID: 200046876

4991. Differential gene expression by suppression of either SOX2 or TP63 in KYSE70 human esophageal squamous carcinoma cell line.
(Submitter supplied) SOX2 is a transcription factor essential for pluripotent stem cells, and development and maintenance of squamous epithelium. We previously reported SOX2 an oncogene subject to highly recurrent genomic amplification in squamous cell carcinomas (SCCs)1.  Here we demonstrate in SCCs that SOX2 interacts with another master squamous transcription factor p63, and through ChIP-seq show that genomic occupancy of SOX2 overlaps with that of p63 at a large number of loci and that they cooperatively regulate gene expression including ETV4, which we find essential for SOX2-amplified SCC cell survival. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE47nnn/GSE47058/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA203388
Series		Accession: GSE47058	ID: 200047058

4992. Global assessment of Antrodia cinnamomea induced microRNA and mRNA transcriptomic alterations in hepatocarcinoma cells
(Submitter supplied) Antrodia cinnamomea (Ac), a traditional medicine and an endemic fungus in Taiwan, has been used in cancer research. Recent research has revealed decreased cell proliferation after treatment of Ac on tumor. In this study, we profiled the 2 hours and 4 hours genome-wide miRNA and mRNA transcriptome by next-generation sequencing techniques to report the early apoptotic effect on Ac fruiting body extract treated human hepatocarcinoma cells, SK-HEP-1, instead of prolonged treatment. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms: GPL9442 GPL15907 GPL16288 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48327/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA209709
Series		Accession: GSE48327	ID: 200048327

4993. 4sUDRB-seq: measuring transcription elongation and initiation genomewide
(Submitter supplied) A new method to measure elongation and intitiation rates
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 14 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57116/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA245468
Series		Accession: GSE57116	ID: 200057116

4994. Developmental transcriptome analysis of human erythropoiesis
(Submitter supplied) We profiled the dynamic, comprehensive transcriptome during human erythroid differentiation in vitro. The erythroid cells at day 4, 8, 11 and 14 differentiation stages were harvested and sequenced by Illumia 72 bp paired-end sequencing format, respectively.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE54nnn/GSE54602/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA237119
Series		Accession: GSE54602	ID: 200054602

4995. A shared transcriptional program in early breast neoplasias despite genetic and clinical distinctions
(Submitter supplied) The earliest recognizable stages of breast neoplasia are lesions that represent a heterogeneous collection of epithelial proliferations currently classified based on morphology. Their role in the development of breast cancer is not well understood but insight into the critical events at this early stage will improve efforts in breast cancer detection and prevention. These microscopic lesions are technically difficult to study so very little is known about their molecular alterations. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL10999 72 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE47nnn/GSE47462/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA205694
Series		Accession: GSE47462	ID: 200047462

4996. RUNX3 Facilitates Growth of Ewing Sarcoma Cells
(Submitter supplied) Ewing sarcoma is an aggressive pediatric small round cell tumor that predominantly occurs in bone.  Approximately 85% of Ewing sarcomas harbor the EWS/FLI fusion protein, which arises from a chromosomal translocation, t(11:22)(q24:q12). EWS/FLI interacts with numerous lineage-essential transcription factors to maintain mesenchymal progenitors in an undifferentiated state. We previously showed that EWS/FLI binds the osteogenic transcription factor RUNX2 and prevents osteoblast differentiation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE56nnn/GSE56900/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA244882
Series		Accession: GSE56900	ID: 200056900

4997. Human intestinal tissue with adult stem cell properties derived from pluripotent stem cells
(Submitter supplied) Genetically engineered human pluripotent stem cells (hPSCs) have been proposed as a source for transplantation therapies and are rapidly becoming valuable tools for human disease modeling. However, many of the potential applications are still limited by the lack of robust differentiation paradigms that allow for the isolation of defined functional tissues. These challenges could be overcome by the use of adult tissue stem cells derived from hPSCs, as their restricted potential could limit the differentiation towards other undesired linages, and allow in vitro expansion and long- term propagation of fully differentiated tissue. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE56nnn/GSE56930/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA245172
Series		Accession: GSE56930	ID: 200056930

4998. Toxic effects of BDE209 in human embryonic kidney 293 cells (HEK 293)
(Submitter supplied) PBDEs are widely used in consumer and household products as flame retardants. Many studies have shown that PBDEs could disrupt thyroid hormone homeostasis and adversely affect brain development. Here, we explored the toxical effects of BDE209 on HEK 293 cells and found that BDE209 may have a role in nucleosome remodeling. Many gene sets involved in cancer are enriched at the BDE209-treated sample. This indicates the carcinogenicity of BDE209. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE56nnn/GSE56361/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA243130
Series		Accession: GSE56361	ID: 200056361

4999. Genome-wide transcriptome profiling of SK-Mel-28, UACC-62 and HCT-116 cells stably expressing scrambled shRNA and RAB7 shRNA
(Submitter supplied) Purpose: Asess the transcritpional changes induced upon RAB7 knock-down in melanoma (SK-Mel-28 and UACC-62) and in colon cancer (HCT-116) cell lines. Methods: mRNA profiles of tumor cell lines (SK-Mel-28, UACC-62, HCT-116) stably expressing scrambled shRNA or RAB7 shRNA (harvested at day 3 after lentiviral infection) were generated by deep sequencing, using three biological replicates per condition. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE42nnn/GSE42735/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA182963
Series		Accession: GSE42735	ID: 200042735

5000. Novel PAX3-MAML3 Fusion in Biphenotypic Sinonasal Sarcoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL14951 42 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE52nnn/GSE52323/
Series		Accession: GSE52323	ID: 200052323

5001. Whole transcriptome analysis of sinonasal sarcoma with translocation t(2;4)(q37.1;q31.3)
(Submitter supplied) Conventioal cytogenetic on 2 sinonasal sarcoma (SNS) cases showed t(2;4)(q37.1;q31.3) translocation previously. The aim of this whole transcriptome analysis is to determine potential candidate genes involved in this translocation.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 1 Sample
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE52nnn/GSE52257/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA227288
Series		Accession: GSE52257	ID: 200052257

5002. Recurrent activating mutation in PRKACA in cortisol-producing adrenal tumors
(Submitter supplied) We performed mRNA-seq of a PRKACA-mutant adrenal tumor and demonstrated that the mutation is expressed at the mRNA level.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 1 Sample
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE56nnn/GSE56016/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA242227
Series		Accession: GSE56016	ID: 200056016

5003. Reconstructing and reprogramming the tumor propagating potential of glioblastoma stem-like cells: RNA-seq
(Submitter supplied) Developmental fate decisions are dictated by master transcription factors (TFs) that interact with cis-regulatory elements to direct transcriptional programs. Certain malignant tumors may also depend on a cellular hierarchy reminiscent of normal development but superimposed on underlying genetic aberrations. In glioblastoma (GBM), a subset of stem-like tumor- propagating cells (TPCs) appears to drive tumor progression and underlie therapeutic resistance, yet remain poorly understood. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL16791 23 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE54nnn/GSE54791/
Series		Accession: GSE54791	ID: 200054791

5004. mRNA expression in C-33A cells expressing HPV1 E2
(Submitter supplied) Profile of RNA expression in a C-33A cell line derived from an HPV negative cervical carcinoma in the presence or absence of HPV1 E2 expression.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE52nnn/GSE52367/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA227505
Series		Accession: GSE52367	ID: 200052367

5005. Epigenomic profiling of stemness, differentiation and primary tissues in human glioblastoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL11154 GPL16791 49 Samples
FTP download: GEO (BED, BIGWIG, BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE54nnn/GSE54792/
Series		Accession: GSE54792	ID: 200054792

5006. RNAseq Analysis of Formalin-Fixed Paraffin-Embedded Prostate Cancer Tissues
(Submitter supplied) In an effort to identify biomarkers of recurrence, we have performed global RNA-sequencing on 106 formalin-fixed, paraffin-embedded (FFPE) prostatectomy samples from 100 patients at three independent sites, and identified a new set of biomarkers of biochemical recurrence composed of a 24-gene panel. We validated this 24-gene panel on an independent publicly available dataset of 140 patients and this new panel outperformed previously published markers based on cell proliferation gene sets in terms of prediction of biochemical recurrence (BCR). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 106 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE54nnn/GSE54460/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA237581
Series		Accession: GSE54460	ID: 200054460

5007. Alternative poladenylation of tumor suppressor genes in small intestinal neuroendocrine tumors
(Submitter supplied) The tumorigenesis of small intestinal neuroendocrine tumors (NETs) is poorly understood. Recent studies have associated alternative polyadenylation with proliferation, cell transformation and cancer. Polyadenylation is the process in which the pre-mRNA is cleaved at a polyA site and a polyA tail is added. Genes with two or more polyA sites can undergo alternative polyadenylation. This produces two or more distinct mRNA isoforms with different 3’ untranslated regions. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL14761 4 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE56nnn/GSE56657/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA244234
Series		Accession: GSE56657	ID: 200056657

5008. RNAseq to investigate transcriptional changes in human MM cell lines due to panobinostat, 5-Azacytidine, panobinostat+5-Azacytidine or n-methyl-2-pyrroldine (NMP) treatments.
(Submitter supplied) Purpose: We applied RNA sequencing technology for high-throughput analysis of transcriptional changes within human MM cell lines JJN3 and U266 due to individual and combination drug treatment. Methods: JJN3 and U266 cells were treated with pan-HDACi panbobinostat, DNMTi 5-Azacytidine, panobinostat+5-Azacytidine or NMP for 4h or 24h in triplicate and transcriptional changes assessed by RNAseq using Illumina HiSeq platform. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 60 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE56nnn/GSE56623/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA244098
Series		Accession: GSE56623	ID: 200056623

5009. Site-Specific Association with Host and Viral Chromatin by KSHV LANA and its Reversal during Lytic Reactivation
(Submitter supplied) Latency-associated nuclear antigen (LANA), a multifunctional protein expressed by the Kaposi sarcoma-associated herpesvirus (KSHV) in latently-infected cells, is required for stable maintenance of the viral episome. This is mediated by two interactions: LANA binds to specific sequences (LBS1 and 2) on viral DNA, and also engages host histones, tethering the viral genome to host chromosomes in mitosis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL9115 GPL16791 33 Samples
FTP download: GEO (BED, GTF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE56nnn/GSE56144/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA242969
Series		Accession: GSE56144	ID: 200056144

5010. Rate of elongation by RNA polymerase II is influenced by specific gene features and histone modifications
(Submitter supplied) The rate of transcription elongation plays important roles in the timing of expression of full-length transcripts as well as for the regulation of alternative splicing. In this study we coupled Bru-Seq technology with 5,6-dichlorobenzimidazole 1-β-D-ribofuranoside (DRB) to estimate the elongation rates of over 2,000 individual genes in human cells. This technique, BruDRB-Seq, revealed gene-specific differences in elongation rates with a median rate of around 1.5 kb/min. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE55nnn/GSE55534/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA239893
Series		Accession: GSE55534	ID: 200055534

5011. Next-generation sequencing facilitates quantitative analysis of AcKLF5 and unAcKLF5 transcriptomes in xenografts of DU-145 cell line
(Submitter supplied) KLF5 possesses both tumor-suppressing and tumor-promoting activities, though the mechanism controlling these opposing functions is unknown. In cultured non-cancerous epithelial cells, KLF5 converts from pro-proliferative to anti-proliferative activity upon TGFβ-induced acetylation, which sequentially alters the KLF5 transcriptional complex and the expression of genes such as p15 and MYC. In nude mice, KLF5 also suppressed tumor growth in an acetylation-dependent manner. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE56nnn/GSE56343/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA242967
Series		Accession: GSE56343	ID: 200056343

5012. RNA-seq of Tumor Initiating Cells (TICs) from Lung Squamous Cell Carcinoma (LSCC) lines reveals PRKCI dependent Hedgehog (HH) Signalling
(Submitter supplied) RNA-seq analysis was performed on TICs and the parental counterparts of 4 LSCC cell lines. In addition, PRKCI knock down (KD) variants of these cells were sequenced. Subsequent analysis revealed that activation of HH signaling, a known driver of the TIC phenotype, is dependent on PRKCI expression.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48599/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA210778
Series		Accession: GSE48599	ID: 200048599

5013. A bioinformatics approach reveals novel mechanisms of the OVOL transcription factors in the regulation of epithelial-mesenchymal cell programming and cancer progression.
(Submitter supplied) We find significant evidence of the OVOL, AP1, STAT1, STAT3, and NFKB1 TFs having important roles in MET. We prioritize known gene/drug targets for follow-up in the clinic, and show that the AP1/MYC TF pair is a strong candidate for intervention.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE51nnn/GSE51975/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA225955
Series		Accession: GSE51975	ID: 200051975

5014. Human endothelial polyA+ RNA expression analysis
(Submitter supplied) The human genome harbors a large number of sequences encoding for RNAs that are not translated but control cellular functions by distinct mechanisms. The expression and function of the longer transcripts namely the long non-coding RNAs (lncRNAs) in the vasculature is largely unknown. Here, we characterized the expression of lncRNAs in human endothelial cells and elucidated the function of the highly expressed metastasis-associated lung adenocarcinoma transcript 1 (MALAT1; also known as MALAT-1 or NEAT2). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE54nnn/GSE54384/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA236375
Series		Accession: GSE54384	ID: 200054384

5015. PAR-CLIP-seq reveals RNAs directly interacting with CTCF in human transformed cell line U2OS
(Submitter supplied) This experiment sought to determine the genome-wide interactome of CTCF in human cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL11154 3 Samples
FTP download: GEO (BB, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53554/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA232376
Series		Accession: GSE53554	ID: 200053554

5016. Integrative Genomic and Transcriptomic Analysis Identified Candidate Genes Implicated in the Pathogenesis of Hepatosplenic T-cell Lymphoma
(Submitter supplied) Hepatosplenic T-cell lymphoma (HSTL) is an aggressive lymphoma cytogenetically characterized by isochromosome 7q   [i(7)(q10)], of which the molecular consequences remain unknown. We report here results of an integrative genomic and transcriptomic (expression microarray and RNA-sequencing) study of six HSTL cases with i(7)(q10) and three cases with ring 7   [r(7)], a rare variant aberration. Using high resolution array CGH, we prove that HSTL is characterized by the common loss of a 34.88 Mb region at 7p22.1p14.1 (3506316-38406226 bp) and duplication/amplification of a 38.77 Mb region at 7q22.11q31.1 (86259620-124892276 bp). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE55nnn/GSE55716/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA240673
Series		Accession: GSE55716	ID: 200055716

5017. Human Hepatocytes with Drug Metabolic Function Induced from Fibroblasts by Lineage Reprogramming
(Submitter supplied) We generated induced human hepatocyte by transduction of several lineage specific transcription factors and analyzed the gene expression profile of generated hepatocytes and freshly isolated human hepatocytes through RNA sequencing.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE54nnn/GSE54066/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA234510
Series		Accession: GSE54066	ID: 200054066

5018. Genome-wide activity of unliganded Estrogen Receptor alpha in breast cancer cells [RNA-Seq]
(Submitter supplied) ERα is essential for the anti-proliferative response of breast cancer cells not only to estrogen antagonists, but also to estrogen withdrawal by means of aromatase inhibitors. We explored here one of the simplest explanation for this, consisting in the possibility that ERα may have a wide genomic function in absence of ligands. The genomic binding of ERα in the complete absence of estrogen was then studied using hormone-dependent MCF7 cells, by chromatin immunoprecipitation sequencing. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 2 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53532/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA232305
Series		Accession: GSE53532	ID: 200053532

5019. Genome-wide activity of unliganded Estrogen Receptor-α in breast cancer cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL9115 5 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53533/
Series		Accession: GSE53533	ID: 200053533

5020. Poly(A) tail length change of miRNA targets in HeLa cells
(Submitter supplied) MicroRNA induces deadenylation of its targets according to the current model in the scientific community, but this model is based on the studies of a few individual genes. We tested the model by examining the global effect of miRNA on poly(A) tail of the targets. Synthetic miR-1 mimic was transfected into HeLa cells, and the poly(A) length was measured by TAIL-seq. Deadenylation of miR-1 targets was evident as early as 3 hours post-transfection without a significant change in mRNA level. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE54nnn/GSE54114/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA235199
Series		Accession: GSE54114	ID: 200054114

5021. Regulation of the KEAP1/NRF2 oxidative stress response pathway by BRD4 in prostate and colorectal cancer
(Submitter supplied) To identify genes regulated by BRD4 and to provide insight into new mechanisms de-regulated by BRD4, such as the response to oxidative stress, we integrated BRD4-binding regions with BRD4 gene expression data. For this analysis we performed BRD4 chromatin immunoprecipitation  experiments and BRD4 knock down experiments followed by RNA-Seq analyses. By integration of both gene lists we identified top candidate genes regulated by BRD4.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL11154 GPL10999 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE50nnn/GSE50491/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA217765
Series		Accession: GSE50491	ID: 200050491

5022. Dynamic Reorganization of the Cardiomyocyte Transcriptome in Response to TNFα-induced Proinflammatory Signaling [GRO-Seq]
(Submitter supplied) Inflammation is associated with many cardiovascular pathologies, but the underlying mechanisms remain unclear.  To explore this in more detail, we characterized the transcriptome of an immortalized adult human ventricular cardiomyocyte cell line (AC16) in response to tumor necrosis factor (TNFa).  Using a combination of genomic approaches, including global nuclear run-on sequencing (GRO-seq) and chromatin immunoprecipitation coupled with sequencing (ChIP-seq), we identified ~30,000 transcribed regions in AC16 cells, which includes a set of RNA polymerases I and III (Pol I and Pol III) transcribed regions revealed in the presence of α-amanitin. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL9052 12 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE51nnn/GSE51224/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA223649
Series		Accession: GSE51224	ID: 200051224

5023. Histone variant H3.3-specific readout of H3K36 trimethylation by ZMYND11 links transcription elongation control to tumour suppression
(Submitter supplied) Recognition of modified histones by “reader” proteins plays a critical role in the regulation of transcription1. H3K36 trimethylation (H3K36me3) is deposited onto the nucleosomes in the transcribed regions following RNA polymerase II (Pol II) elongation. In yeast, this mark in turn recruits epigenetic regulators to reset the chromatin at an appropriate state to suppress cryptic transcription2,3. However, much less is known about the role of H3K36me3 in transcription regulation in mammals. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 13 Samples
FTP download: GEO (TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48423/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA210152
Series		Accession: GSE48423	ID: 200048423

5024. Energy Metabolism during Anchorage-Independence
(Submitter supplied) The detachment of epithelial cells, but not cancer cells, causes anoikis due to reduced energy production. Invasive tumor cells generate three splice variants of the metastasis gene osteopontin. The cancer-specific form osteopontin-c supports anchorage-independence through inducing oxidoreductases and upregulating intermediates/enzymes in the hexose monophosphate shunt, glutathione cycle, glycolysis, glycerol phosphate shuttle, and mitochondrial respiratory chain. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE55nnn/GSE55193/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA238877
Series		Accession: GSE55193	ID: 200055193

5025. RNA m5C Methylation in breast cancer using MeRIP-Seq
(Submitter supplied) RNA m5C methylation profile of MCF10A and MDA486 by using MeRIP-Seq protocol
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 10 Samples
FTP download: GEO (BED, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53370/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA231850
Series		Accession: GSE53370	ID: 200053370

5026. Classification of cancer cell lines using a promoter-targeted liquid hybridization capture-based bisulfite sequencing approach
(Submitter supplied) DNA methylation plays a significant role in assuring cell identity, thus potentiating its application in molecular classification of cancers in respect of tissue origins or clinically and aetiologically distinct subtypes. In this study, we adapted our liquid hybridization capture-based bisulfite sequencing approach on the targeted sequencing of promoter methylomes. We detected ten cell lines originated from different tissue origins and demonstrated a similar potentiality of promoter methylomes as classifiers for cancer cell lines from different tissue origins in comparison with gene expression profiles. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE44nnn/GSE44866/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA192520
Series		Accession: GSE44866	ID: 200044866

5027. mRNA and RNC-mRNA deep sequencing of three hepatocellular carcinoma cell lines
(Submitter supplied) We sequenced the total mRNA and translating mRNA (RNC-mRNA) of three hepatocellular carcinoma cell lines Hep3B, HCCLM3 and MHCC97H
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL11154 6 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE49nnn/GSE49994/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA215765
Series		Accession: GSE49994	ID: 200049994

