
3001. Gene expression signature of vemurafenib resistance in WM989 and WM983B melanoma cells
(Submitter supplied) Therapies targeting signaling molecules mutated in cancers can often have striking short-term effects, but the emergence of resistant cancer cells is a major barrier to full cures. Resistance can sometimes result from a secondary mutations in rare cells, but other times, there is no clear genetic cause, raising leaving the possibility of non-genetic rare cell variability. Here, we show that melanoma cells can display profound transcriptional variability at the single cell level that predicts which cells will ultimately resist drug treatment. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 122 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97681/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA382674
Series		Accession: GSE97681	ID: 200097681

3002. Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance [RNA-seq]
(Submitter supplied) Therapies targeting signaling molecules mutated in cancers can often have striking short-term effects, but the emergence of resistant cancer cells is a major barrier to full cures. Resistance can sometimes result from a secondary mutations in rare cells, but other times, there is no clear genetic cause, raising leaving the possibility of non-genetic rare cell variability. Here, we show that melanoma cells can display profound transcriptional variability at the single cell level that predicts which cells will ultimately resist drug treatment. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 16 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97679/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA382752
Series		Accession: GSE97679	ID: 200097679

3003. Cell Cycle-Targeting MicroRNAs as Therapeutic Tools Against Refractory Cancers
(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: GPL16356 GPL11154 3 Samples
FTP download: GEO (CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77230/
Series		Accession: GSE77230	ID: 200077230

3004. Cell Cycle-Targeting MicroRNAs as Therapeutic Tools   Against Refractory Cancers [SW900 cells]
(Submitter supplied) Cyclins and cyclin-dependent kinases (CDKs) are hyperactivated in nearly all human tumor types. To identify new approaches for interfering with cyclins/CDKs, we systematically searched for microRNAs (miRNAs) regulating these proteins. We uncovered a group of miRNAs that target nearly all cyclins and CDKs, and demonstrated that these miRNAs are very effective in shutting off cancer cell expansion. By profiling the response of over 120 human cancer cell lines representing 12 tumor types to these cell-cycle-targeting miRNAs, we identified miRNAs particularly effective against triple-negative breast cancers and KRAS-mutated cancers. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77229/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA309820
Series		Accession: GSE77229	ID: 200077229

3005. Modeling Trilateral Retinoblastoma using Human Embryonic Stem Cells
(Submitter supplied) Human embryonic stem cells (hESCs) provide a platform for understanding mechanisms underlying diseases and finding ways to treat them. Trilateral retinoblastoma (TRb) is a condition in which retinoblastoma, the most common congenital intraocular malignancy, is associated with an intracranial neural tumor. This mostly fatal disease is caused by biallelic inactivation of the retinoblastoma-1 (RB1) gene, transcribing pRB. 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/GSE84nnn/GSE84504/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA329518
Series		Accession: GSE84504	ID: 200084504

3006. Effect of PKN1 inhibition on androgen responsive genes.
(Submitter supplied) To study and compare the effect of siRNA-mediated PKN1 silencing and CEP701-mediated PKN1 inhibition on androgen-responsive genes.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 24 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97398/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA380418
Series		Accession: GSE97398	ID: 200097398

3007. PLATE-Seq for Genome-Wide Regulatory Network Analysis of High-Throughput Screens
(Submitter supplied) Pharmacological and functional genomic screens play an essential role in the discovery and characterization of therapeutic targets and associated pharmacological inhibitors. Although these screens affect thousands of gene products, the typical readout is based on low-complexity rather than genome-wide assays. To address this limitation, we introduce Pooled Library Amplification for Transcriptome Expression (PLATE-Seq), a low-cost, genome-wide mRNA profiling methodology specifically designed to complement high-throughput screening (HTS) assays. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL16791 GPL20301 688 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97460/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA381890
Series		Accession: GSE97460	ID: 200097460

3008. Gene and transcript expression in a G1S Cell Cycle Phase Marker (G1S-CCPM) recombinant U2OS cell line that stably expresses the Cas9 nuclease from a CAG promoter
(Submitter supplied) The purpose of this experiment is to determine the gene/transcript expression levels in the G1S-CCPM-Cas9 cell line to help interpret gene editing experiments.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 2 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97404/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA381692
Series		Accession: GSE97404	ID: 200097404