5028. Genome-wide maps of WT and over-expressing CenH3/CENP-A in Human HeLa S3 cells
(Submitter supplied) Centromeres are essential to ensure proper chromosome segregation in eukaryotes. Their definition relies on the presence of a centromere-specific H3 histone variant CenH3, known as CENP-A in mammals. Its overexpression in aggressive cancers raises questions concerning its effect on chromatin dynamics and contribution to tumorigenesis. We find that CenH3 overexpression in human cells leads to ectopic enrichment at sites of active histone turnover. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 16 Samples
FTP download: GEO (BED, TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE42nnn/GSE42951/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA183936
Series		Accession: GSE42951	ID: 200042951

5029. Genomic analyses reveal miR-137 broad impact on genes associated with malignant transformation and neuronal differentiation in glioblastoma cells
(Submitter supplied) miR-137 plays critical roles in the nervous system and tumor development. An increase in its expression is required for neuronal differentiation while its reduction is implicated in gliomagenesis. To evaluate the potential of miR-137 in glioblastoma therapy, we conducted genome-wide target mapping in glioblastoma cells by measuring levels of associations between PABP and mRNAs in cells transfected with miR-137 mimics vs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL10999 16 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53220/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA231155
Series		Accession: GSE53220	ID: 200053220

5030. Transcriptome sequencing of nasopharyngeal carcinoma model system
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL10999 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE54nnn/GSE54174/
Series		Accession: GSE54174	ID: 200054174

5031. Transcriptome sequencing of nasopharyngeal carcinoma model system (mRNA)
(Submitter supplied) Nasopharyngeal carcinoma (NPC) is a prevalent malignancyt disease in Southeast Asia among the Chinese population. Aberrant regulation of transcripts has been implicated in many types of cancers including NPC. Herein, we characterized mRNA and miRNA transcriptomes by RNA sequencing (RNASeq) of NPC model systems.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE54nnn/GSE54159/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA235326
Series		Accession: GSE54159	ID: 200054159

5032. Leucegene: AML sequencing (part 2)
(Submitter supplied) RNA sequencing of human leukemia
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 27 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE52nnn/GSE52656/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA229548
Series		Accession: GSE52656	ID: 200052656

5033. RNA helicase A is necessary for KIF1Bβ tumor suppression in neuroblastoma
(Submitter supplied) During development neuronal progenitors compete for growth factors such as nerve growth factor NGF and require the prolyl hydroxylase EglN3 and the kinesin KIF1Bβ for developmental apoptosis. Inherited KIF1Bβ loss-of-function mutations in neuroblastomas and pheochromocytomas implicate KIF1Bβ as a 1p36.2 tumor suppressor, however the mechanism of tumor suppression is unknown. We found that KIF1Bβ interacts with the RNA helicase A (DHX9) resulting in DHX9 nuclear accumulation to regulate apoptosis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE44nnn/GSE44585/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA190911
Series		Accession: GSE44585	ID: 200044585

5034. A GNAS mutation found in pancreatic intraductal papillary mucinous neoplasms induces drastic alterations of gene expression profiles with upregulation of mucin genes.
(Submitter supplied) GNAS, a gene encoding G-protein stimulating alpha subunit, is frequently mutated in intraductal papillary mucinous neoplasms (IPMNs), which is an indolent and slow-growing pancreatic neoplasm that secretes abundant mucin. GNAS mutation is not observed in conventional ductal adenocarcinomas of the pancreas. To determine the functional significance of GNAS mutation in pancreatic ductal cells, we examined in vitro phenotypes and gene expression profiles of cells of pancreatic ductal lineage, HPDE, PK-8, PCI-35, and MIA PaCa-2, with exogenous expression of either wild-type or mutated (R201H) GNAS. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16288 6 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53350/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA231774
Series		Accession: GSE53350	ID: 200053350

5035. Integrative Analyses of Gene Expression and DNA Methylation Profiles in a Breast Cancer Cell Line Model of Tamoxifen-Resistance Indicate a Crucial Role of Cells with Stem-like Properties
(Submitter supplied) Purpose: Development of resistance to tamoxifen is an important clinical issue in the treatment of patients with breast cancer. Tamoxifen resistance may be the result of the acquisition of epigenetic regulation such as DNA methylation within breast cancer cells resulting in changed mRNA expression of genes being pivotal for estrogen dependent growth. Alternatively, tamoxifen resistance may be due to selection of preexisting resistant cells, which may exhibit cancer stem-like characteristics or a combination of the two mechanisms. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform: GPL11154 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE40nnn/GSE40665/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA174525
Series		Accession: GSE40665	ID: 200040665

5036. A genome-wide map of transcription start sites specific for acute promyelocytic leukemia reveals deregulation of full-length transcripts
(Submitter supplied) Transcription start sites are the focal points of transcriptional regulation, where information from regulatory elements is integrated to stabilize initiation of transcription. In humans, most genes have more than one transcription start site, and these often exhibit different tissue specificity, serving as distinct regulatory frameworks for the same gene.  Usage of such promoters can also result in differential gene function manifested on the protein level. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 4 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE46nnn/GSE46561/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA200968
Series		Accession: GSE46561	ID: 200046561

5037. Oct4 affects E-cadherin expression via regulating Rnd1 associated cytoskeleton rearrangement in breast cancer cells
(Submitter supplied) Oct4, a key transcription factor for maintaining the pluripotency and self-renewal of stem cells has been reported previously. It also plays an important role in tumor proliferation and apoptosis, but the role of Oct4 been in tumor metastasis is still not very clear. Here, we found that ectopic expression of Oct4 in breast cancer cells can inhibit their migration and invasion. Detailed examinations revealed that Oct4 up-regulates expression of E-cadherin, indicative of its inhibitory role in epithelial-mesenchymal transition (EMT). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE54nnn/GSE54392/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA236383
Series		Accession: GSE54392	ID: 200054392

5038. Inhibition of Androgen Receptor and β-catenin activity in prostate cancer
(Submitter supplied) Androgen receptor (AR) is the major therapeutic target in aggressive prostate cancer. However, targeting AR alone can result in drug resistance and disease recurrence. Therefore, simultaneous targeting of multiple pathways could in principle be an effective new approach to treating prostate cancer. Here we provide proof-of-concept that a small molecule inhibitor of nuclear β-catenin activity (called C3) can inhibit both the AR and β-catenin signaling pathways that are often misregulated in prostate cancer. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 10 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE49nnn/GSE49295/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA213558
Series		Accession: GSE49295	ID: 200049295

5039. WTAP is a novel oncogenic protein in Acute Myeloid Leukemia
(Submitter supplied) Acute myeloid leukemia (AML) continues to have the lowest survival rates of all leukemias. Therefore, new therapeutic strategies are urgently needed to improve clinical outcomes for AML patients. Here, we report a novel role for Wilms’ tumor 1-associated protein (WTAP) in pathogenesis of AML. We have performed RNA-Seq in K562 cells with knockdown of WTAP to ascertain which genes it regulates.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 4 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE46nnn/GSE46718/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA202085
Series		Accession: GSE46718	ID: 200046718

5040. Next Generation Sequencing of MCF-7 and MDA-MB-435 cells
(Submitter supplied) Human breast cancer cells MDA-MB-435 had higher metastatic potential and other aggressive characteristics than MCF-7 cells.  Next-generation RNA sequencing (RNA-Seq) was used to clear this concern through comparison the transcriptomic expression profiles of these two cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE54nnn/GSE54122/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA235273
Series		Accession: GSE54122	ID: 200054122

5041. Brd4 and JMJD6-associated Anti-pause Enhancers in Regulation of Transcriptional Pause Release
(Submitter supplied) Distal enhancers characterized by H3K4me1 mark play critical roles in developmental and transcriptional programs. However, potential roles of specific distal regulatory elements in regulating RNA Polymerase II (Pol II) promoter-proximal pause release remain poorly investigated. Here we report that a unique cohort of jumonji C domain-containing protein 6 (JMJD6) and bromodomain-containing protein 4 (Brd4) co-bound distal enhancers, termed anti-pause enhancers (A-PEs), regulate promoter-proximal pause release of a large subset of transcription units via long-range interactions. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL9115 GPL11154 40 Samples
FTP download: GEO (BIGWIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE51nnn/GSE51633/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA224140
Series		Accession: GSE51633	ID: 200051633

5042. RNA-seq differential expression studies: more sequence, or more replication?
(Submitter supplied) Motivation: RNA-seq is replacing microarrays as the primary tool for gene expression studies. Many RNA-seq studies have used insufficient biological replicates, resulting in low statistical power and inefficient use of sequencing resources. Results: We show the explicit trade-off between more biological replicates and deeper sequencing in increasing power to detect differentially expressed (DE) genes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE51nnn/GSE51403/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA222975
Series		Accession: GSE51403	ID: 200051403

5043. RNA-seq melanoma
(Submitter supplied) Using a chromatin regulator-focused shRNA library, we found that suppression of sex determining region Y-box 10 (SOX10) in melanoma causes  resistance to BRAF and MEK inhibitors. To investigate how SOX10 loss leads to drug resistance, we performed transcriptome sequencing (RNAseq) of both parental A375 (Ctrl. PLKO) and A375-SOX10KD (shSOX10-1, shSOX10-2) cells. To ask directly whether SOX10 is involved indrug resistance in BRAF(V600E) melanoma patients, we isolated RNA from paired biopsies from melanoma patients (pre- and post- treatment) , that had gained  BRAF or MEK inhibitor resistance . more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE50nnn/GSE50535/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA217909
Series		Accession: GSE50535	ID: 200050535

5044. The RON receptor tyrosine kinase promotes metastasis by triggering epigenetic reprogramming through the thymine glycosylase MBD4
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform: GPL9052 27 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE52nnn/GSE52689/
Series		Accession: GSE52689	ID: 200052689

5045. The RON receptor tyrosine kinase promotes metastasis by triggering epigenetic reprogramming through the thymine glycosylase MBD4 (RNA-Seq)
(Submitter supplied) Metastasis is the major cause of death in cancer patients, yet the genetic/epigenetic programs that drive metastasis are poorly understood. Here, we report a novel epigenetic reprogramming pathway that is required for breast cancer metastasis. Concerted differential DNA methylation is initiated by activation of the RON receptor tyrosine kinase by its ligand, macrophage stimulating protein (MSP). Through PI3K signaling, RON/MSP promotes expression of the G:T mismatch-specific thymine glycosylase MBD4. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE52nnn/GSE52687/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA229803
Series		Accession: GSE52687	ID: 200052687

5046. Widespread Transcription beyond mRNA 3’ Ends Yields Abundant Regulatory RNAs
(Submitter supplied) Through RNA-seq analyses of nascent transcripts, we found large numbers of RNA transcripts that extend beyond the 3’ ends of protein-coding genes; we refer to these extended transcripts as geRNAs. These findings demonstrate that transcription of most human protein-coding genes does not terminate within close proximity to poly(A) signals; rather, it terminates at sites far beyond these signals (up to 50 kb).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (BIGWIG, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE46nnn/GSE46228/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA198440
Series		Accession: GSE46228	ID: 200046228

5047. Whole Genome sequencing of a normal karyotype AML cell line
(Submitter supplied) Normal Karyotype acute myeloid leukemia (NK-AML) represents approximately 50% of all cases of AML which patients develop.  Most AML cell lines are highly abnormal and therefore not good models for investigating NK-AML biology a novel AML cell line, CG-SH, was recently estabished and here we characterize the gene expression and mutations present through high-throughput sequencing of RNA and genomic DNA using a HiSeq 2000
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL11154 2 Samples
FTP download: GEO (BCF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE40nnn/GSE40199/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA173077
Series		Accession: GSE40199	ID: 200040199

5048. Global Target mRNA Specification and Regulation by RNA-Binding Protein ZFP36/Tristetraprolin/TTP [PAR-CLIP]
(Submitter supplied) Tristetraprolin/ZFP36/TTP and ELAVL1/HuR are two disease-relevant RNA-binding proteins (RBPs) that both interact with AU-rich sequences but have antagonistic roles. While ELAVL1 binding has been profiled in several studies, the precise in vivo binding specificity of ZFP36 has not been investigated on a global scale. We determined ZFP36 binding preferences using cross-linking and immunoprecipitation in human embyonic kidney cells and examined combinatorial regulation of AU-rich elements by ZFP36 and ELAVL1. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 1 Sample
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53184/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA231063
Series		Accession: GSE53184	ID: 200053184

5049. Regulation of NUMB alternative splicing by RBM5, RBM6 and RBM10 controls cancer cell proliferation (CLIP-Seq)
(Submitter supplied) RBM5, a regulator of alternative splicing of apoptotic genes, and its close homologues, RBM6 and RBM10, are RNA binding proteins frequently deleted or mutated in lung cancer. We report that RBM5/6 and RBM10 antagonistically regulate the proliferative capacity of cancer cells and display distinct positional effects in alternative splicing regulation. We identify the Notch pathway regulator NUMB as a key target of these factors in the control of cell proliferation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 9 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48066/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA208845
Series		Accession: GSE48066	ID: 200048066

5050. RNAseq of PRMT4KD in human cord blood derived CD34+ cells
(Submitter supplied) Defining the role of epigenetic regulators in normal hematopoiesis has become critically important, as recurrent mutations or aberrant expression of these genes has been identified in both myeloid and lymphoid hematological malignancies. We have found that PRMT4, a type I arginine methyltransferase, whose function in normal and malignant hematopoiesis is unknown, is overexpressed in AML patient samples. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE46nnn/GSE46056/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA197140
Series		Accession: GSE46056	ID: 200046056

5051. Correlation between STAT3 binding presence and gene expression levels in subtypes of diffuse large B cell lymphoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL10999 27 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE50nnn/GSE50724/
Series		Accession: GSE50724	ID: 200050724

5052. Whole transcriptome profiling of the two major subtypes of diffuse large B cell lymphoma
(Submitter supplied) The goal of this study is to identify the transcriptome differences between the two major subtypes of diffuse large B cell lymphoma (DLBCL).  DLBCL is the most common form of non-Hodgkin’s lymphoma and has two major subtypes: germinal center B-cell-like (GCB) and activated B-cell-like (ABC).  When compared to the GCB form, ABC lymphomas respond much more poorly to current therapies. To investigate how gene expression changes might contribute to this aggressive phenotype, we have used RNA-Seq to profile the whole transcriptome in 8 DLBCL cell lines (4 GCB subtype, 4 ABC) that are derived from patient tumors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE50nnn/GSE50721/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA218585
Series		Accession: GSE50721	ID: 200050721

5053. Architecture of Epigenetic Reprogramming Following Twist1 Mediated Epithelial-Mesenchymal Transition [RNA-seq]
(Submitter supplied) Purpose: to characterize epigenetic changes following Twist1 mediated Epithelial-Mesenchymal Transition in human  Methods: we characterized the epigenetic and transcriptome landscapes using whole genome transcriptome analysis by RNA-seq, DNA methylation by digital restriction enzyme analysis of methylation (DREAM) and histone modifications by CHIP-seq of H3K4me3 and H3K27me3 in immortalized human mammary epithelial cells relative to cells induced to undergo EMT by Twist1. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9442 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53024/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA230693
Series		Accession: GSE53024	ID: 200053024

5054. A RNA-seq-based gene expression profiling of radiation-induced tumorigenic mammary epithelial cells
(Submitter supplied) To understand tumorigenesis and cancer progression of mammary epithelium, we established a cell model combining over-expression of human telomerase reverse transcriptase gene (hTERT) and heavy-ion radiation from normal human mammary epithelial cells. We subsequently used RNA-seq method to acquire their transcriptomes from two characteristic cell lines, an immortal epithelial cell line (I_hMEC) and a tumorigenic epithelial cell line (T_hMEC), and to look for differentially expressed genes (DEGs) between immortalization and tumorigenicity. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9442 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE31nnn/GSE31310/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA146017
Series		Accession: GSE31310	ID: 200031310

5055. Gene expression, single nucleotide variant and fusion transcript discovery in archival material from breast tumors
(Submitter supplied) Advantages of RNA-Seq over array based platforms are quantitative gene expression and discovery of expressed single nucleotide variants (eSNVs) and fusion transcripts from a single platform, but the sensitivity for each of these characteristics is unknown. We measured gene expression in a set of manually degraded RNAs, nine pairs of matched fresh-frozen, and FFPE RNA isolated from breast tumor with the hybridization based, NanoString nCounter, (226 gene panel) and with whole transcriptome RNA-Seq using RiboZeroGold ScriptSeq V2 library preparation kits. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 27 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE51nnn/GSE51124/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA221234
Series		Accession: GSE51124	ID: 200051124

5056. An Integrated Model of the Transcriptome Landscape of HER2-Positive Breast Cancer
(Submitter supplied) The goal of our study is to build an integrated transcriptome landscape model for HER2 positive breast tumors and identify the crucial signaling pathways associated with HER2 tumors. Genomic features include, 685 genes that were differentially expressed only in HER2-positive tumors, 102 genes that were alternatively spliced in a pattern that is unique to HER2-positive tumors, and 303 genes that expressed single nucleotide sequence variants (eSNVs) that were unique to HER2-positive tumors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 32 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE45nnn/GSE45419/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA193673
Series		Accession: GSE45419	ID: 200045419

5057. Modelling and rescuing neurodevelopmental defect of Down syndrome using induced pluripotent stem cells from monozygotic twins discordant for trisomy 21 [RNA-seq]
(Submitter supplied) Down syndrome (trisomy 21) is the most common viable chromosomal disorder with intellectual impairment and several other developmental abnormalities. Here, we report the generation and characterization of induced pluripotent stem cells (iPSCs) derived from monozygotic twins discordant for trisomy 21 in order to eliminate the effects of the variability of genomic background. The alterations observed by genetic analysis at the iPSC level and at first approximation in early development illustrate the developmental disease transcriptional signature of Down syndrome. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 7 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE52nnn/GSE52249/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA227902
Series		Accession: GSE52249	ID: 200052249

5058. Identification of miR-181a target genes in Epithelial Ovarian Cancer
(Submitter supplied) We have identified a single miRNA, miR-181a, that can modulate TGF-β signaling to induce and maintain EMT, and effect further downstream events of tumour cell survival, altered response to chemotherapy, migration, invasion and dissemination in vivo. Our present study provides an understanding of how enhanced expression of miR-181a can confer malignant and invasive traits through the modulation of a canonical signaling pathway and a consequent maintenance of a mesenchymal state. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE52nnn/GSE52077/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA226708
Series		Accession: GSE52077	ID: 200052077

5059. RNA-seq analysis generated a comprehensive landscape of transcriptomes and revealed complex patterns of transcripts in Chinese HBV-related hepatocellular carcinoma
(Submitter supplied) RNA-seq is a powerful tool for comprehensive characterization of whole transcriptome at both gene and exon levels and with a unique ability of identifying novel splicing variants. To date, RNA-seq analysis of HBV-related HCC has not been reported. In this study, we performed transcriptome analyses for 10 matched pairs of cancer and non-cancerous tissues from Chinese HBV-related hepatocelluar carcinoma patients using 36bp single-end sequencing approach on Solexa/Illumina GAII platform. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 20 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE25nnn/GSE25599/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA134241
Series		Accession: GSE25599	ID: 200025599

5060. Fusion discovery in breast cancer cell line
(Submitter supplied) SnowShoes-FTD, a fusion transcript discovery tool, was used to identify fusions in breast cancer cell lines using the RNA-Seq data
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE52nnn/GSE52643/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA229558
Series		Accession: GSE52643	ID: 200052643

5061. Two New Stromal Signatures Stratify Breast Cancers with Different Prognosis
(Submitter supplied) Purpose:  Multiple studies from last decades have shown that the microenvironment of carcinomas plays an important role in the initiation, progression and metastasis of cancer.  Our group has previously identified novel cancer stroma gene expression signatures associated with outcome differences in breast cancer by gene expression profiling of two tumors of fibroblasts as surrogates for physiologic stromal expression patterns. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 53 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE42nnn/GSE42948/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA183925
Series		Accession: GSE42948	ID: 200042948

5062. mRNA-sequencing of breast cancer subtypes and normal tissue
(Submitter supplied) Goal: To define the digital transcriptome of three breast cancer subtypes (TNBC, Non-TNBC, and HER2-positive) using RNA-sequencing technology. To elucidate differentially expressed known and novel transcripts, alternatively spliced genes and differential isoforms and lastly expressed variants in our dataset. Method: Dr. Suzanne Fuqua (Baylor College of Medicine) provided the human breast cancer tissue RNA samples. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 20 Samples
FTP download: GEO (GTF, VCF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE52nnn/GSE52194/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA227137
Series		Accession: GSE52194	ID: 200052194

5063. Leucegene: AML sequencing (part 1)
(Submitter supplied) RNA sequencing of human leukemia
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 43 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE49nnn/GSE49642/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA214592
Series		Accession: GSE49642	ID: 200049642

5064. Leucegene: ALL sequencing
(Submitter supplied) RNA sequencing of human leukemia
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE49nnn/GSE49601/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA214428
Series		Accession: GSE49601	ID: 200049601

5065. Leucegene
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 72 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48173/
Series		Accession: GSE48173	ID: 200048173

5066. Translating transcriptome of cancer cells in situ in mesenchymal-rich tumor microenvironment
(Submitter supplied) A mesenchymal rich stroma such as cancer-associated fibroblasts (CAFs) in breast tumors favors the selection of cancer clones with enhanced bone metastatic ability. To determine the cancer cell transcriptomic response to the mesenchymal stroma, we supplemented experimental mammary tumours with or without exogenous mesenchymal cells. We used bone marrow-derived human mesenchymal stem cells (MSCs) as a source of mesenchymal stroma, as MSCs have been shown to undergo CAF-like differentiation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE43nnn/GSE43306/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA185392
Series		Accession: GSE43306	ID: 200043306

5067. Polysome-associated mRNA profiling of cancer cells in response to CXCL12 and IGF1
(Submitter supplied) CXCL12 and IGF1 are key secreting molecules produced by cancer-associated fibroblasts in breast cancer. These factors promote the survival of disseminated cancer cells in the bone marrow. To assess the combined responses elicited by CXCL12 and IGF1, we examined the translating transcriptome of cancer cells in response to these two factors by Translating Ribosome Affinity Purification (TRAP)-RNAseq.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE43nnn/GSE43296/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA185391
Series		Accession: GSE43296	ID: 200043296

5068. RNA-seq (Illumina and PacBio) of hESC
(Submitter supplied) We used PacBio data to identify more reliable transcripts from hESC, based on which we can estimate gene/transcript abundance better from Illumina data.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 2 Samples
FTP download: GEO (FA, GTF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE51nnn/GSE51861/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA225616
Series		Accession: GSE51861	ID: 200051861

5069. Genome-Wide Transcriptional Effects of the Anti-Cancer Agent Camptothecin
(Submitter supplied) The anti-cancer drug camptothecin inhibits replication and transcription by trapping DNA topoisomerase I (Top1) covalently to DNA in a “cleavable complex”. To examine the effects of camptothecin on RNA synthesis genome-wide we used Bru-Seq and show that camptothecin treatment affected transcription initiation, elongation, termination, splicing and enhancer activity. Following removal of camptothecin, transcription spread as a wave from the 5’-end of genes with no recovery of transcription apparent from RNA polymerases stalled in the body of genes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48678/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA211115
Series		Accession: GSE48678	ID: 200048678

5070. Novel kinase fusion oncogenes in post-Chernobyl radiation-induced pediatric thyroid cancers
(Submitter supplied) Exposure to ionizing radiation during childhood markedly increases the risk of developing papillary thyroid cancer. We identified non-overlapping somatic driver mutations in all 26 cases of post-Chernobyl thyroid cancers we studied through candidate gene assays and next generation RNA-sequencing. We found that 22/26 harbored fusion oncogenes arising primarily through intrachromosomal rearrangements. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 11 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48850/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA211959
Series		Accession: GSE48850	ID: 200048850

5071. Transcriptional super-enhancers connected to cell identity and disease
(Submitter supplied) Super-enhancers are large clusters of transcriptional enhancers that drive expression of genes that control and define cell identity. Improved understanding of the roles super-enhancers play in biology would be afforded by knowing the constellation of factors that constitute these domains and by identifying super-enhancers across the spectrum of human cell types. We describe here the population of transcription factors, cofactors, chromatin regulators and core transcription apparatus that occupy super-enhancers in embryonic stem cells (ESCs) and evidence that super-enhancers are highly transcribed. more...
Organism:	Homo sapiens; Mus musculus
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL9115 GPL9250 5 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE51nnn/GSE51522/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA223352
Series		Accession: GSE51522	ID: 200051522

5072. Long Noncoding RNA HNF1A-AS1 Regulates Proliferation and Migration in Esophageal Adenocarcinoma  Cells
(Submitter supplied) Objectives: Long non-coding RNAs (lncRNAs) have been shown to play important roles in the development and progression of cancer. However, functional lncRNAs and their downstream mechanisms are largely unknown in the molecular pathogenesis of esophageal adenocarcinoma (EAC) and its progression. Design: lncRNAs that are abnormally upregulated in EACs were identified by RNA-seq analysis, followed by quantitative RT-PCR (qRTPCR) validation using tissues from 31 EAC patients. more...
Organism:	Homo sapiens
Type:		Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL16791 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48240/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA209632
Series		Accession: GSE48240	ID: 200048240

5073. Genome-wide Analysis of Chromatin Interactions in Human Cells
(Submitter supplied) Millions of cis-regulatory sequences have recently been found in the human genome, but the function of most cis-elements are not yet clear, in part due to the difficulty in determining their regulatory targets, which are often located millions of base pairs away and separated by one or more unrelated genes. To address this problem, the Hi-C method has been developed to identify long-range looping interactions in a genome-wide, unbiased fashion. more...
Organism:	Homo sapiens
Type:		Other; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL10999 GPL11154 53 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE43nnn/GSE43070/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA184350
Series		Accession: GSE43070	ID: 200043070

5074. Altered Epigenetic Regulation of Homeobox Genes in Human Oral Squamous Cell Carcinoma Cells
(Submitter supplied) To gain insight into the molecular changes during OSCC carcinogenesis, we performed unbiased, whole genome deep sequencing (RNA-seq) using RNA isolated from cultured, human TERT-immortalized, non-tumorigenic OKF6-TERT1R and OSCC SCC-9 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE51nnn/GSE51415/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA222994
Series		Accession: GSE51415	ID: 200051415

5075. Ribosome profiling reveals features of normal and disease-associated mitochondrial translation
(Submitter supplied) Ribosome profiling and RNAseq data on human BJ fibroblasts and cybrid cells using an adapted ribosome profiling protocol to improve detection of mitochondrial ribosome protected fragments
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL15520 GPL11154 10 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48933/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA212323
Series		Accession: GSE48933	ID: 200048933

5076. Global response to chemotherapy-induced apoptosis
(Submitter supplied) Here we use an integrated systems-level examination of transcription, translation, and proteolysis to explore how cancer cells struggle with a chemotherapeutic drug prior to succumbing to apoptosis. As a model system we study myeloma cells exposed to the proteasome inhibitor bortezomib, a first-line clinical treatment. Despite robust transcriptional changes, unbiased quantitative proteomics detects production of only a few critical anti-apoptotic proteins against a background of general translation inhibition. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48785/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA211752
Series		Accession: GSE48785	ID: 200048785

5077. RNA-seq for gastric cancer and normal tissues/cells
(Submitter supplied) We performed RNA-seq experiments to identify differentially expressed intergenic transcripts between gastric cancer and normal tissues/cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL9115 8 Samples
FTP download: GEO (GTF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE41nnn/GSE41476/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA178120
Series		Accession: GSE41476	ID: 200041476

5078. Dynamic transcriptomes of human myeloid leukemia cells
(Submitter supplied) To identify the mechanisms controlling chronic myeloid leukemia (CML) and acute myeloid leukemia (AML) in humans, we analyzed genome-wide transcription dynamics in three myeloid leukemia cell lines (K562, HL-60, and THP1) using high-throughput sequencing technology. Using KEGG analysis, we found that the ERK/MAPK, JAK-STAT and ErbB pathways promoted proliferation and metabolism in CML. However, in AML, differentiation and apoptosis blocking resulted in the accumulation of blast cells in marrow. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9520 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE46nnn/GSE46164/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA197429
Series		Accession: GSE46164	ID: 200046164

5079. The Wnt/β-catenin-signaling pathway is modulated by androgen ablation therapy for advanced clinical prostate cancer and contributes to androgen independent cell growth
(Submitter supplied) Androgen ablation therapy (AAT) is standard treatment for locally-advanced/metastatic prostate cancer (PCa).  Many patients develop castration-resistance (CRPCa) after ~2-3 years, with a poor prognosis.  The molecular mechanisms underlying CRPCa progression are unclear.  mRNA-Seq was performed on tumours from 7 patients with locally-advanced/metastatic PCa before and ~22 weeks after AAT initiation.  Differentially regulated genes were identified in treatment pairs.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 14 Samples
FTP download: GEO (TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48403/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA209978
Series		Accession: GSE48403	ID: 200048403

5080. Genome-wide total RNA and MBD-sequencing in HCT116 and DKO cells as a global re-expression model
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform: GPL10999 25 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE45nnn/GSE45334/
Series		Accession: GSE45334	ID: 200045334

5081. Genome-wide total RNA and MBD-sequencing in HCT116 and DKO cells as a global re-expression model [RNA-Seq]
(Submitter supplied) Genome-wide view of the interplay between methylation and RNA expression in this colorectal cancer model was obtained.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 17 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE45nnn/GSE45332/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA193485
Series		Accession: GSE45332	ID: 200045332

5082. Scrambled Control and EGFR Knockdown Cells Cultured under Normoxia and Hypoxia
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL13393 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE44nnn/GSE44804/
Series		Accession: GSE44804	ID: 200044804

5083. Next-Generation Sequencing for Whole Transcriptome Analysis in Scrambled Control and EGFR Knockdown Cells Cultured under Normoxia and Hypoxia
(Submitter supplied) Purpose: The goal of this study is to identify the mRNA clusters that are regulated by EGFR under normoxia or hypoxia. Method: Total RNAs were extracted from HeLa cells expressing scrambled control or EGFR shRNA-E1 that cultured under normoxia or hypoxia (1% O2) for 24h. Customized Next-Generation RNA Deep Sequencing, including both small RNA application and whole transcriptome analysis, was performed according to the standard procedure instructed by Applied Biosystems. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL13393 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE44nnn/GSE44801/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA191817
Series		Accession: GSE44801	ID: 200044801

5084. Genome-wide analysis of BRCA1 and PALB2
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by array
Platforms: GPL10999 GPL10558 53 Samples
FTP download: GEO (BEDGRAPH, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE45nnn/GSE45715/
Series		Accession: GSE45715	ID: 200045715

5085. Genome-wide analysis of BRCA1 and PALB2 [ChIP-seq and RNA-seq]
(Submitter supplied) Breast and ovarian cancer susceptibility genes, BRCA1 and PALB2 have enigmatic roles in cellular growth and mammalian development.  While these genes are essential for growth during early developmental programs, inactivation later in adulthood leads to increased growth and formation of tumors, leading to their designation as tumor suppressors.  We performed genome-wide analysis assessing their chromatin residence and gene expression responsiveness using high throughput sequencing in breast epithelial cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL10999 12 Samples
FTP download: GEO (BEDGRAPH, BW, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE40nnn/GSE40591/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA174355
Series		Accession: GSE40591	ID: 200040591

5086. Integrated profiling of microRNAs and mRNAs: microRNAs located on Xq27.3 associate with clear cell renal cell carcinoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL9115 40 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE24nnn/GSE24952/
Series		Accession: GSE24952	ID: 200024952

5087. Digital gene expression (DGE) sequencing of 10 pairs samples between kidney normal tissue and cancer tissue
(Submitter supplied) we combined their genome-wide profiles of tumors and normal adjacent tissues in 10 ccRCC patients. The results showed that 283 miRNAs were down-regulated and 187 up-regulated, meanwhile 7473 mRNAs were up-regulated and 3439 down-regulated in ccRCC. Expressions of 12 miRNAs and genes were validated in 10 patients we studied by RT-qPCR (validation rate from 60% to 100%). Differentially expressed gene analysis showed the collective change of miR-200 and SLC22A gene family, and pathway analysis revealed down-regulation of multiple metabolic pathways and up-regulation of focal adhesion, ECM-receptor interaction, etc. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 20 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE24nnn/GSE24455/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA133499
Series		Accession: GSE24455	ID: 200024455

5088. Promiscuous RNA binding by PRC2
(Submitter supplied) Polycomb repressive complex-2 (PRC2) is a histone methyltransferase required for epigenetic silencing during development and cancer. Long non-coding RNAs (lncRNAs) recruit PRC2 to chromatin, but the general role of RNA in maintaining repressed chromatin is unknown. ChIP-seq, combined with RNA-seq, indicating that PRC2 is also associated with active genes, but most of these are not regulated by PRC2. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (BED, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE50nnn/GSE50177/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA217298
Series		Accession: GSE50177	ID: 200050177

5089. High-throughput sequencing of matched colorectal normal, tumor and metastasis tissues and proof-of principal bioinformatics modeling of therapeutic consequences of miRNA applications
(Submitter supplied) MiRNAs are discussed as diagnostic and therapeutic molecules. However, effective miRNA drug treatments with miRNAs are so far hampered by the complexity of the miRNA networks. To identify potential miRNA drugs in colorectal cancer, we profiled miRNA and mRNA expression in matching normal, tumor and metastasis tissues of eight patients by Illumina sequencing. We identified miRNA-1 as top candidate differentially expressed in tumor and metastasis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL10999 36 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE46nnn/GSE46622/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA201245
Series		Accession: GSE46622	ID: 200046622

5090. Expression data for HT29 cells treated with 5-aza-deoxy-cytidine
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL570 GPL11154 18 Samples
FTP download: GEO (CEL, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE41nnn/GSE41588/
Series		Accession: GSE41588	ID: 200041588

5091. Expression data for HT29 cells treated with 5-aza-deoxy-cytidine [RNA-Seq]
(Submitter supplied) The RNA samples from HT-29 (ATCC) colon cancer cell line were reverse transcribed to build cDNA libraries and categorized into 3 groups with different concentrations of 5-aza-deoxy-cytidine (5-Aza); in each group three replicative 150 mm cultures were treated with: 1) dimethyl sulfoxide (vehicle alone, 0 μM 5-Aza); 2) 5μM 5-Aza and 3) 10 μM 5-Aza; for five days. This experiment was also performed parallel on a commercial Affymetrix microarray [GSE41364] and the aim of the study was to compare the two platforms on gene expression measurements and differentially expressed gene (DEG) detection. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE41nnn/GSE41586/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA177604
Series		Accession: GSE41586	ID: 200041586

5092. A compendium of hematopoietic regulators, chromatin modifiers and basal transcription factors occupy CBF-MYH11/RUNX1 target genes
(Submitter supplied) Different mechanisms for CBF-MYH11 function in acute myeloid Leukemia (AML) with inv(16) have been proposed such as tethering of RUNX1 outside the nucleus, interference with transcription factor complex assembly and recruitment of histone deacetylases, all resulting in transcriptional repression of RUNX1 target genes. Here, through genome-wide CBF-MYH11 binding site analysis and quantitative interaction proteomics we found that CBF-MYH11 localizes to RUNX1 occupied promoters where it interacts with TAL1, FLI1 and TBP associated factors (TAFs) in the context of the hematopoietic transcription factors ERG, GATA2 and PU.1/SPI1 and the co regulators EP300 and HDAC1. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL10999 GPL11154 27 Samples
FTP download: GEO (BEDGRAPH, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE46nnn/GSE46044/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA197000
Series		Accession: GSE46044	ID: 200046044

5093. Non-IG Aberrations of FOXP1 in B-Cell Malignancies Lead to an Aberrant Expression of N-Truncated Isoforms of FOXP1
(Submitter supplied) The transcription factor FOXP1 is implicated in the pathogenesis of B-cell lymphomas through immunoglobulin heavy chain (IGH) locus-related chromosomal translocations leading to dysregulated expression of FOXP1. Translocations of FOXP1 with non-IG gene sequences have been also reported, but the molecular consequences of such aberrations remain undetermined. Here, using molecular cytogenetics and molecular biology studies, we comprehensively analyzed four lymphoma cases with non-IG rearrangements of FOXP1 and compared these with cases harboring t(3;14)(p13;q32)/IGH-FOXP1 and FOXP1-expressing lymphomas without underlying t(3p13/FOXP1). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE50nnn/GSE50514/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA217945
Series		Accession: GSE50514	ID: 200050514

5094. Genome-wide Analysis of Transcriptional Regulators in Human Blood Stem/Progenitor Cells reveals a densely interconnected network of coding and non-coding genes.
(Submitter supplied) Combinatorial transcription factor (TF) interactions regulate hematopoietic stem cell formation, maintenance and differentiation, and are increasingly recognised as drivers of stem cell signatures in cancer.  However, genome-wide combinatorial binding patterns for key regulators do not exist in primary human hematopoietic stem/progenitor cells (HSPCs) and have constrained analysis of the global architecture of the molecular circuits controlling these cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 10 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE45nnn/GSE45144/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA193088
Series		Accession: GSE45144	ID: 200045144

5095. Comparative mRNA and microRNA expression profiling of three genitourinary cancers reveals common hallmarks and cancer-specific molecular events
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL9115 68 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE31nnn/GSE31617/
Series		Accession: GSE31617	ID: 200031617

5096. mRNA expression of cancer and matched adjacent tissues of 7 testicular germ cell tumors and 10 transitional cell carcinomas of bladder
(Submitter supplied) Genome-wide gene expression profile using deep sequencing technologies can drive the discovery of cancer biomarkers and therapeutic targets. Such efforts are often limited to profiling the expression signature of either mRNA or microRNA (miRNA) in a single type of cancer.Here we provided an integrated analysis of the genome-wide mRNA and miRNA expression profiles of three different genitourinary cancers: carcinomas of the bladder, kidney and testis.Our results highlight the general or cancer-specific roles of several genes and miRNAs that may serve as candidate oncogenes or suppressors of tumor development. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 34 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE31nnn/GSE31614/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA154991
Series		Accession: GSE31614	ID: 200031614

5097. Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
(Submitter supplied) A large number of computational methods have been recently developed for analyzing differential gene expression (DE) in RNA-seq data. We report on a comprehensive evaluation of the commonly used DE methods using the SEQC benchmark data set and data from ENCODE project. We evaluated a number of key features including: normalization, accuracy of DE detection and DE analysis when one condition has no detectable expression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Third-party reanalysis
Platform: GPL11154 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE49nnn/GSE49712/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA214799
Series		Accession: GSE49712	ID: 200049712

5098. Modeling precision treatment of breast cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL10999 131 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48216/
Series		Accession: GSE48216	ID: 200048216

5099. Transcriptional profiling of a breast cancer cell line panel using RNAseq technology
(Submitter supplied) 56 breast cancer cell lines were profiled to identify patterns of gene expression associated with subtype and response to therapeutic compounds.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 56 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48213/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA210428
Series		Accession: GSE48213	ID: 200048213

5100. LncRNA-dependent mechanisms of androgen receptor-regulated gene activation programs [GRO-seq II]
(Submitter supplied) While thousands of long non-coding RNAs (lncRNAs) are expressed in higher eukaryotes, the potential regulatory roles of lncRNAs in regulated gene transcription programs remain rather poorly understood. Here, we report that two lncRNAs highly overexpressed in aggressive prostate cancer, PRNCR1 and PCGEM1, bind successively to the androgen receptor (AR) and strongly enhance both ligand-dependent and ligand-independent AR-mediated gene activation programs and proliferation in prostate cancer cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (BED, BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE47nnn/GSE47806/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA207828
Series		Accession: GSE47806	ID: 200047806

5101. LncRNA-dependent mechanisms of androgen receptor-regulated gene activation programs [GRO-seq I]
(Submitter supplied) While thousands of long non-coding RNAs (lncRNAs) are expressed in higher eukaryotes, the potential regulatory roles of lncRNAs in regulated gene transcription programs remain rather poorly understood. Here, we report that two lncRNAs highly overexpressed in aggressive prostate cancer, PRNCR1 and PCGEM1, bind successively to the androgen receptor (AR) and strongly enhance both ligand-dependent and ligand-independent AR-mediated gene activation programs and proliferation in prostate cancer cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (BED, BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE47nnn/GSE47805/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA207829
Series		Accession: GSE47805	ID: 200047805

5102. RNA-seq analysis of HT-29, MCF10A, and MDA-MB-436 cells
(Submitter supplied) RNA-seq data from HT-29 cells treated with IFN-γ for 24 hr, MCF10A cells, and MDA-MB-436 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE45nnn/GSE45258/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA193502
Series		Accession: GSE45258	ID: 200045258

5103. A Hybrid Mechanism of Action for BCL6 in B Cells Defined by Formation of Functionally Distinct Complexes at Enhancers and Promoters 
(Submitter supplied) BCL6 is crucial for B-cell activation and lymphomagenesis. We used integrative genomics to explore BCL6 mechanism in normal and malignant B-cells. Surprisingly, BCL6 assembled distinct complexes at enhancers vs. promoters. At enhancers BCL6 preferentially recruited SMRT, which mediated H3K27 deacetylation through HDAC3, antagonized p300 activity and repressed transcription, but without decommissioning enhancers. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL15433 GPL10999 GPL11154 46 Samples
FTP download: GEO (BED, BW, TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE29nnn/GSE29282/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA138597
Series		Accession: GSE29282	ID: 200029282

5104. Genome wide mapping of effects of U6atac knockdown on pre-mRNA splicing
(Submitter supplied) This project looks into experimentally identifying all minor introns by knocking down the minor spliceosome's catalytic snRNP, U6atac.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48263/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA209423
Series		Accession: GSE48263	ID: 200048263

5105. Transcription factors OVOL1 and OVOL2 induce the mesenchymal to epithelial transition in human cancer
(Submitter supplied) This paper shows, for the first time, a novel function of the OVO-like proteins (OVOL1and OVOL2) as critical inducers of mesenchymal to epithelial transition (MET) in human cancer.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48230/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA209306
Series		Accession: GSE48230	ID: 200048230

5106. Wnt-signaling potentiates nevogenesis.
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL570 GPL10999 18 Samples
FTP download: GEO (BIGWIG, CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE46nnn/GSE46818/
Series		Accession: GSE46818	ID: 200046818

5107. Expression data from 7 Human Melanomas
(Submitter supplied) Melanocytes within benign human nevi are the paradigm for tumor suppressive senescent cells in a pre-malignant neoplasm. These cells typically contain mutations in either the BRAF or N-RAS oncogene and express markers of senescence, including p16. However, a nevus can contain 10s to 100s of thousands of clonal melanocytes and approximately 20-30% of melanoma are thought to arise in association with a pre-existing nevus. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 7 Samples
FTP download: GEO (BIGWIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE46nnn/GSE46817/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA202398
Series		Accession: GSE46817	ID: 200046817

5108. Expression data from Uninfected and BRAF600V induced melanocytes
(Submitter supplied) Melanocytes within benign human nevi are the paradigm for tumor suppressive senescent cells in a pre-malignant neoplasm. These cells typically contain mutations in either the BRAF or N-RAS oncogene and express markers of senescence, including p16. However, a nevus can contain 10s to 100s of thousands of clonal melanocytes and approximately 20-30% of melanoma are thought to arise in association with a pre-existing nevus. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 2 Samples
FTP download: GEO (BIGWIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE46nnn/GSE46805/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA202399
Series		Accession: GSE46805	ID: 200046805

5109. USP49 deubiquitinates histone H2B and regulates pre-mRNA splicing
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL15433 GPL9115 10 Samples
FTP download: GEO (BEDGRAPH, GTF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE38nnn/GSE38101/
Series		Accession: GSE38101	ID: 200038101

5110. Examination of gene expression in wild type and USP49 knockdown cells [RNA-Seq]
(Submitter supplied) Posttranslational histone modifications play important roles in regulating chromatin structure and function. Histone H2B ubiquitination and deubiquitination have been implicated in transcriptional regulation, but the function of H2B deubiquitination is not well defined, particularly in higher eukaryotes. Here we report the purification of USP49 as a histone H2B specific deubiquitinase and demonstrate that H2B deubiquitination by USP49 is required for efficient co-transcriptional splicing of a large set of exons. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 2 Samples
FTP download: GEO (BEDGRAPH, GTF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE38nnn/GSE38100/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA167216
Series		Accession: GSE38100	ID: 200038100

5111. Transcriptomes of K562 cell line
(Submitter supplied) To investigate the expression level of genes in K562 cells
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9442 1 Sample
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE39nnn/GSE39374/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA171143
Series		Accession: GSE39374	ID: 200039374

5112. Differences in gastric carcinoma microenvironment stratify according to EBV infection intensity; implications for possible immune adjuvant therapy
(Submitter supplied) Our goal of this study was to perform quantitative and global assessment of EBV gene expression in gastric carcinomas and assess EBV associated cellular pathway alterations.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE45nnn/GSE45453/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA194069
Series		Accession: GSE45453	ID: 200045453

5113. Mapping ERβ genomic binding sites reveals unique genomic features and identifies EBF1 as an ERβ interactor
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL11154 GPL9115 8 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48161/
Series		Accession: GSE48161	ID: 200048161

5114. Mapping ERβ genomic binding sites reveals unique genomic features and identifies EBF1 as an ERβ interactor [Gro-Seq]
(Submitter supplied) The C4-12/Flag.ERβ cell line which stably expressed Flag.ERβ is used to study ERβ genomic functions without ERα interference. Mapping ERβ binding sites in these cells reveals ERβ unique distribution and motif enrichment patterns. Accompanying our mapping results, nascent RNA profiling is performed on cells at the same treatment time. The combined results allow the identification of ERβ target genes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL9115 GPL11154 4 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48159/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA209071
Series		Accession: GSE48159	ID: 200048159

5115. A Stable Transcription Factor Complex Nucleated by Dimeric AML1-ETO Controls Leukaemogenesis
(Submitter supplied) AML1-ETO, a fusion protein generated by the t(8;21) translocation in acute myeloid leukemia, is a transcription factor implicated in both gene repression and activation. We now show that, in leukemic cells, AML1-ETO resides in and functions through a stable protein complex (AETFC) that contains several hematopoietic transcription factors and cofactors. In conjunction with biochemical and leukemia pathological studies, the ChIP-seq and RNA-seq analyses of the AETFC components in leukemic cells reveal that these components stabilize the complex through multivalent interactions, provide multiple DNA-binding domains for diverse target genes, colocalize genome-wide, cooperatively regulate gene expression, and contribute to leukemogenesis.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL10999 GPL11154 17 Samples
FTP download: GEO (TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE43nnn/GSE43834/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA187930
Series		Accession: GSE43834	ID: 200043834

5116. Global regulation of alternative splicing by adenosine deaminase acting on RNA (ADAR) [RNA-seq]
(Submitter supplied) Alternative mRNA splicing is a major mechanism for gene regulation and transcriptome diversity. Despite the extent of the phenomenon, the regulation and specificity of the splicing machinery are only partially understood. Adenosine-to-inosine (A-to-I) RNA editing of pre-mRNA by ADAR enzymes has been linked to splicing regulation in several cases. Here we used bioinformatics approaches, RNA-seq and exon-specific microarray of ADAR knockdown cells to globally examine how ADAR and its A-to-I RNA editing activity influence alternative mRNA splicing. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 4 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE47nnn/GSE47997/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA208620
Series		Accession: GSE47997	ID: 200047997

5117. Genome-wide methylation and expression analysis of two breast cancer cell lines
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms: GPL10999 GPL9442 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE45nnn/GSE45337/
Series		Accession: GSE45337	ID: 200045337

5118. Genome-wide methylation and expression analysis of two breast cancer cell lines [RNA-Seq]
(Submitter supplied) To improve our understanding of the relationships between methylation and expression we profiled mRNA expression and single-base resolution methylation levels for two breast cancer cell lines, MCF7 and T47D. Expression was profiled using RNA-seq.  Methylation was assayed using Methyl-MAPS, which uses methylation-sensitive and -dependent restriction enzyme digests followed by high-throughput sequencing to identify methylation levels at individual CpGs (Edwards et al. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE45nnn/GSE45335/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA193492
Series		Accession: GSE45335	ID: 200045335

5119. Molecular profiling of human mammary gland links breast cancer risk to a p27+ cell population with progenitor characteristics
(Submitter supplied) Gene expression, DNA and histone methylation profiles were performed on multiple cell types purified from normal human nulliparous and parous breast tissue using SAGE-seq, MSDK-seq and ChIP-seq [GSE26141].
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform: GPL9052 42 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE32nnn/GSE32017/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA147521
Series		Accession: GSE32017	ID: 200032017

5120. Lung adenocarcinoma metastasis is suppressed by the alveolar lineage transcription factors GATA6 and HOPX.
(Submitter supplied) Molecular programs that mediate normal cell differentiation are required for oncogenesis and tumor cell survival in certain cancers. How cell-lineage-restricted genes specifically influence metastasis is poorly defined. In lung cancers, we uncovered a transcriptional program that is preferentially associated with distal airway epithelial differentiation and lung adenocarcinoma (ADC) progression. This program is regulated in part by the lineage transcription factors GATA6 and HOPX. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE39nnn/GSE39121/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA170053
Series		Accession: GSE39121	ID: 200039121

5121. Breakpoint analysis of transcriptional and genomic profiles uncovers novel gene fusions spanning multiple human cancer types
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL9115 GPL15797 GPL11154 23 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE45nnn/GSE45137/
Series		Accession: GSE45137	ID: 200045137

5122. Breakpoint analysis of transcriptional and genomic profiles uncovers novel gene fusions spanning multiple human cancer types (RNA-seq)
(Submitter supplied) We report the design and implementation of a "breakpoint analysis" pipeline to discover novel gene fusions by tell-tale transcript level or genomic DNA copy number transitions occurring within genes.  We use this method to prioritize candidate rearrangements from high density array CGH datasets as well as exon-resolution expression microarrays.  We mine both publicly available data as well as datasets generated in our laboratory. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL9115 GPL11154 7 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE45nnn/GSE45133/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA192951
Series		Accession: GSE45133	ID: 200045133

5123. Argonaute 2
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Non-coding RNA profiling by array; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms: GPL10999 GPL14767 GPL10850 17 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE41nnn/GSE41081/
Series		Accession: GSE41081	ID: 200041081

5124. Next Generation Sequencing Facilitates Quantitative Analysis of Argonaute 2 (Ago2)-immunoprecipitation (IP) after miR-195 or miR-497 overexpression in HepG2
(Submitter supplied) To explore functionally crucial tumor-suppressive (TS)-miRNAs in hepatocellular carcinoma (HCC), we performed integrative function- and expression-based screenings of TS-miRNAs in six HCC cell lines.  The screenings identified seven miRNAs, which showed growth-suppressive activities through the overexpression of each miRNA and were endogenously downregulated in HCC cell lines.  Further expression analyses using a large panel of HCC cell lines and primary tumors demonstrated four miRNAs, miR-101, -195, -378 and -497, as candidate TS-miRNAs frequently silenced in HCCs. more...
Organism:	Homo sapiens
Type:		Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL10999 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE41nnn/GSE41074/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA175701
Series		Accession: GSE41074	ID: 200041074

5125. Functional Identification of Critical Bmi1 target genes in Neural Progenitor and Malignant Glioma cells
(Submitter supplied) In this study, we combined a genome-wide analysis of the Polycomb protein Bmi1 and an in vivo RNAi screening to identify critical targets whose repression in neural progenitor and Malignant Glioma cells enables normal and aberrant self-renewal.
Organism:	Homo sapiens; Mus musculus
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
4 related Platforms 42 Samples
FTP download: GEO (BAM, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE33nnn/GSE33912/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA148249
Series		Accession: GSE33912	ID: 200033912

5126. EZH2 is required for germinal center formation and somatic EZH2 mutations promote lymphoid transformation
(Submitter supplied) The EZH2 histone methyltransferase is highly expressed in germinal center (GC) B-cells and targeted by somatic mutations in B-cell lymphomas. Here we find that EZH2 deletion or pharmacologic inhibition suppresses GC formation and functions in mice. EZH2 represses proliferation checkpoint genes and helps establish bivalent chromatin domains at key regulatory loci to transiently suppress GC B-cell differentiation. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL13112 GPL10999 GPL11154 61 Samples
FTP download: GEO (BED, TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE45nnn/GSE45982/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA198866
Series		Accession: GSE45982	ID: 200045982

5127. A high dimensional deep sequencing study of non-small cell lung adenocarcinoma in never-smoker Korean females
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome variation profiling by array; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms: GPL10153 GPL10999 48 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE37nnn/GSE37765/
Series		Accession: GSE37765	ID: 200037765

5128. A high dimensional deep sequencing study of non-small cell lung adenocarcinoma in never-smoker Korean females [Seq]
(Submitter supplied) One of the most fertile applications of next generation sequencing will be in the field of cancer genomics. Here, we report a high-throughput multi-dimensional sequencing study of primary non-small cell lung adenocarcinoma tumors and adjacent normal tissues of 6 never-smoker Korean female patients. Our data encompass results from exome-seq, RNA-seq, small RNA-seq, and MeDIP-seq. We identified and validated novel genetic aberrations including 47 somatic mutations and 20 fusion transcripts. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL10999 36 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE37nnn/GSE37764/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA163279
Series		Accession: GSE37764	ID: 200037764

5129. Enhancer Transcripts Mark Active Estrogen Receptor Binding Sites
(Submitter supplied) In this study, we used Global Run-On sequencing (GRO-seq), a method that assays the genome-wide location and orientation of all active RNA polymerases. We generated a global profile of active transcription at ERα binding sites in MCF-7 human breast cancer cells in response to short time course of E2 treatment. This method enabled us to detect active transcription at enhancers and define a class of primary transcripts transcribed uni- or bidirectionally from the ERα binding sites. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 6 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE43nnn/GSE43835/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA187528
Series		Accession: GSE43835	ID: 200043835

5130. A receptor tyrosine kinase network comprised of FGFRs, EGFR, ERBB2, and MET drives growth and survival of HNSCC cell lines.
(Submitter supplied) We have previously shown that some gefitinib insensitive head and neck squamous cell carcinoma (HNSCC) cell lines exhibit dominant autocrine fibroblast growth factor receptor (FGFR) signaling. Herein, we deployed a whole genome loss-of-function screen to identify genes whose knockdown potentiated the inhibitory effect of the FGFR inhibitor, AZ12908010, in HNSCC cell lines. Three HNSCC cell lines expressing a genome-wide shRNA library were treated with AZ8010 and the abundance of shRNA sequences was assessed by deep sequencing. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 21 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE39nnn/GSE39305/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA170525
Series		Accession: GSE39305	ID: 200039305

5131. Comparing proteomics and RISC immunoprecipitations to identify targets of Epstein-Barr viral miRNAs [RISC-IP-seq]
(Submitter supplied) Epstein-Barr virus is a gamma-herpes virus that is causally associated with several lymphomas and carcinomas. This virus encodes at least 25 pre-miRNAs, which are expressed in infected cells to yield more than 50 detected mature miRNAs. miRNAs are small, non-coding RNAs that inhibit gene expression by promoting the inhibition of translation or of degradation of mRNAs. Currently, the function of these viral miRNAs and the contribution they provide to EBV's life-cycle remain largely unknown, due to difficulties in identifying cellular and viral genes regulated by these miRNAs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE46nnn/GSE46514/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA200712
Series		Accession: GSE46514	ID: 200046514

5132. RNA-seq in breast cancer cell lines after manipulation of miR-23b expression
(Submitter supplied) RNA sequencing technology has been carried out in order to evaluate mRNA expression changes after manipulation of miR-23b in both MCF-7 and MDA-MB-231 breast cancer cell lines
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE37nnn/GSE37918/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA165157
Series		Accession: GSE37918	ID: 200037918

5133. Epstein-Barr virus maintains lymphomas via its miRNAs
(Submitter supplied) Epstein‐Barr virus (EBV) has evolved exquisite controls over its host cells, human B lymphocytes, not only directing these cells during latency to proliferate and thereby expand the pool of infected cells, but also to survive and thereby persist for the lifetime of the infected individual.  Although these activities ensure the virus is successful, they also make the virus oncogenic, particularly when infected people are immunosuppressed. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 4 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE44nnn/GSE44769/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA192693
Series		Accession: GSE44769	ID: 200044769

5134. Human PA-1 cells treated with scrambled or specific ASOs
(Submitter supplied) We describe the discovery of sno-lncRNAs, a class of nuclear-enriched intron-derived long noncoding RNAs (lncRNAs) that are processed on both ends by the snoRNA machinery. During exonucleolytic trimming, the sequences between the snoRNAs are not degraded, leading to the accumulation of lncRNAs flanked by snoRNA sequences but lacking 5' caps and 3' poly(A) tails. Such RNAs are widely expressed in cells and tissues and can be produced by either box C/D or box H/ACA snoRNAs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE38nnn/GSE38541/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA200086
Series		Accession: GSE38541	ID: 200038541

5135. Inactive or moderately active human promoters are enriched for inter-individual epialleles [Seq]
(Submitter supplied) We first demonstrate that non-genetically determined inter-individual differentially methylated regions (iiDMRs) can be temporally stable for at least two years. Then, we show that iiDMRS are associated with concomitant changes in chromatin state as measured by inter-individual differences in the levels of the histone variant H2A.Z. However, the correlation of promoter iiDMRs with gene expression is negligible and this correlation is not improved even by integrating H2A.Z information. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL10999 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE46nnn/GSE46217/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA198092
Series		Accession: GSE46217	ID: 200046217

5136. Signaling Pathways Deferentially Affect RNA Polymerase II Initiation, Pausing, and Elongation in Human Cells: Estrogen dependent signaling in MCF-7 cells
(Submitter supplied) We used Global Run-on and Sequencing (GRO-seq) to measure the rate of transcription elongation by RNA polymerase II (Pol II) following gene activation.  We observed that Pol II elongation rates can vary as much as 4-fold at different genomic loci and in response to two distinct cellular signaling pathways (i.e., estrogen and TNFα).  Elongation rates are slowest near the promoter and increase during the first ~15 kb transcribed into the gene body. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 11 Samples
FTP download: GEO (BED, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE41nnn/GSE41324/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA176560
Series		Accession: GSE41324	ID: 200041324

5137. KRAB/KAP1-microRNA cascade regulates erythropoiesis through the stage-specific control of mitophagy
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Expression profiling by array
Platforms: GPL9250 GPL11154 GPL6887 15 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE44nnn/GSE44065/
Series		Accession: GSE44065	ID: 200044065

5138. KRAB/KAP1-microRNA cascade regulates erythropoiesis through the stage-specific control of mitophagy [Seq]
(Submitter supplied) A multilayered transcription regulatory system is unveiled, where protein- and RNA-based repressors are super-imposed in combinatorial fashion to govern the timely triggering of an essential step of erythropoiesis
Organism:	Homo sapiens; Mus musculus
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL9250 7 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE44nnn/GSE44061/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA188561
Series		Accession: GSE44061	ID: 200044061

5139. Transcriptome sequencing of human hepatocellular carcinoma
(Submitter supplied) Deep high-throughput transcriptome sequencing (RNA-seq) performed on 3 pairs of matched tumor and adjacent non-tumorours (NT) tissues from HCC patients of Chinese origin generated 183.6-million reads that could be aligned. We discovered a number of differentially expressed genes and multiple types of somatic single nucleotide variations (SNVs) in expressed genes.  After the removal of the error alignments, high-quality reads were mapped to the human reference sequence (GRCh37/hg19) using three different softwares TopHat, Burrows-Wheeler Aligner (BWA) and CLC Genomics Workbench (CLC). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE33nnn/GSE33294/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA149267
Series		Accession: GSE33294	ID: 200033294

5140. Examination of gene expression in human placenta using RNA-seq
(Submitter supplied) As genome-scale DNA methylation sequencing technologies have improved it has become apparent that tissue-specific methylation can occur not only at promoters, enhancers, and CpG islands but also over larger genomic regions. In most human tissues, the vast majority of the genome is highly methylated (>70%). However, genomic sequencing of bisulfite-treated DNA (MethylC-seq) has revealed large partially methylated domains (PMDs) in some human cell lines. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE39nnn/GSE39776/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA171704
Series		Accession: GSE39776	ID: 200039776

5141. High-throughput transcriptome sequencing of an AML-M2 patient in two stages: primary tumor and remission.
(Submitter supplied) In order to detect the transcriptomic differences during chemotherapy treatment of de novo AML, we adopted massively parallel pyrosequencing of mRNAs (RNA-seq) using blood tissues of an patient with AML (FAB subtype M2) in tumor stage and remission stage. We obtained a total of 34.6 and 30.8 million paired reads from the two samples. The RNA-seq data derived from the sample illustrated the differentially expression genes between the two stages.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 2 Samples
FTP download: GEO (DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36866/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA157037
Series		Accession: GSE36866	ID: 200036866

5142. Transcriptome-profiling (RNA-seq) and Ribosome-profiling (Ribo-seq) in proliferation, quiescence, senescence and transformed states.
(Submitter supplied) We applied in parallel RNA-Seq and Ribosome-profiling analyses to immortalized human primary BJ fibroblast cells under the following conditions: normal proliferation, quiescence (induced by serum depletion), senescence (induced by activation of the oncogenic RASG12V gene, and examined at early (5 days; pre-senescent state) and late (14 days; fully senescent state) time points), and neoplastic transformation (induced by RASG12V in the background of stable p53 and p16INK4A knockdowns and SV40 small-T expression.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL11154 17 Samples
FTP download: GEO (TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE42nnn/GSE42509/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA182756
Series		Accession: GSE42509	ID: 200042509

5143. Amplitude modulation of androgen signaling by c-MYC
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE45nnn/GSE45203/
Series		Accession: GSE45203	ID: 200045203

5144. Amplitude modulation of androgen signaling by c-MYC [RNA-Seq]
(Submitter supplied) Androgen-stimulated growth of the molecular apocrine breast cancer is mediated by an androgen receptor (AR)-regulated transcriptional program.  Through profiling the genomic licalizations of AR and its co-regulators FOXA1 and TCF7L2 in MDA-MB-453 breast cancer cells, we revealed the molecular details of the AR-centered regulatory network. We further identified that  c-MYC is a key downstream target co-regulated by AR, FOXA1 and TCF7L2, and reinforces the transctiopnal activation of androgen-responsive genes in this subtype of breast cancers.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 3 Samples
FTP download: GEO (TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE45nnn/GSE45202/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA193203
Series		Accession: GSE45202	ID: 200045202

5145. Transcriptome of chronic myeloid leukemia blood in early disease based on RNA-seq method
(Submitter supplied) In order to support our research of chronic myeloid leukemia in human genome, we conducted massively parallel pyrosequencing of mRNAs (RNA-seq) using chronic myeloid leukemia blood in early disease. We obtained a total of 17.74 million read pairs from blood in early disease.The RNA-seq data derived from the sample illustrated the expreesion genes in chronic myeloid leukemia blood in early disease of human.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 1 Sample
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36522/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA153477
Series		Accession: GSE36522	ID: 200036522

5146. Stability, Delivery and Functions of Human Sperm RNAs at Fertilization
(Submitter supplied) We report on abundance and transcript profile characteristics of sperm RNAs.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 5 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE42nnn/GSE42326/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA181058
Series		Accession: GSE42326	ID: 200042326

5147. Translatome of A549, H1299 and HBE cells
(Submitter supplied) We performed translatome and transcriptome sequencing of A549, H1299 and HBE cells and analyzed the translation ratio (TR) of all genes
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL10999 GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE42nnn/GSE42006/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA178748
Series		Accession: GSE42006	ID: 200042006

5148. miR-139-5p induced gene expression alteration in glioma cells
(Submitter supplied) To evaluate gene expression alteration following miR-139-5p transfection in glioma cells. We find a significant downregulation of two transcriptional factors, E2F3 and HoxA9.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL6480 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE44nnn/GSE44728/
Series		Accession: GSE44728	ID: 200044728

5149. GRO-seq from HCT116 cells
(Submitter supplied) The majority of transcription studies examine steady-state RNA . However steady-state RNA is not a true reflection of the transcriptome, because the RNA levels are affected by both transcription rate and degradation rate. In this experiment we measured the amount of transcription occurring in HCT116 colon cancer cells, regardless of degradation, using GRO-seq (global nuclear run-on sequencing). This information demonstrates that many genes have a pile-up of transcriptionally-engaged polymerase near their 5'-end.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL11154 1 Sample
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE38nnn/GSE38140/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA167277
Series		Accession: GSE38140	ID: 200038140

5150. Modulation of gene expression by ZNF143, THAP11 and NOTCH1 via overlapping binding sites in mammalian cells
(Submitter supplied) In this study we investigated the genome wide DNA binding profile of ZNF143 and ICN1 in human and murine cells. We also analyzed the expression profile in human cells after overexpression or knockdown of ZNF143.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL10999 GPL11002 GPL11154 17 Samples
FTP download: GEO (TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE39nnn/GSE39263/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA170436
Series		Accession: GSE39263	ID: 200039263

5151. Transcriptional profiles of PA1 teratoma cells transfected by RIPK1, RIPK2, RIPK3, or RIPK4
(Submitter supplied) RIPK4 but not the related kinases RIPK1, RIPK2, and RIPK3 caused similar transcriptional changes to Wnt3a.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE43nnn/GSE43362/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA185828
Series		Accession: GSE43362	ID: 200043362

5152. Circulating Breast Tumor Cells Exhibit Dynamic Changes in Epithelial and Mesenchymal Cell Composition
(Submitter supplied) By applying RNA-ISH and RNAseq to circulating tumor cells (CTCs), the study provides definitive evidence of epithelial to mesenchymal transition (EMT) across all histological types of breast cancer, identifying mediators such as FOXC1 and TGF-β signaling, and demonstrating dynamic treatment-associated changes in EMT within clusters of CTCs.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL14761 30 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE41nnn/GSE41245/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA176307
Series		Accession: GSE41245	ID: 200041245

5153. Enhancer Transcripts Mark Active Estrogen Receptor Binding Sites using GRO-seq
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 14 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE43nnn/GSE43836/
Series		Accession: GSE43836	ID: 200043836

5154. Transcriptome of normal, paracancerouse and cancerous bladder tissues based on RNA-Seq method
(Submitter supplied) In order to support our research of bladder cancer in human genome, we conducted massively parallel pyrosequencing of mRNAs (RNA-Seq) using normal, paracancerouse and cancerous human bladder tissues. We obtained a total of 30.0 million read pairs from normal, 33.1 million read pairs from paracancerous and 36.5 million read pairs from cancerous. The RNA-Seq data derived from the sample illustrated the differencially expression genes among normal, paracancerous and cancerous bladder tissues of human.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 3 Samples
FTP download: GEO (DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE35nnn/GSE35178/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA150663
Series		Accession: GSE35178	ID: 200035178

5155. Characteristics of Cross-Hybridization and Cross-Alignment in Pseudo-Xenograft samples by RNA-Seq and Microarrays
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by array; Expression profiling by high throughput sequencing
5 related Platforms 49 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE40nnn/GSE40892/
Series		Accession: GSE40892	ID: 200040892

5156. Characteristics of Cross-Hybridization and Cross-Alignment in Pseudo-Xenograft samples by RNA-Seq and Microarrays [RNA-Seq]
(Submitter supplied) In order to study molecular changes in the stroma from tissue samples it is recommended to separate tumor tissue from stromal tissue. This is particularly relevant to mouse tumor xenograft models where tumor, particularly metastatic tumors, can be small and difficult to separate from the host tissue. In our research we compared qualitatively the ability of high-throughput mRNA sequencing, RNA-Seq, and microarrays to detect tumor (human) and stromal (mouse) expression from mixed tumor-stromal samples in terms of the genes and pathways that are involved in cross-alignment (RNA-Seq) and cross-hybridization (microarrays).
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11002 GPL10999 GPL16061 19 Samples
FTP download: GEO (GTF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE40nnn/GSE40890/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA175327
Series		Accession: GSE40890	ID: 200040890

5157. RECURRENT SETBP1 MUTATIONS IN ATYPICAL CHRONIC MYELOID LEUKEMIA
(Submitter supplied) RNA-Seq analysis of atypical chronic myeloid leukemia samples
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 13 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE42nnn/GSE42146/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA179284
Series		Accession: GSE42146	ID: 200042146

5158. Identification of a Novel Angiogenesis and Tumor Suppressor Gene   Rab25 in Esophageal Squamous Cell Carcinoma
(Submitter supplied) Twelve clinical samples from human esophageal squamous cell carcinoma (ESCC) (seven tumors and five non-tumors) were sequenced using Illumina high-throughput sequencing and the RNA-Seq profiling was investigated with 1730 genes significantly differentially expressed. The gene Rab25 was found to be down-regulated in tumors (p-value < 1E-20) and identified as a novel candidate tumor suppressor gene. The down-regulation of Rab25 was examined in a large cohort of ESCC and non-tumor cases by qPCR and immunohistochemistry analyses. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 12 Samples
FTP download: GEO (BAM, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE32nnn/GSE32424/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA147913
Series		Accession: GSE32424	ID: 200032424

5159. RNA-seq HL60 cells
(Submitter supplied) Identification of the all RNA species coding and non-coding in total RNA
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (GTF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE41nnn/GSE41279/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA176438
Series		Accession: GSE41279	ID: 200041279

5160. Relationship between DNMT1-RNA interactions, DNA methylation and gene expression
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms: GPL11154 GPL6244 GPL10999 8 Samples
FTP download: GEO (BSP, CEL, GTF, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE32nnn/GSE32260/
Series		Accession: GSE32260	ID: 200032260

5161. Mapping of Transcription Start Sites of Normal and Cancerous Prostate Cells
(Submitter supplied) Capped analysis of gene expression (CAGE) sequencing was done on a normal and a cancer cell line to examine how promoter usage changes between these two states.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 2 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE38nnn/GSE38677/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA168461
Series		Accession: GSE38677	ID: 200038677

5162. Expression Analysis of Normal and Cancerous Prostate Cells
(Submitter supplied) Strand-specific RNA sequencing was done on a normal and a cancer cell line to examine how isoforms are used differently between these two states.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 2 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE38nnn/GSE38676/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA168460
Series		Accession: GSE38676	ID: 200038676

5163. Transcriptomic response to benzo[a]pyrene treatment in HepG2 cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL9052 GPL13695 16 Samples
FTP download: GEO (CEL, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36244/
Series		Accession: GSE36244	ID: 200036244

5164. Transcriptomic response to benzo[a]pyrene treatment in HepG2 cells (RNA-Seq)
(Submitter supplied) Whole-genome transcriptome measurements are pivotal for characterizing carcinogenic mechanisms of chemicals and predicting toxic classes, such as genotoxicity, from in vitro and in vivo assays. DNA microarrays have evolved as the gold standard for this purpose. In recent years deep sequencing technologies have been developed that hold the promise of measuring the transcriptome with RNA-seq in a more accurate and unbiased manner than microarrays. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36242/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA155821
Series		Accession: GSE36242	ID: 200036242

5165. K562 polyA RNA-Seq
(Submitter supplied) RNA-Seq reads and TopHat (Trapnell et al. Bioinformatics 2009) alignments of K562 cell-line transcriptome.  These were used to validate the expression of short peptides idenitified by Mass-Spectrometry in K562 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL9115 GPL11154 9 Samples
FTP download: GEO (BAM) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE34nnn/GSE34740/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA150405
Series		Accession: GSE34740	ID: 200034740

5166. A model system for assessing the ability of exon microarray and tag sequencing to detect genes specific for malignant B-cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL9052 GPL15981 16 Samples
FTP download: GEO (CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE40nnn/GSE40311/
Series		Accession: GSE40311	ID: 200040311

5167. A model system for assessing the ability of tag sequencing to detect genes specific for malignant B-cells
(Submitter supplied) The purpose of this study was to develop a quantification method that can be used to assess the ability of tag-seq to detect malignant B-cell transcripts. The data support that tumour cell concentration is an important variable with fundamental impact on gene expression pattern.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE40nnn/GSE40310/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA173462
Series		Accession: GSE40310	ID: 200040310

5168. Histone acetylation regulates intracellular pH
(Submitter supplied) Differences in global levels of histone acetylation occur in normal and cancer cells, although the reason cells regulate these levels has remained unclear. Here we demonstrate a role for histone acetylation in regulating intracellular pH (pHi). As pHi decreases, histones are globally deacetylated by histone deacetylases (HDACs) and the released acetate anions are co-exported with protons out of the cell by monocarboxylate transporters (MCTs), preventing further reductions in pHi. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (BED, TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE40nnn/GSE40114/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA172856
Series		Accession: GSE40114	ID: 200040114

5169. Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues
(Submitter supplied) In our study we applied a genome-wide DNA methylation analysis approach, MethylCap-seq, to map the differentially methylated regions in 24 tumor and matched normal colon samples. In total, 2687 frequently hypermethylated and 468 frequently hypomethylated regions were identified, which include potential biomarkers for CRC diagnosis. Hypermethylation in the tumor samples was enriched at CpG islands and gene promoters, while hypomethylation was distributed throughout the genome. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL10999 68 Samples
FTP download: GEO (BED, TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE39nnn/GSE39068/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA169875
Series		Accession: GSE39068	ID: 200039068

5170. Revisiting Global Gene Expression Analysis
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL16043 GPL11154 8 Samples
FTP download: GEO (CEL, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE40nnn/GSE40784/
Series		Accession: GSE40784	ID: 200040784

5171. Revisiting Global Gene Expression Analysis (RNA-Seq)
(Submitter supplied) Gene expression analysis is a widely used and powerful method for investigating the transcriptional behavior of biological systems, for classifying cell states in disease and for many other purposes.  Recent studies indicate that common assumptions currently embedded in experimental and analytical practices can lead to misinterpretation of global gene expression data.  We discuss these assumptions and describe solutions that should minimize erroneous interpretation of gene expression data from multiple analysis platforms.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE40nnn/GSE40783/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA174954
Series		Accession: GSE40783	ID: 200040783

5172. Transcriptional Profiling of Psoriasis Using RNA-seq Reveals Previously Unidentified Differentially Expressed genes
(Submitter supplied) The transcriptomic profiling of psoriasis has led to an increased understanding of disease pathogenesis. Although microarray technologies have been instrumental in this regard, it is clear that these tools detect an incomplete set of DEGs. RNA-seq can be used to supplement these prior technologies. Here, the use of RNAseq methods substantially increased the number of psoriasis-related DEGs. Furthermore, DEGs that were uniquely identified by RNA-seq, but not in other published microarray studies, further supported the role of IL-17 and tumor necrosis factor-a synergy in psoriasis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE41nnn/GSE41745/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA178116
Series		Accession: GSE41745	ID: 200041745

5173. The viral and cellular microRNA targetome in lymphoblastoid cell lines
(Submitter supplied) Epstein-Barr virus (EBV) is a human herpesvirus linked to a number of B cell cancers and lymphoproliferative disorders. During latent infection, EBV expresses 25 viral pre-microRNAs (miRNAs) and induces the expression of specific host miRNAs, such as miR-155 and miR-21, which potentially play a role in viral oncogenesis. To date, a limited number of EBV miRNA targets have been identified; thus, the role of EBV miRNAs in viral pathogenesis is not well defined. more...
Organism:	Homo sapiens
Type:		Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL10999 11 Samples
FTP download: GEO (BED, TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE41nnn/GSE41437/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA177675
Series		Accession: GSE41437	ID: 200041437

5174. Small RNA and mRNA profiles following TUT knock-down in HeLa
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL9115 GPL10999 7 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE40nnn/GSE40236/
Series		Accession: GSE40236	ID: 200040236

5175. mRNA profiles following TUT knock-down in HeLa
(Submitter supplied) The precise control of microRNA (miRNA) biogenesis is important for various cellular functions, and its dysregulation is often associated with human diseases.  We previously reported that Terminal   uridylyl transferase 4 (TUT4) down-regulates let-7 miRNA biogenesis by oligo-uridylating let-7 precursor (pre-let-7) in mouse embryonic stem cells and that a pluripotency marker Lin28 promotes   a processivity of TUT4. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE40nnn/GSE40228/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA173241
Series		Accession: GSE40228	ID: 200040228

5176. Ago HITS-CLIP in KSHV-infected primary effusion lymphoma (PEL) cell lines BCBL-1 and BC-3
(Submitter supplied) We performed Ago HITS-CLIP to identify targets of viral and human miRNAs in latently KSHV-infected PEL cells
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL10999 7 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE41nnn/GSE41357/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA176666
Series		Accession: GSE41357	ID: 200041357

5177. DNMT3B7, an aberrant DNMT3B isoform, suppresses growth, induces differentiation, and alters DNA methylation in human neuroblastoma
(Submitter supplied) In adult cancers, epigenetic changes and aberrant splicing of the DNMT3B is commonly observed, and the pattern of gene methylation and expression has been shown to be modified by DNMT3B7, a truncated protein of DNMT3B.  Much less is known about the mechanism of epigenetic changes in the pediatric cancer neuroblastoma.  To investigate if aberrant DNMT3B transcripts alter DNA methylation, gene expression and tumor phenotype in neuroblastoma, we measured DNMT3B isoform expression in primary tumors and cell lines. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 3 Samples
FTP download: GEO (TAR) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36350/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA153309
Series		Accession: GSE36350	ID: 200036350

5178. Genetically-driven target tissue over-expression of CD40: A novel mechanism in autoimmune disease
(Submitter supplied) The CD40 gene, an important immune regulatory gene, is also expressed and functional on non-myeloid derived cells, many of which are targets for tissue specific autoimmune diseases, including d thyroid follicular cells in Graves’ disease (GD). Whether target tissue CD40 expression plays a role in autoimmune disease etiology has yet to be determined. Here we show for the first time, that target-tissue over-expression of CD40 plays a key role in the etiology of autoimmunity. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL13112 GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE39nnn/GSE39081/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA169916
Series		Accession: GSE39081	ID: 200039081

5179. Gene Expression Changes in a Tumor Xenograft by a Py-Im Polyamide
(Submitter supplied) Gene regulation by DNA binding small molecules could have important therapeutic applications. This study reports the investigation of a DNA-binding pyrrole-imidazole polyamide targeted to bind the DNA sequence 5’-WGGWWW-3’ with reference to its potency in a subcutaneous xenograft tumor model. The molecule is capable of trafficking to the tumor site following subcutaneous injection and modulates transcription of select genes in vivo. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL13112 GPL11154 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE40nnn/GSE40218/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA173215
Series		Accession: GSE40218	ID: 200040218

5180. Persistent androgen receptor-mediated transcription in castration-resistant prostate cancer under androgen-deprived conditions
(Submitter supplied) The androgen receptor (AR) is a ligand-inducible transcription factor that mediates androgen action in target tissues. Upon ligand binding, the AR binds to thousands of genomic loci and activates a cell-type specific gene program. Prostate cancer growth and progression depend on androgen-induced AR signalling. Treatment of advanced prostate cancer through medical or surgical castration leads to initial response and durable remission, but resistance inevitably develops. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms: GPL10999 GPL11154 35 Samples
FTP download: GEO (BEDGRAPH, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE40nnn/GSE40050/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA172760
Series		Accession: GSE40050	ID: 200040050

5181. DPN and Tamoxifen treatments of parathyroid adenoma cells
(Submitter supplied) Stimulation of estrogen receptor beta in PHPT, genetic changes after 24 and 48h of treatments vs. Control
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 23 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE37nnn/GSE37211/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA158975
Series		Accession: GSE37211	ID: 200037211

5182. Oncofusion protein AML1-ETO targets ERG factor binding sites in AML
(Submitter supplied) ERG has been identified as an essential factor for the function and maintenance of adult hematopoietic stem cells and high ERG expression is a negative prognostic marker for treatment outcome in AML. The molecular function of ERG and its interplay with other factors is however largely unknown. Here we demonstrate that ERG has cell type specific distributions in normal CD34+ myeloid progenitors and in AML cells and identify ERG as a potential pioneering protein for binding of oncofusion protein complexes. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL9052 42 Samples
FTP download: GEO (BED, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE23nnn/GSE23730/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA130783
Series		Accession: GSE23730	ID: 200023730

5183. The transcriptional landscape and mutational profile of lung adenocarcinoma
(Submitter supplied) Understanding the molecular signatures of cancer is important to apply appropriate targeted therapies. Here we present the first large scale RNA sequencing study of lung adenocarcinoma demonstrating its power to identify somatic point mutations as well as transcriptional variants such as gene fusions, alternative splicing events and expression outliers. Our results reveal the genetic basis of 200 lung adenocarcinomas in Koreans including deep characterization of 87 surgical specimens by transcriptome sequencing. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 164 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE40nnn/GSE40419/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJEB3132
Series		Accession: GSE40419	ID: 200040419

5184. SOX2 gene regulates the transcriptional network of oncogenes and affects tumorigenesis of human lung cancer cells
(Submitter supplied) Recent studies demonstrated that cancer stem cells (CSCs) have higher tumorigenesis properties than those of differentiated cancer cells and that transcriptional factor-SOX2 plays a vital role in maintaining the unique properties of CSCs; however, the function and underlying mechanism of SOX2 in carcinogenesis of lung cancer are still elusive. This study applied immunohistochemistry to analyze the expression of SOX2 in human lung tissues of normal individuals as well as patients with adenocarcinoma, squamous cell carcinoma, large cell and small cell carcinoma and demonstrated specific overexpression of SOX2 in all types of lung cancer tissues. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36597/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA153681
Series		Accession: GSE36597	ID: 200036597

5185. Transcriptional profiling of lncRNAs and novel transcribed regions across a diverse panel of archived human cancers
(Submitter supplied) Molecular characterization of tumors has been critical for identifying important genes in cancer biology and for improving tumor classification and diagnosis. Long non-coding RNAs (lncRNAs), as a new, relatively unstudied class of transcripts, provide a rich opportunity to identify both functional drivers and cancer-type specific biomarkers. However, despite the potential importance of lncRNAs to the cancer field, no comprehensive survey of lncRNA expression across various cancers has been reported. more...
Organism:	Homo sapiens
Type:		Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL10999 99 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE28nnn/GSE28866/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA140583
Series		Accession: GSE28866	ID: 200028866

5186. Transcriptome of normal,paracancerous and cancerous colon tissues based on RNA-seq method
(Submitter supplied) To support our research of colon cancer in human genome, we conducted massively parallel pyrosequencing of mRNAs (RNA-seq) using normal,paracancerouse and cancerous human colon tissues. We obtained a total of 29.9M reads from normal,33.0M reads from paracancerous and 36.5M reads from cancerous.The RNA-seq data derived from the sample illustrated the differencially expreesion genes among normal,paracancerous and cancerous colon tissues of human.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 3 Samples
FTP download: GEO (BAM, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE33nnn/GSE33782/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA148603
Series		Accession: GSE33782	ID: 200033782

5187. RNA sequencing of circulating tumour cells implicates WNT signaling in pancreatic cancer metastasis
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL14761 GPL14759 44 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE40nnn/GSE40176/
Series		Accession: GSE40176	ID: 200040176

5188. RNA sequencing of circulating tumour cells implicates WNT signaling in pancreatic cancer metastasis (human data)
(Submitter supplied) Circulating tumour cells (CTCs) shed into blood from primary cancers include putative precursors that initiate distal metastases. While these cells are extraordinarily rare, they may identify cellular pathways contributing to the blood-borne dissemination of cancer. Here, we adapted a microfluidic device for efficient capture of CTCs from an endogenous mouse pancreatic cancer model and subjected CTCs to single-molecule RNA sequencing, identifying Wnt2 as enriched in CTCs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL14761 32 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE40nnn/GSE40174/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA173018
Series		Accession: GSE40174	ID: 200040174

5189. Chromatin Accessibility Reveals Insight into Androgen Receptor Activation and Transcriptional Specificity
(Submitter supplied) Using DNase-seq, mRNA-seq and publicly available ChIP-seq data sets, we examined the role of chromatin accessibility (DNase-seq) in androgen receptor binding to the genome (ChIP-seq) and AR-mediated transcriptional changes (mRNA-seq). Our data reveals genome-wide changes in chromatin structure that correspond to AR binding and  differential gene expression.  A focused examination of DNase-seq data around androgen receptor motifs within androgen receptor ChIP-seq peaks reveals distinct patterns of protection from DNaseI cleavage.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE34nnn/GSE34780/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA150331
Series		Accession: GSE34780	ID: 200034780

5190. Genome-wide analysis of histone methylation reveals chromatin state-based regulation of host cellular gene expression induced by hepatitis B viruses
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE35nnn/GSE35465/
Series		Accession: GSE35465	ID: 200035465

5191. Genome-wide analysis of histone methylation reveals chromatin state-based regulation of host cellular gene expression induced by hepatitis B viruses (DGE dataset)
(Submitter supplied) Hepatitis B virus (HBV) is a hepatotropic virus that can regulate many host cellular gene expressions participating in the HBV life cycle, liver inflammation and hepatocellular injury. However, the underlying mechanism of differential gene expression is not understood. We report here a genome-wide analysis of histone methylation on two histone H3 lysine residues (H3K4me3 and H3K27me3) and gene expression profiles in HepG2 and HepG2.2.15 cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE35nnn/GSE35464/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA156115
Series		Accession: GSE35464	ID: 200035464

5192. Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells
(Submitter supplied) We assessed Smart-Seq, a new single-cell RNA-Seq library preparation method, on a variety of mouse and human RNA samples or cells.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
4 related Platforms 121 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE38nnn/GSE38495/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA170814
Series		Accession: GSE38495	ID: 200038495

5193. miRNA sensor and decoy libraries permit high-throughput assessment of miRNA activity and function
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE37nnn/GSE37771/
Series		Accession: GSE37771	ID: 200037771

5194. mRNA profiling of THP1 cell line
(Submitter supplied) Analysis of mRNA in THP1 (human monocytic leukemia) cell line in order to correlate miRNA activity with target abundance.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 1 Sample
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE37nnn/GSE37769/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA163281
Series		Accession: GSE37769	ID: 200037769

5195. Genome-wide characterization of long nonpolyadenylated RNAs
(Submitter supplied) We have used deep sequencing to explore the repertoire of both poly(A)+ and poly(A)- RNAs from two standard cell lines, HeLa cells and human embryonic stem cell (hESC) H9 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 4 Samples
FTP download: GEO (BEDGRAPH, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE22nnn/GSE22666/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA128275
Series		Accession: GSE22666	ID: 200022666

5196. Targeted RT-PCR assays spanning unannotated splice junctions sequenced by Roche 454.
(Submitter supplied) The ENCODE projects seeks to identify and characterize functional elements in the human genome.  Throughout the scale-up phase of ENCODE, the transcriptome group has generate Long RNA-Seq, Small RNA-Seq, Cap-Analysis of Gene Expression (CAGE), and RNA-PET short read data on the Illumina platform for ~ 40 different human primary and transformed cell lines in replicate.   From these data several high-resolution and discrete features/elements have been mined out (5’ caps, splice junctions, polyadenylation sites, small RNAs, etc…). more...
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9186 3 Samples
FTP download: GEO (PSL, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE38nnn/GSE38886/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA169392
Series		Accession: GSE38886	ID: 200038886

5197. Genistein and bisphenol A exposure cause estrogen receptor 1 to bind thousands of binding sites in a cell type-specific manner
(Submitter supplied) To obtain an integrated view of gene regulation in response to environmental and endogenous estrogens on a genome-wide scale, we performed ChIP-seq, to identify estrogen receptor 1 (ER) binding sites, and RNA-seq in endometrial cancer cells exposed to bisphenol A (BPA; found in plastics), genistein (GEN; found in soybean), or 17β-estradiol (E2; an endogenous estrogen).  GEN and BPA treatment induces thousands of ER binding sites and >50 gene expression changes, representing a subset of E2‑induced gene regulation changes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE38nnn/GSE38234/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA167511
Series		Accession: GSE38234	ID: 200038234

5198. Deep Sequence Analysis of non-small cell lung cancer: Integrated analysis of gene expression, alternative splicing, and single nucleotide variations in lung adenocarcinomas with and without oncogenic KRAS mutations
(Submitter supplied) In this manuscript, we have used RNA-Sequencing experiment to obtain and integrate a variety of genomic features in order to identify signaling pathways that are associated to mutant KRAS lung tumors.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE34nnn/GSE34914/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA150161
Series		Accession: GSE34914	ID: 200034914

5199. Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3
(Submitter supplied) The TCF7L2 transcription factor is linked to a variety of human diseases, including type 2 diabetes and cancer. One mechanism by which TCF7L2 could influence expression of genes involved in diverse diseases is by binding  to distinct regulatory regions in different tissues. To test this hypothesis, we performed ChIP-seq for TCF7L2 in 6 human cell lines. We identified 116,000 non-redundant TCF7L2 binding sites, with only 1,864  sites common to the 6 cell lines. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (GFF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE38nnn/GSE38447/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA168032
Series		Accession: GSE38447	ID: 200038447

5200. RNA Sequencing Analysis Generates Comprehensive Transcriptomic Landscape and Identifies PTK6 as a Novel Tumor Suppressor Gene in Esophageal Squamous Cell Carcinoma
(Submitter supplied) We performed the integrative transcriptome analysis of human esophageal squamous cell carcinoma (ESCC) using Illumina high-throughput sequencing. A total of 187 million 38bp sequencing reads were generated containing 7 billion bases for three pairs of matched patient-derived ESCC clinical specimens and their adjacent non-tumorous tissues. By investigating the digital gene expression profiling, we found 1425 genes significantly differentially expressed and detected more than 9000 SNPs across all six samples. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 6 Samples
FTP download: GEO (BAM) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE29nnn/GSE29968/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA140847
Series		Accession: GSE29968	ID: 200029968

5201. CBX3 Regulates Efficient RNA Processing Genome Wide
(Submitter supplied) HP1 alpha, beta, and gamma play an evolutionarily conserved role in the formation and maintenance of heterochromatin. In addition, some HP1 family members may also participate in transcriptional regulation of genes. Recently, HP1 gamma binding to the bodies of a subset of genes has been observed in human and murine cells. However, the generality of this phenomenon and the role HP1 gamma may play in this context are unknown. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by genome tiling array; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
8 related Platforms 39 Samples
FTP download: GEO (BED, BEDGRAPH, GFF, GPR, PAIR) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE28nnn/GSE28115/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA139835
Series		Accession: GSE28115	ID: 200028115

5202. Oncogene-Mediated Alterations in Chromatin Conformation
(Submitter supplied) Emerging evidence suggests that chromatin adopts a non-random three-dimensional (3D) topology and that the organization of genes into structural hubs and domains affects their transcriptional status. How chromatin conformation changes in diseases such as cancer is poorly understood. Moreover, how oncogenic transcription factors, which bind to thousands of sites across the genome, influence gene regulation by globally altering the topology of chromatin requires further investigation. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL10999 14 Samples
FTP download: GEO (BED, SIF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE37nnn/GSE37752/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA163079
Series		Accession: GSE37752	ID: 200037752

5203. Genome-wide analysis of pre-mRNA 3' end processing reveals a decisive role of human cleavage factor I in the regulation of 3' UTR length: CLIP
(Submitter supplied) Through alternative polyadenylation, human mRNAs acquire longer or shorter 3' untranslated regions, the latter typically associated with higher transcript stability and increased protein production. To understand the dynamics of polyadenylation site usage, we mapped transcriptome‐wide both binding sites of 3' end processing factors CPSF‐160, CPSF‐100, CPSF‐73, CPSF‐30, Fip1, CstF‐64, CstF-64tau, CF Im25, CF Im59, and CF Im68 and 3' end processing sites in HEK293 cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 18 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE37nnn/GSE37398/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA159827
Series		Accession: GSE37398	ID: 200037398

5204. Genome‐wide analysis of pre‐mRNA 3' end processing reveals a decisive role of human cleavage factor I in the regulation of 3' UTR length: A-seq
(Submitter supplied) Through alternative polyadenylation, human mRNAs acquire longer or shorter 3' untranslated regions, the latter typically associated with higher transcript stability and increased protein production. To understand the dynamics of polyadenylation site usage, we mapped transcriptome‐wide both binding sites of 3' end processing factors CPSF‐160, CPSF‐100, CPSF‐73, CPSF‐30, Fip1, CstF‐64, CstF-64tau, CF Im25, CF Im59, and CF Im68 and 3' end processing sites in HEK293 cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL11154 4 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE37nnn/GSE37037/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA157987
Series		Accession: GSE37037	ID: 200037037

5205. The SEC family of RNA Polymerase II elongation factors: gene target specificity and transcriptional output
(Submitter supplied) The elongation stage of transcription is a highly regulated in metazoan. We previously purified the AFF1/AFF4-containing Super Elongation Complex (SEC) as a major regulator of development and cancer pathogenesis. Here, we report the biochemical isolation of SEC-like 2 (SEC-L2) and SEC-like 3 (SEC-L3) containing AFF2 and AFF3 in association with P-TEFb, ENL, and AF9. The SEC family members demonstrate high levels of Pol II CTD kinase activity, however, only SEC is required for the proper induction of the HSP70 gene upon stress. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL10999 13 Samples
FTP download: GEO (BAM, BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE34nnn/GSE34097/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA149901
Series		Accession: GSE34097	ID: 200034097

5206. Oncogenic BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Expression profiling by array
Platforms: GPL570 GPL11154 7 Samples
FTP download: GEO (BW, CEL, GTF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE37nnn/GSE37169/
Series		Accession: GSE37169	ID: 200037169

5207. Oncogenic BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration [HT-seq]
(Submitter supplied) Most cancer genomics papers to date have focused on aberrations in genomic DNA and protein-coding transcripts. However, around 50% of transcripts have no coding potential and may exist as non-coding RNA. We performed RNA-seq in BRAFv600e melanoma skin cancer and on melanocytes over-expressing oncogenic BRAF to catalog transcriptome remodeling. We discovered that BRAF regulates expression of 1027 protein coding transcripts, 39 annotated lncRNAs and 70 novel transcripts. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (BW, GTF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE33nnn/GSE33092/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA149345
Series		Accession: GSE33092	ID: 200033092

5208. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Saccharomyces cerevisiae; Homo sapiens; Schizosaccharomyces pombe; Mus musculus
Type:		Expression profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL2529 GPL10999 GPL11002 32 Samples
FTP download: GEO (CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE37nnn/GSE37005/
Series		Accession: GSE37005	ID: 200037005

5209. m6A mapping in human RNA (untreated)
(Submitter supplied) We developed a novel approach, m6A-seq, for high-resolution mapping of the transcriptome-wide m6A landscape, based on antibody-mediated capture followed by massively parallel sequencing.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 7 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE37nnn/GSE37003/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA158111
Series		Accession: GSE37003	ID: 200037003

5210. m6A mapping in human RNA (with treatments)
(Submitter supplied) We developed a novel approach, m6A-seq, for high-resolution mapping of the transcriptome-wide m6A landscape, based on antibody-mediated capture followed by massively parallel sequencing.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE37nnn/GSE37002/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA158109
Series		Accession: GSE37002	ID: 200037002

5211. METTL3 KD in HepG2 cells
(Submitter supplied) To gain insight into possible processes that require m6A for their function, METTL3 was knocked down (KD) in HepG2 cells by siRNA transfections
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE37nnn/GSE37001/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA158107
Series		Accession: GSE37001	ID: 200037001

5212. RNA-seq from ENCODE/Stanford/Yale/USC/Harvard
(Submitter supplied) This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Gerstein Lab mailto:datasubmission@gersteinlab.org). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).  The tracks show enrichment of RNA sequence tags generated by high throughput sequencing (RNA-seq) and mapped to the human genome. more...
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 4 Samples
FTP download: GEO (BIGWIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE35nnn/GSE35587/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA30709
Series		Accession: GSE35587	ID: 200035587

5213. RNA-sequencing analysis of NB4 cells overexpressing miR-125b
(Submitter supplied) To better understand the mechanisms of blockage of myeloid differentiation and apoptosis and induction of proliferation by miR-125b, we proceeded to identify miR-125b target genes involved in these pathways. We analyzed the total cellular gene expression pattern by RNA-sequencing of the parental NB4 myeloid cell line and that transiently transfected with miR-125b. We generated four cDNA libraries corresponding to duplicates of miR-125b and control cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE37nnn/GSE37061/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA158085
Series		Accession: GSE37061	ID: 200037061

5214. Effects of Cardiac Glycosides on RNA Expression in Prostate Cancer LNCaP-abl Cells
(Submitter supplied) Prostate cancer is the most common cancer in men and cardiac glycosides inhibit prostate cancer cell proliferation. In order to investigate the mechanism by which cardiac glycosides inhibit  prostate cancer cells, we observed genome-wide RNA expression in prostate cancer LNCaP-abl cells, hormone resistant cells, after the cardiac glycoside treatment using RNA-Seq. In addition, we profiled LNCaP-abl cells after androgen receptor (AR) knockdown to observe whether cardiac glycoside effect on RNA expression is similar to that of  AR knockdown.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL9115 GPL11154 18 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE35nnn/GSE35126/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA150723
Series		Accession: GSE35126	ID: 200035126

5215. AMPKα Modulation in Cancer Progression: Multilayer Integrative Analysis of the Whole Transcriptome in Asian Gastric Cancer
(Submitter supplied) Gastric cancer is the most common cancer in Asia and most developing countries. To identify the molecular underpinnings of gastric cancer in the Asian population, we applied an RNA-sequencing approach to gastric tumor and noncancerous specimens to quantitatively characterize the entire transcriptome of gastric cancer (including mRNAs and microRNAs). A multi-layer analysis was then developed to identify multiple types of transcriptional aberrations associated with different stages of gastric cancer, including differentially expressed mRNAs, recurrent somatic mutations and key differentially expressed microRNAs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL9442 55 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36968/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA157511
Series		Accession: GSE36968	ID: 200036968

5216. Identification of allele-specific alternative mRNA processing via transcriptome sequencing
(Submitter supplied) Establishing the functional roles of genetic variants remains a significant challenge in the post-genomic era. Here, we present a method, allele-specific alternative mRNA processing (ASARP), to identify genetically influenced mRNA processing events using transcriptome sequencing (RNA-Seq) data. The method examines RNA-Seq data at both single nucleotide and whole-gene/isoform levels to identify allele-specific expression (ASE) and existence of allele-specific regulation of mRNA processing. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 1 Sample
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE29nnn/GSE29738/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA141163
Series		Accession: GSE29738	ID: 200029738

5217. DEEP SEQUENCING OF MODELS OF BREAST DUCTAL CARCINOMA IN SITU REVEALS ALDH5A1 AS A NOVEL POTENTIAL THERAPEUTIC TARGET
(Submitter supplied) We attempted to identify alterations in gene expression that occur during the progression from normal breast to ductal carcinoma in situ (DCIS) with the aim to elucidate significant genes and pathways underlying the premalignant transformation.  To determine the expression changes that are common to multiple DCIS models (MCF10.DCIS, SUM102 and SUM225) and normal mammary epithelial cells (MCF10A), we grew the cells in three dimensional overlay culture with reconstituted basement membrane and used the extracted RNA for 76 cycles of deep sequencing (mRNA-Seq) using Illumina Genome Analyzer GAIIx. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 4 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36863/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA157137
Series		Accession: GSE36863	ID: 200036863

5218. Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk
(Submitter supplied) Cross-talk between DNA methylation and histone modifications drives the establishment of composite epigenetic signatures and is traditionally studied using correlative rather than direct approaches. Here we present sequential ChIP-bisulfite-sequencing (ChIP- BS-seq) as an approach to quantitatively assess DNA methylation patterns associated with chromatin modifications or chromatin-associated factors directly. more...
Organism:	Homo sapiens; Mus musculus
Type:		Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL11002 GPL13112 GPL10999 15 Samples
FTP download: GEO (BED, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE28nnn/GSE28254/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA139563
Series		Accession: GSE28254	ID: 200028254

5219. Integrated genome-wide analysis of transcription factor occupancy, RNA polymerase II binding and steady-state RNA levels identify differentially regulated functional gene classes
(Submitter supplied) Routine methods for assaying steady-state mRNA levels such as RNA-seq and micro-arrays are commonly used as readouts to study the role of transcription factors (TFs) in gene expression regulation. However, cellular RNA levels do not solely depend on activity of TFs and subsequent transcription by RNA polymerase II (Pol II), but are also affected by RNA turnover rate. Here, we demonstrate that integrated analysis of genome-wide TF occupancy, Pol II binding and steady-state RNA levels provide important insights in gene regulatory mechanisms. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL9520 12 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36349/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA153307
Series		Accession: GSE36349	ID: 200036349

5220. The human pancreatic islet transcriptome: impact of pro-inflammatory cytokines
(Submitter supplied) We have used RNA-seq to identify transcripts, including splice variants, expressed in human islets of Langerhans under control condition or following exposure to the pro-inflammatory cytokines interleukin-1β (IL-1β) and interferon-γ (IFN-γ). A total of 29,776 transcripts were identified as expressed in human islets. Expression of around 20% of these transcripts was modified by pro-inflammatory cytokines, including apoptosis- and inflammation-related genes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 10 Samples
FTP download: GEO (BED, GTF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE35nnn/GSE35296/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA151601
Series		Accession: GSE35296	ID: 200035296

5221. Genome-wide maps of chromatin state in NCCIT cells
(Submitter supplied) H2B mono-ubiquitylation is required for multiple methylations of both H3K4 and H3K79 and has been implicated in gene expression from yeast to human. However, molecular crosstalk between H2BUb1 and other modifications, especially H3K4 and H3K79 methylations, remains unclear in vertebrates. To understand the functional role of H2BUb1, genome-wide histone modification patterns were measured in human cells. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL9052 14 Samples
FTP download: GEO (BED, SAM, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE25nnn/GSE25882/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA135813
Series		Accession: GSE25882	ID: 200025882

5222. The translational landscape of mTOR signaling steers cancer initiation and metastasis
(Submitter supplied) The mammalian target of rapamycin (mTOR) kinase is a master regulator of protein synthesis that couples nutrient sensing to cell growth and cancer. However, the downstream translationally regulated nodes of gene expression that may direct cancer development are poorly characterized. Employing ribosome profiling we uncover specialized translation of the prostate cancer genome by oncogenic mTOR signaling, revealing a remarkably specific repertoire of genes involved in cell proliferation, metabolism, and invasion. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE35nnn/GSE35469/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA152347
Series		Accession: GSE35469	ID: 200035469

5223. Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (RNA-Seq)
(Submitter supplied) Understanding how RNA binding proteins control the splicing code is fundamental to human biology and disease. Here we present a comprehensive study to elucidate how heterogeneous nuclear ribonucleoparticle (hnRNP) proteins, among the most abundant RNA binding proteins, coordinate to regulate alternative pre-mRNA splicing (AS) in human cells. Using splicing-sensitive microarrays, cross-linking and immunoprecipitation coupled with high-throughput sequencing, and cDNA sequencing, we find that more than half of all AS events are regulated by multiple hnRNP proteins, and that some combinations of hnRNP proteins exhibit significant synergy, whereas others act antagonistically. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL9115 GPL11154 31 Samples
FTP download: GEO (BOWTIE) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE34nnn/GSE34995/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA156297
Series		Accession: GSE34995	ID: 200034995

5224. Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins  (CLIP-Seq)
(Submitter supplied) Understanding how RNA binding proteins control the splicing code is fundamental to human biology and disease. Here we present a comprehensive study to elucidate how heterogeneous nuclear ribonucleoparticle (hnRNP) proteins, among the most abundant RNA binding proteins, coordinate to regulate alternative pre-mRNA splicing (AS) in human cells. Using splicing-sensitive microarrays, cross-linking and immunoprecipitation coupled with high-throughput sequencing, and cDNA sequencing, we find that more than half of all AS events are regulated by multiple hnRNP proteins, and that some combinations of hnRNP proteins exhibit significant synergy, whereas others act antagonistically. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL9115 GPL9052 15 Samples
FTP download: GEO (BOWTIE) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE34nnn/GSE34993/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA156301
Series		Accession: GSE34993	ID: 200034993

5225. "Calling Cards" for DNA-binding proteins in mammalian cells
(Submitter supplied) The ability to chronicle transcription factor binding events throughout the development of an organism would facilitate mapping of transcriptional networks that control cell fate decisions. We describe a method for permanently recording protein-DNA interactions in mammalian cells.  We endow transcription factors with the ability to deposit a transposon into the genome near to where they bind. The transposon becomes a “Calling Card” the transcription factor leaves behind to record its visit to the genome. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL10999 7 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE34nnn/GSE34791/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA151051
Series		Accession: GSE34791	ID: 200034791

5226. Digital gene and expression profiling of primary acute lymphoblastic leukemia (ALL) cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL570 GPL10999 GPL9115 48 Samples
FTP download: GEO (CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE26nnn/GSE26878/
Series		Accession: GSE26878	ID: 200026878

5227. Digital gene expression profiling of primary acute lymphoblastic leukemia cells
(Submitter supplied) We determined the genome-wide digital gene expression (DGE) profiles of primary acute lymphoblastic leukemia (ALL) cells from 28 patients and fractionated blood cells from healthy blood donors taking advantage of “second generation” sequencing technology. The patients included in the study represent distinct subtypes of B-cell precursor (BCP) ALL and T-cell lineage ALL (T-ALL) and the controls are fractionated CD19+ and CD3+ cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL10999 GPL9115 36 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE26nnn/GSE26530/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA142169
Series		Accession: GSE26530	ID: 200026530

5228. RNA Subcellular CAGE Localization from ENCODE/RIKEN
(Submitter supplied) This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Piero Carninci mailto:carninci@riken.jp). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).  This track shows 5' cap analysis gene expression (CAGE) tags and clusters in RNA extracts (http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?type=rnaExtract) from different sub-cellular localizations (http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?type=localization) in multiple cell lines (http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?type=cellType). more...
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL9052 GPL10999 GPL11154 78 Samples
FTP download: GEO (BED, BEDRNAELEMENTS, BIGWIG, GTF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE34nnn/GSE34448/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA30709
Series		Accession: GSE34448	ID: 200034448

5229. Modulation of NF-kB-Dependent Gene Transcription Using Programmable DNA Minor Groove Binders
(Submitter supplied) Nuclear factor kappaB (NF-kB) is a transcription factor that regulates various aspects of immune response, cell death and differentiation as well as cancer. In this study we introduce the Py-Im polyamide 1 that binds preferentially to the sequences 5'-WGGWWW-3' and 5' GGGWWW-3'. The compound is capable of binding to kB sites and reducing the expression of various NF-kB driven genes including IL6 and IL8 by qRT-PCR. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL10999 11 Samples
FTP download: GEO (DIFF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE34nnn/GSE34329/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA151489
Series		Accession: GSE34329	ID: 200034329

5230. Revealing novel transcribed sequences absent from the human reference genome by RNA-Seq
(Submitter supplied) These two transcriptome sequencing datasets were generated from two reference RNA samples established by the US FDA-led MicroArray Quality Control project with Illumina next-generation sequencing technology. The reference RNA sample A (UHRR, Catalog #740000) consists of total RNA extracted from 10 human cell lines of various origins: Blymphocyte, brain, breast, cervix, liposarcoma, liver, macrophage, skin, testis and Tlymphocyte. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL9115 2 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE30nnn/GSE30251/
Series		Accession: GSE30251	ID: 200030251

5231. Comparative analysis of human protein-coding and noncoding RNAs between brain and various cell lines by RNA-Seq
(Submitter supplied) These two transcriptome sequencing datasets were generated from two reference RNA samples established by the US FDA-led MicroArray Quality Control project with Illumina next-generation sequencing technology. The reference RNA sample A (UHRR, Catalog #740000) consists of total RNA extracted from 10 human cell lines of various origins: Blymphocyte, brain, breast, cervix, liposarcoma, liver, macrophage, skin, testis and Tlymphocyte. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL9115 2 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE30nnn/GSE30250/
Series		Accession: GSE30250	ID: 200030250

5232. RNA-seq of brain and various cell lines
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL9115 4 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE30nnn/GSE30222/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA143717
Series		Accession: GSE30222	ID: 200030222

5233. RNA Subcellular Localization by Paired End diTag Sequencing from ENCODE/GIS
(Submitter supplied) This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Yijun Ruan mailto:ruanyj@gis.a-star.edu.sg). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).  This track is produced as part of the ENCODE Transcriptome Project. It shows the starts and ends of full length mRNA transcripts determined by GIS paired-end ditag (PET) sequencing using RNA extracts (http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?type=rnaExtract) from different sub-cellular localizations (http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?type=localization) in different cell lines (http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?type=cellType). more...
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL9115 GPL10999 31 Samples
FTP download: GEO (BED, BIGWIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE33nnn/GSE33600/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA30709
Series		Accession: GSE33600	ID: 200033600

5234. Interferon-alpha mediates the development of autoimmunity by direct tissue toxicity and through immune-cell recruitment mechanisms
(Submitter supplied) Interferon-alpha is a major therapeutic agent for many diverse diseases.  However, the interferon-alpha mechanism of therapeutic action and associated side effects are not well understood. In particular, thyroiditis is a common unexplained complication.  We hypothesized that direct thyroid-toxic actions coupled with immune mechanisms play a major role in the thyroiditis etiology. To test this hypothesis, we investigated the actions of interferon-alpha on cultured thyrocytes in vitro, and in vivo by creating transgenic mice overexpressing interferon-alpha tissue specifically in thyrocytes. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL10999 GPL11002 5 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE25nnn/GSE25115/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA134511
Series		Accession: GSE25115	ID: 200025115

5235. Transcriptomic profiling of a glioblastoma multiforme patient with matched control brain tissue
(Submitter supplied) To investigate differential gene expression, we analyzed the entire transcriptomes of tumor and matched normal brain tissues obtained from a patient who had glioblastoma multiforme.  We extracted and sequenced the mRNA using Illumina GA2 platform. The raw data was analyzed using our recently developed program called RNASEQR, as well as ERANGE, MapSplice, SpliceMap, and TopHat.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 2 Samples
FTP download: GEO (BAM) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE33nnn/GSE33328/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA148993
Series		Accession: GSE33328	ID: 200033328

5236. Identification of stromally expressed molecules in the prostate by Tag profiling of cancer-associated fibroblasts, normal fibroblasts and fetal prostate
(Submitter supplied) The stromal microenvironment plays key roles in prostate development and cancer. Cancer associated fibroblasts (CAFs) and other stromal cells stimulate tumourigenesis via several mechanisms including the expression of pro-tumourigenic factors. Mesenchyme (embryonic stroma) controls prostate organogenesis, and in some circumstances can re-differentiate prostate tumours. Epithelia are regulated by powerful paracrine signalling from the stroma in both development and disease, and identification of these stromal signals is important. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE25nnn/GSE25018/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA134387
Series		Accession: GSE25018	ID: 200025018

5237. ENCODE Cold Spring Harbor Labs Long RNA-seq (hg18)
(Submitter supplied) This track depicts high throughput sequencing of long RNAs (>200 nt) from RNA samples from tissues or subcellular compartments from ENCODE cell lines. The overall goal of the ENCODE project is to identify and characterize all functional elements in the sequence of the human genome. For data usage terms and conditions, please refer to http://www.genome.gov/27528022  and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL9052 3 Samples
FTP download: GEO (BB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE32nnn/GSE32931/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA30709
Series		Accession: GSE32931	ID: 200032931

5238. Transposon-based construction of strand-specific RNA-seq libraries
(Submitter supplied) We have developed two methods for efficiently consructing RNA-seq libraries using transposition.  Each method constructs high quality RNA-seq libraries when compared to standard approaches. One of the methods (Directional Tn-RNA-seq) maintains strand-of-origin information and exhibits strand specificity comparable to current approaches.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL10999 GPL11154 15 Samples
FTP download: GEO (RPKM) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE32nnn/GSE32307/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA147303
Series		Accession: GSE32307	ID: 200032307

5239. CTCF promotes RNA pol II pausing and links DNA methylation to alternative splicing [RNA-Seq]
(Submitter supplied) The goal of this study was to investigate the role of intragenic CTCF in alternative pre-mRNA splicing through a combined CTCF-ChIP-seq and RNA-seq approach. CTCF depletion led to decreased inclusion of weak upstream exons.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE31nnn/GSE31486/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA154053
Series		Accession: GSE31486	ID: 200031486

5240. CTCF promotes RNA pol II pausing and links DNA methylation to alternative splicing
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL10999 10 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE31nnn/GSE31278/
Series		Accession: GSE31278	ID: 200031278

5241. Accurate Identification of A-to-I RNA editing in human by transcriptome sequencing
(Submitter supplied) RNA editing enhances the diversity of gene products at the post-transcriptional level. Approaches for genome-wide identification of RNA editing face two main challenges: separating true editing sites from false discoveries and accurate estimation of editing levels. We developed an approach to analyze transcriptome sequencing data (RNA-Seq) for global identification of RNA editing in cells for which whole-genome sequencing data are available. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 2 Samples
FTP download: GEO (TAR, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE28nnn/GSE28040/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA137951
Series		Accession: GSE28040	ID: 200028040

5242. Gene expression analysis of breast cancer (HCC1954) and normal breast cells (HMEC)
(Submitter supplied) While genetic mutation is a hallmark of cancer, many cancers also acquire epigenetic alterations during tumorigenesis including aberrant DNA hypermethylation of tumor suppressors as well as changes in chromatin modifications as caused by genetic mutations of the chromatin-modifying machinery. However, the extent of epigenetic alterations in cancer cells has not been fully characterized. Here, we describe the first complete methylome maps at single nucleotide resolution of a low-passage breast cancer cell line and primary human mammary epithelial cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 2 Samples
FTP download: GEO (BAM) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE29nnn/GSE29119/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA142887
Series		Accession: GSE29119	ID: 200029119

5243. Global DNA Hypomethylation Coupled to Repressive Chromatin Domain Formation and Gene Silencing in Breast Cancer
(Submitter supplied) While genetic mutation is a hallmark of cancer, many cancers also acquire epigenetic alterations during tumorigenesis including aberrant DNA hypermethylation of tumor suppressors as well as changes in chromatin modifications as caused by genetic mutations of the chromatin-modifying machinery. However, the extent of epigenetic alterations in cancer cells has not been fully characterized. Here, we describe the first complete methylome maps at single nucleotide resolution of a low-passage breast cancer cell line and primary human mammary epithelial cells. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms: GPL11154 GPL10999 14 Samples
FTP download: GEO (BAM) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE29nnn/GSE29069/
Series		Accession: GSE29069	ID: 200029069

5244. SAGE-Seq gene expression profiles of Hs578T, MCF7, and SUM159PT cells treated with STAT3 or non-targeting siRNAs, DMSO, or CXCR2, PTGIS, HAS1, PFKFB3, JAK, or NQO1 inhibitor
(Submitter supplied) To investigate potential links between Stat3 transcriptional activity and other signaling pathways in breast cancer, we determined the gene expression profiles of three breast cancer cell lines treated with JAK, PTGIS, PFKFB3, CXCR2, HAS1, or NQO1 inhibitor (all of which decreased Stat3 transcriptional activity in Hs 578T cells except for the NQO1 inhibitor), inhibitor treatment vehicle alone (DMSO), STAT3 siRNAs, or non-targeting siRNAs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 27 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE22nnn/GSE22917/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA127973
Series		Accession: GSE22917	ID: 200022917

5245. ChimeraScan: A tool for identifying chimeric transcription in sequencing data
(Submitter supplied) Next Generation Sequencing technologies have enabled de novo gene fusion discovery that could reveal candidates with therapeutic significance in cancer. Here we present an open-source software package, ChimeraScan, for the discovery of chimeric transcription between two independent transcripts.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 3 Samples
FTP download: GEO (BAM, BEDPE) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE29nnn/GSE29098/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA140329
Series		Accession: GSE29098	ID: 200029098

5246. Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Expression profiling by array
Platforms: GPL4133 GPL9052 GPL9115 67 Samples
FTP download: GEO (BAM, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE31nnn/GSE31728/
Series		Accession: GSE31728	ID: 200031728

5247. Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression (RNA-Seq data)
(Submitter supplied) Noncoding RNAs (ncRNAs) are emerging as key molecules in human cancer, with the potential to serve as novel markers of disease and to reveal uncharacterized aspects of tumor biology. Here we discover 121 unannotated prostate cancer–associated ncRNA transcripts (PCATs) by ab initio assembly of high-throughput sequencing of polyA+ RNA (RNA-Seq) from a cohort of 102 prostate tissues and cells lines. We characterized one ncRNA, PCAT-1, as a prostate-specific regulator of cell proliferation and show that it is a target of the polycomb repressive complex 2 (PRC2). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms: GPL9115 GPL9052 58 Samples
FTP download: GEO (BAM) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE25nnn/GSE25183/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA153913
Series		Accession: GSE25183	ID: 200025183

5248. The tumor antigen PRAME is a substrate recognition subunit of a Cul2-based ubiquitin ligase and is associated with active NFY promoters
(Submitter supplied) The human tumor antigen PRAME (Preferentially expressed antigen of melanoma) is frequently overexpressed in tumors. High PRAME levels correlate with poor clinical outcome of several cancers, but the mechanisms by which PRAME could be involved in tumorigenesis remain largely elusive. We applied protein-complex purification strategies and identified PRAME as a substrate recognition subunit of a Cullin2-based E3 ubiquitin ligase. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL9115 5 Samples
FTP download: GEO (BED, TSV, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE26nnn/GSE26439/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA136821
Series		Accession: GSE26439	ID: 200026439

5249. The human mitochondrial transcriptome
(Submitter supplied) The human mitochondrial genome comprises a distinct genetic system transcribed as precursor polycistronic transcripts that are subsequently cleaved to generate individual mRNAs, tRNAs and rRNAs. Here we provide a comprehensive analysis of the human mitochondrial transcriptome across multiple cell lines and tissues. Using directional deep sequencing and parallel analysis of RNA ends, we demonstrate wide variation in mitochondrial transcript abundance, and precisely resolve transcript processing and maturation events. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL9115 7 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE30nnn/GSE30772/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA144321
Series		Accession: GSE30772	ID: 200030772

5250. Determination of transcript abundance before and after serum induction in human HCT-116 colon cancer cell line.
(Submitter supplied) Transcriptional regulation of developmentally controlled genes is at the heart of differentiation and organogenesis. In this study, we have performed mRNA transcript abdundance analyses in human cells in response to serum activation signal by RNA-seq.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE30nnn/GSE30786/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA154711
Series		Accession: GSE30786	ID: 200030786

5251. Dynamic transcriptional events in embryonic stem cells mediated by the super elongation complex (SEC).
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL11002 GPL10999 GPL1261 34 Samples
FTP download: GEO (CEL, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE30nnn/GSE30268/
Series		Accession: GSE30268	ID: 200030268

5252. Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis
(Submitter supplied) Epidermal growth factor (EGF) is a key regulatory growth factor activating a myriad of processes affecting cell proliferation and survival that are relevant to normal development and disease. Here we have used a combined approach to study the EGF dependent transcriptome of HeLa cells. We obtained mRNA expression profiles using multiple long oligonucleotide based microarray platforms (from Agilent, Operon, Febit, and Illumina) in combination with digital gene expression profiling (DGE) with the Illumina Genome Analyzer I (GA-I). more...
Organism:	Homo sapiens
Type:		Expression profiling by array; Genome variation profiling by genome tiling array; Expression profiling by high throughput sequencing
6 related Platforms 60 Samples
FTP download: GEO (FA, GPR, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE17nnn/GSE17403/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA118851
Series		Accession: GSE17403	ID: 200017403

5253. An EMT-driven alternative splicing program occurs in human breast cancer and modulates cellular phenotype.
(Submitter supplied) Regulation of cell-cell junction formation and regulation of cell migration were enriched among EMT (Epithelial-Mesenchymal Transition)-associated alternatively splicing events. Our analysis suggested that most EMT-associated alternative splicing events are regulated by one or more members of the RBFOX, MBNL, CELF, hnRNP or ESRP classes of splicing factors. The EMT alternative splicing signature was confirmed in human breast cancer cell lines, which could be classified into basal and luminal subtypes based exclusively on their EMTassociated splicing pattern. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 2 Samples
FTP download: GEO (MAP) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE30nnn/GSE30290/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA143595
Series		Accession: GSE30290	ID: 200030290

5254. ENCODE Cold Spring Harbor Labs Long RNA-seq (hg19)
(Submitter supplied) This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Carrie Davis mailto:davisc@cshl.edu (experimental), Alex Dobin mailto:dobin@cshl.edu (computational), Felix Schlesinger mailto:schlesin@cshl.edu (computational), Tom Gingeras mailto:gingeras@cshl.edu (primary investigator), and Roderic Guigo's group mailto:rguigo@imim.es at the CRG). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).  These tracks were generate by the ENCODE Consortium. They contain information about human RNAs > 200 nucleotides in length obtained as short reads off the Illumina GAIIx platform. Data is available from biological replicates of several cell lines. In addition to profiling Poly-A+ and Poly-A- RNA from whole cells, we have also gather data from various subcellular compartments. In many cases, there are Cap Analysis of Gene Expression (CAGE, RIKEN Institute) and Small RNA-Seq (<200 nucleotides, CSHL) and Pair-End di-TAG-RNA (PET-RNA, Genome Institute of Singapore) datasets available from the same biological replicates.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL10999 GPL11154 GPL9115 99 Samples
FTP download: GEO (BAM, BEDRNAELEMENTS, BIGWIG, GFF, GTF, PDF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE30nnn/GSE30567/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA30709
Series		Accession: GSE30567	ID: 200030567

5255. Human Large Airway Epithelial Cells from healthy never and current smoker and smokers with and without lung cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL13447 GPL10999 21 Samples
FTP download: GEO (BEDGRAPH, CEL, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE29nnn/GSE29007/
Series		Accession: GSE29007	ID: 200029007

5256. mRNA-seq of Human Airway Epithelial Cells
(Submitter supplied) mRNA expression was profiled from pooled bronchial airway epithelial cell brushings (n=3 patients/pool) obtained during bronchoscopy from healthy never (NS) and current smokers (S) and smokers with (C) and without (NC) lung cancer
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 8 Samples
FTP download: GEO (BEDGRAPH, GTF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE29nnn/GSE29006/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA153969
Series		Accession: GSE29006	ID: 200029006

5257. RNA-seq of two paired normal and cancer tissues in two stage III colorectal cancer patients
(Submitter supplied) The RNA from two paired normal and colorectal tumor tissue were sequenced by Illumina genome analyzer. 0.8 to 1.1 million reads were generated. Sequencing data was aligned with human RNA, human mitochondrial DNA and human genomic DNA by BWA.  Base calling and Phred-like score was calculated by SAMTools.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 4 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE29nnn/GSE29580/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA141411
Series		Accession: GSE29580	ID: 200029580

5258. Reprogramming Transcriptional Responses through Functionally-Distinct Classes of Enhancers in Prostate Cancer Cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL9115 GPL6102 42 Samples
FTP download: GEO (BED, BEDGRAPH, FA) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE27nnn/GSE27824/
Series		Accession: GSE27824	ID: 200027824

5259. Reprogramming Transcriptional Responses through Functionally-Distinct Classes of Enhancers in Prostate Cancer Cells [ChIP-Seq, Gro-Seq]
(Submitter supplied) Mammalian genomes are populated with thousands of transcriptional enhancers that orchestrate cell type-specific gene expression programs; however, the potential that there are pre-established enhancers in different functional classes that permit alternative signal-dependent transcriptional responses has remained unexplored. Here we present evidence that cell lineage-specific factors, such as FoxA1, can simultaneously facilitate and restrict key regulated transcription factors, exemplified by the androgen receptor (AR), acting at structurally- and functionally-distinct classes of pre-established enhancers, thus licensing specific signal-activated responses while restricting others. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL9115 30 Samples
FTP download: GEO (BED, BEDGRAPH, FA) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE27nnn/GSE27823/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA141903
Series		Accession: GSE27823	ID: 200027823

5260. RNA-Seq anlalysis of prostate cancer cell lines using Next Generation Sequencing
(Submitter supplied) Beginning with precursor lesions, aberrant DNA methylation marks the entire spectrum of prostate cancer progression. We mapped the global DNA methylation patterns in selected prostate tissues and cell lines using Methylplex-Next Generation Sequencing (M-NGS). Hidden Markov Model based next generation sequence analysis identified ~68,000 methylated regions per sample. While global CpG Island (CGI) methylation was not differential between benign adjacent and cancer samples, overall promoter CGI methylation increased from ~12.6% in benign samples to 19.3% and 21.8% in localized and metastatic cancer tissues, respectively. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL9052 GPL9115 11 Samples
FTP download: GEO (BAM) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE29nnn/GSE29155/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA142987
Series		Accession: GSE29155	ID: 200029155

5261. Global Analysis of the Immediate Transcriptional Effects of Estrogen Signaling Reveals a Rapid, Extensive, and Transient Response
(Submitter supplied) We report the immediate effects of estrogen signaling on the transcriptome of breast cancer cells using Global Run-On and sequencing (GRO-seq). We found that estrogen signaling directly regulates a strikingly large fraction of the transcriptome in a rapid, robust, and unexpectedly transient manner. In addition to protein-coding genes, estrogen regulates the distribution and activity of all three RNA polymerases, and virtually every class of non-coding RNA that has been described to date. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 8 Samples
FTP download: GEO (BED, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE27nnn/GSE27463/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA138459
Series		Accession: GSE27463	ID: 200027463

5262. Deep sequencing reveals distinct patterns of DNA methylation and transcript isoform regulation in prostate cancer
(Submitter supplied) Beginning with precursor lesions, aberrant DNA methylation marks the entire spectrum of prostate cancer progression.  We mapped the global DNA methylation patterns in selected prostate tissues and cell lines using Methylplex-Next Generation Sequencing (M-NGS).  Hidden Markov Model based next generation sequence analysis identified ~68,000 methylated regions per sample.  While global CpG Island (CGI) methylation was not differential between benign adjacent and cancer samples, overall promoter CGI methylation increased from ~12.6% in benign samples to 19.3% and 21.8% in localized and metastatic cancer tissues, respectively. more...
Organism:	Homo sapiens
Type:		Expression profiling by array; Methylation profiling by genome tiling array; Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
4 related Platforms 39 Samples
FTP download: GEO (BAM, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE27nnn/GSE27619/
Series		Accession: GSE27619	ID: 200027619

5263. Comparative transcriptomic analysis of prostate cancer and matched normal tissue using RNA-seq
(Submitter supplied) We used RNA-seq to interrogate prostate cancer specific gene fusions, alternative splicings, somatic mutations and novel transcripts.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 30 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE22nnn/GSE22260/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA128733
Series		Accession: GSE22260	ID: 200022260

5264. Genome-Wide Analysis of Somatic Copy Number Alterations and Gene Expression in Metastatic Melanoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome variation profiling by SNP array; Genome variation profiling by genome tiling array
4 related Platforms 36 Samples
FTP download: GEO (CEL, CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE23nnn/GSE23056/
Series		Accession: GSE23056	ID: 200023056

5265. Genome-Wide Analysis of Somatic Copy Number Alterations and Gene Expression in Metastatic Melanoma: RNA-Seq
(Submitter supplied) All cancers are diseases of the genome. A combination of somatic point mutations, focal amplifications and deletions, and chromosome level aberrations conspire to disrupt gene expression and the interplay between signaling pathways that control normal growth and tissue homeostasis. Here we investigate transcript levels in 7 melanomas and a pool of melanocytes.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9186 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE22nnn/GSE22932/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA133097
Series		Accession: GSE22932	ID: 200022932

5266. The C-Terminal Domain of RNA Polymerase II is Modified by Site-Specific Methylation
(Submitter supplied) The Carboxy-terminal domain (CTD) of RNA Polymerase II (RNAPII) in mammals undergoes extensive post-translational modification, which is essential for transcriptional initiation and elongation. Here, we show that the CTD of RNAPII is methylated at a single arginine (R1810) by the transcriptional co-activator CARM1. Although methylation at R1810 is present on the hyper-phosphorylated form of RNAPII in vivo, Ser-2 or Ser-5 phosphorylation inhibit CARM1 activity towards this site in vitro, suggesting that methylation occurs before transcription initiation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE27nnn/GSE27315/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA137181
Series		Accession: GSE27315	ID: 200027315

5267. Deep Sequence Analysis of the Relationship between Gene Expression, CpG Island Methylation, and Gene Copy Number in Breast Cancer Cells
(Submitter supplied) We used deep sequencinge technology to profile the transcriptome, gene copy number, and CpG island methylation status simultaneously in eight commonly used breast cell lines to develop a model for how these genomic features are integrated in estrogen receptor positive (ER+) and negative breast cancer. Total mRNA sequence, gene copy number, and genomic CpG island methylation were carried out using the Illumina Genome Analyzer. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL9115 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE27nnn/GSE27003/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA137657
Series		Accession: GSE27003	ID: 200027003

5268. Interplay between c-Jun and TAp73α/β contributes to the apoptosis-survival balance
(Submitter supplied) The p53-family member p73 functions in various cellular signaling pathways and can have tumor suppressor properties. Several isoforms of p73 exist that differ considerably in their function. Whereas the functions of the N-terminal isoforms (TA and ΔNp73) and their opposing pro- and anti-apoptotic roles became evident, the functional differences of the distinct C-terminal spliceforms of TAp73 have remained unclear. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL9052 15 Samples
FTP download: GEO (BED, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE15nnn/GSE15780/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA116853
Series		Accession: GSE15780	ID: 200015780

5269. ENCODE Genome Institute of Singapore RNA-Seq
(Submitter supplied) This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Ruan Xiaoan mailto:ruanx@gis.a-star.edu.sg). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).  This track is produced as part of the ENCODE Project. It shows high throughput sequencing of RNA samples from tissues or sub cellular compartments from cell lines included in the ENCODE Transcriptome subproject. more...
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL9442 GPL9115 4 Samples
FTP download: GEO (BAM, BIGWIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE27nnn/GSE27221/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA30709
Series		Accession: GSE27221	ID: 200027221

5270. Regulation of alternative splicing by the core spliceosomal machinery
(Submitter supplied) Abstract: Alternative splicing (AS) plays a major role in the generation of proteomic diversity and in gene regulation. However, the role of the basal splicing machinery in regulating AS remains poorly understood. Here we show that the core snRNP protein SmB/B’ self-regulates its expression by promoting the inclusion of a highly-conserved alternative exon in its own pre-mRNA that targets the spliced transcript for nonsense-mediated mRNA decay (NMD). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 3 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE26nnn/GSE26463/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA136533
Series		Accession: GSE26463	ID: 200026463

5271. ENCODE Cold Spring Harbor Labs Long RNA-seq
(Submitter supplied) For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf  This SuperSeries is composed of the SubSeries listed below.
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
4 related Platforms 84 Samples
FTP download: GEO (BAM, BB, BEDRNAELEMENTS, BIGWIG, GFF, GTF, PDF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE26nnn/GSE26284/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA30709
Series		Accession: GSE26284	ID: 200026284

5272. Altered antisense-to-sense transcript ratios in breast cancer: ASSAGE
(Submitter supplied) Transcriptome profiling studies suggest that a large fraction of the genome is transcribed and many transcripts function independent of their protein coding potential. The relevance of noncoding RNAs (ncRNAs) in normal physiological processes and in tumorigenesis is increasingly recognized. Here, we describe consistent and significant differences in the distribution of sense and antisense transcripts between normal and neoplastic breast tissues. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 3 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE25nnn/GSE25932/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA142511
Series		Accession: GSE25932	ID: 200025932

5273. Altered antisense-to-sense transcript ratios in breast cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Expression profiling by array
Platforms: GPL9052 GPL11305 28 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE25nnn/GSE25292/
Series		Accession: GSE25292	ID: 200025292

5274. Altered antisense-to-sense transcript ratios in breast cancer: Sage-Seq
(Submitter supplied) Transcriptome profiling studies suggest that a large fraction of the genome is transcribed and many transcripts function independent of their protein coding potential. The relevance of noncoding RNAs (ncRNAs) in normal physiological processes and in tumorigenesis is increasingly recognized. Here, we describe consistent and significant differences in the distribution of sense and antisense transcripts between normal and neoplastic breast tissues. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 21 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE25nnn/GSE25291/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA142565
Series		Accession: GSE25291	ID: 200025291

5275. Gene expression profiling of human tissue samples using SAGE-Seq
(Submitter supplied) We present a powerful application of ultra high-throughput sequencing, SAGE-Seq, for the accurate quantification of normal and neoplastic mammary epithelial cell transcriptomes. We develop data analysis pipelines that allow the mapping of sense and antisense strands of mitochondrial and RefSeq genes, the normalization between libraries, and the identification of differentially expressed genes. We find that the diversity of cancer transcriptomes is significantly higher than that of normal cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE24nnn/GSE24491/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA132527
Series		Accession: GSE24491	ID: 200024491

5276. Elucidating the stromal expression pattern in response to tumor-derived Shh
(Submitter supplied) Most tumors of the upper gastrointestinal tract are known to depend on an excessive expression of Shh. It was recently discovered that this Shh does not signal on the tumor cells, but rather the stromal cells that in turn produce an unknown set of reciprocal signals that act as growth- or survival cues for the tumor cells. This sequencing effort aims to identify the reciprocal signals.
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL9185 GPL9052 GPL10329 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE18nnn/GSE18245/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA119635
Series		Accession: GSE18245	ID: 200018245

5277. Deep sequencing analysis of transcription-induced chimeras in human prostate adenocarcinoma and reference samples
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome variation profiling by genome tiling array
Platforms: GPL4091 GPL9052 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE24nnn/GSE24284/
Series		Accession: GSE24284	ID: 200024284

5278. Deep transcriptional sequencing analysis of human prostate adenocarcinoma and reference samples
(Submitter supplied) Prostate adenocarcinoma and matched adjacent normal samples were profiled by deep transcriptional sequencing to analyze transcription-induced chimeras and gene fusions.  Reference samples from the MAQC and brain and universal reference libraries were also sequenced.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 8 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE24nnn/GSE24283/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA133719
Series		Accession: GSE24283	ID: 200024283

5279. Alternative expression analysis by RNA sequencing (comparison of 5-FU sensitive and resistant colorectal cancer cell lines)
(Submitter supplied) In Alternative Expression Analysis (ALEXA)-Seq we developed a method to analyze massively parallel RNA sequence data to catalogue transcripts and assess differential and alternative expression of known and predicted messenger RNA (mRNA) isoforms in cells and tissues. As proof-of-principle, we applied the approach to a comparison of fluorouracil responsive and non-responsive human colorectal cancer cell lines. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE23nnn/GSE23776/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA130627
Series		Accession: GSE23776	ID: 200023776

5280. ENCODE Caltech RNA-seq
(Submitter supplied) This data was produced by the Wold lab at Caltech as part of the ENCODE Project. RNA-Seq is a method for mapping and quantifying the transcriptome of any organism that has a genomic DNA sequence assembly. RNA-Seq is performed by reverse-transcribing an RNA sample into cDNA, followed by high throughput DNA sequencing. The resulting sequence reads are then informatically mapped onto the genome sequence. more...
Project: ENCODE
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 36 Samples
FTP download: GEO (BED12, BEDGRAPH, BOWTIE, FASTA, PSL, RPKM) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE23nnn/GSE23316/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA30709
Series		Accession: GSE23316	ID: 200023316

5281. An Integrated Network of Androgen Receptor and TMPRSS2-ERG Gene Fusion in Prostate Cancer Progression
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL4133 GPL9052 75 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE14nnn/GSE14097/
Series		Accession: GSE14097	ID: 200014097

5282. An Integrated Network of Androgen Receptor and TMPRSS2-ERG Gene Fusion in Prostate Cancer Progression (II)
(Submitter supplied) Androgen receptor (AR) is a transcription factor that plays a central role in the growth and development of the normal prostate and its malignant transformation.  More recently, a majority of prostate cancers have been shown to harbor recurrent gene fusions of the androgen-regulated gene, TMPRSS2, to the oncogenic ETS transcription factor ERG.  Here we employed chromatin immunoprecipitation coupled to massively parallel sequencing (ChIP-Seq) to explore the genome-wide localization of these transcription factors in human prostate cancer cell lines as well as tissues. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL9052 60 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE14nnn/GSE14092/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA114515
Series		Accession: GSE14092	ID: 200014092

5283. RNA-Seq of oral squamous cell carcinomas and matched normal tissues
(Submitter supplied) RNA-Seq was applied to oral squamous cell carcinomas and matched normal oral tissue to measure gene expression patterns and identify examples of allelic imbalance.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9442 6 Samples
FTP download: GEO (PDF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE20nnn/GSE20116/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA124251
Series		Accession: GSE20116	ID: 200020116

5284. RNA-Seq of melanoma short-term cultures and cell lines
(Submitter supplied) Identification of RNA-based alterations in melanoma by RNA-Seq, including gene fusions, sequence mutations, and aberrant gene expression levels (to compare to expression level estimates obtained by microarray).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 14 Samples
FTP download: GEO (BAM) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE20nnn/GSE20156/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA39289
Series		Accession: GSE20156	ID: 200020156

5285. Melanoma short-term cultures and cell lines: expression profiling and CNV analyses
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Genome variation profiling by SNP array; Expression profiling by high throughput sequencing
Platforms: GPL9115 GPL6801 GPL5175 41 Samples
FTP download: GEO (BAM, CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE17nnn/GSE17593/
Series		Accession: GSE17593	ID: 200017593

5286. University of Washington Human Reference Epigenome Mapping Project
(Submitter supplied) The NIH Roadmap Epigenomics Mapping Consortium aims to produce a public resource of epigenomic maps for stem cells and primary ex vivo tissues selected to represent the normal counterparts of tissues and organ systems frequently involved in human disease.  Study of chromatin accessibility and expression using exon arrays.   **************** For data usage terms and conditions, please refer to: http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies **************** 
Project: Roadmap Epigenomics
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by array; Expression profiling by high throughput sequencing
5 related Platforms 758 Samples
FTP download: GEO (BAM, BED, CEL, TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE18nnn/GSE18927/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA34535
Series		Accession: GSE18927	ID: 200018927

5287. UCSF-UBC Human Reference Epigenome Mapping Project
(Submitter supplied) The epigenome is the dynamic interface between our changing environment and the static genome, and understanding it is a goal of immense importance to human health. We will map reference cell epigenomes of the brain, breast, blood and approved embryonic stem cells, inclusive of males and females and different racial groups. This cooperative work will transform our understanding of the short and long-lasting consequences of environment impact on human health and disease. more...
Project: Roadmap Epigenomics
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms: GPL10999 GPL9115 GPL11154 529 Samples
FTP download: GEO (BAM, BED, TAB, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE16nnn/GSE16368/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA34535
Series		Accession: GSE16368	ID: 200016368

5288. UCSD Human Reference Epigenome Mapping Project
(Submitter supplied) The human embryonic stem cells (hESCs) are a unique model system for investigating the mechanisms of human development due to their ability to replicate indefinitely while retaining the capacity to differentiate into a host of functionally distinct cell types. In addition, these cells could be potentially used as therapeutic agents in regenerative medicine. Differentiation of hESCs involves selective activation or silencing of genes, a process controlled in part by the epigenetic state of the cell. more...
Project: Roadmap Epigenomics
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
6 related Platforms 878 Samples
FTP download: GEO (BAM, BED, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE16nnn/GSE16256/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA34535
Series		Accession: GSE16256	ID: 200016256

5289. Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq
(Submitter supplied) Whole genome re-sequencing is still a costly method to detect genetic mutations that lead to altered forms of proteins and may be associated with disease development. Since the majority of disease-related single nucleotide variations (SNVs) are found in protein-coding regions, we propose to identify SNVs in expressed exons of the human genome using the recently developed RNA-Seq technique. We identify 12,176 and 10,621 SNVs, respectively, in Jurkat T cells and CD4+ T cells from a healthy donor. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE16nnn/GSE16190/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA117197
Series		Accession: GSE16190	ID: 200016190

5290. A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome
(Submitter supplied) Transcriptome of HEK and B cells were analyzed by microarray and RNA-Seq parallely. Both platforms were then compared in terms of sensitivity. To assess whether values were a reliable indicator of gene activity, we correlated these values with hypophosphorylated RNA polymerase II (PolIIa) occupancy, used as a landmark of transcription initiation. For HEK, we identified PolIIa islands by chromatin immunoprecipitation and sequencing (ChIP-Seq).
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL6104 GPL9052 11 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE11nnn/GSE11892/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA105719
Series		Accession: GSE11892	ID: 200011892

5291. Expression of microRNAs and Protein-coding Genes Associated with Perineural Invasion in Prostate Cancer
(Submitter supplied) BACKGROUND. Perineural invasion (PNI) is the dominant pathway for local invasion in prostate cancer. To date, only few studies have investigated the molecular differences between prostate tumors with PNI and those without it.  METHODS. To evaluate the involvement of both microRNAs and protein-coding genes in PNI, we determined their genome-wide expression with a custom microRNA microarray and Affymetrix GeneChips in 50 prostate adenocarcinomas with PNI and 7 without it. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by array; Non-coding RNA profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL4700 GPL571 114 Samples
FTP download: GEO (CEL, GPR) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE7nnn/GSE7055/
Series		Accession: GSE7055	ID: 200007055