3009. Novel BET protein Proteolysis Targeting Chimera (BET-PROTAC) exerts superior lethal activity than Bromodomain Inhibitor (BETi) against post-myeloproliferative Neoplasm (MPN) Secondary (s) AML Cells
(Submitter supplied) The PROTAC (proteolysis-targeting chimera) ARV-825 recruits bromodomain and extraterminal (BET) proteins to the E3 ubiquitin ligase cereblon, leading to degradation of BET proteins, including BRD4. Whereas the BET-protein inhibitor (BETi) OTX015 caused accumulation of BRD4, treatment with equimolar concentrations of ARV-825 caused sustained and profound depletion (>90%) of BRD4 and induced significantly more apoptosis in cultured and patient-derived (PD) CD34+ post-MPN sAML cells, while relatively sparing the CD34+ normal hematopoietic progenitor cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93578/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA361174
Series		Accession: GSE93578	ID: 200093578

3010. ENL Links Histone Acetylation to Oncogenic Gene Expression in AML
(Submitter supplied) Cancer cells are characterized by aberrant epigenetic landscapes and often exploit the chromatin machinery to activate oncogenic gene expression programs1. The recognition of modified histones by “reader” proteins constitutes a key mechanism underlying these processes; therefore targeting such pathways holds clinical promise, as exemplified by the recent development of BET bromodomain inhibitors2,3. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL11154 39 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80774/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA319965
Series		Accession: GSE80774	ID: 200080774

3011. Discovering the miR-26a/targetome in prostate cancer cells
(Submitter supplied) In this work, we showed that the re-expression of miR-26a in DU-145 prostate cancer cells restored the tumor suppressor activity of miR-26a. To discover the genes and pathways elicited by miR-26a re-expression, we used the miRNA pull out assay to capture and the Next Generation Sequencing to identify the miR-26a targets. Data showed that: i) miR-26a captured both non-coding and coding RNAs; ii) 46% of transcripts were putative miR-26a targets according to target prediction algorithms; iii) 21 pathways were significantly enriched and the “Pathway in Cancer” was among those comprising the largest number of genes, including BIRC5 that we experimentally validated. 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/GSE85nnn/GSE85306/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA338150
Series		Accession: GSE85306	ID: 200085306

3012. Generation and functional characterization of MDSC-like cells
(Submitter supplied) Myeloid derived suppressor cells (MDSC) are critical in regulating immune responses by suppressing antigen presenting cells (APC) and T cells. We previously observed that incubation of peripheral blood monocytes with IL-10 during their differentiation to dendritic cells (moDC) results in the generation of an APC population with a CD14+HLA-DRlow phenotype (IL-10-APC) with reduced stimulatory capacity similar to human MDSC. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE92nnn/GSE92852/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA358618
Series		Accession: GSE92852	ID: 200092852

3013. 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 is essential for p53-null cancer cells
(Submitter supplied) The bifunctional enzyme 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase-4 (PFKFB4) controls metabolic flux through allosteric regulation of glycolysis. Here we show that p53 regulates the expression of PFKFB4 and that p53-deficient cancer cells are highly dependent on the function of this enzyme. We found that p53 down-regulates PFKFB4 expression by binding to its promoter and mediating transcriptional repression via histone deacetylases. 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/GSE89nnn/GSE89110/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA350308
Series		Accession: GSE89110	ID: 200089110

3014. Crenolanib in combination with azacitidine abrogates stromal protection and survival of leukemia-initiating cells in FLT3-ITD+ AML
(Submitter supplied) Effectively targeting leukemia-initiating cells (LIC) in FLT3-internal-tandem-duplication (ITD)-mutated acute myeloid leukemia (AML) remains a crucial goal for achievement of cure. FLT3 tyrosine kinase inhibitors (TKI) have limited impact as single agents and have thus far been unable to eradicate LIC enriched in the CD34+CD38- bone marrow compartment and protected by contact with niche cells.Using primary AML samples in vitro as well as in an in vivo xenograft model, we investigated whether combining the novel FLT3-selective TKI crenolanib with the hypomethylating agent azacitidine (AZA) can eliminate LIC in FLT3-ITD+ AML and determined whether efficacy of this combination is dependent on coexisting genetic mutations in DNMT3A, NPM1 and TET2. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18460 GPL18480 42 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86021/
Series		Accession: GSE86021	ID: 200086021

3015. The Project for High-Confidence Coding and Noncoding Transcriptome Maps
(Submitter supplied) The advent of high-throughput RNA sequencing (RNA-seq) has led to the discovery of unprecedentedly immense transcriptomes encoded by eukaryotic genomes. However, the transcriptome maps are still incomplete partly because they were mostly reconstructed based on RNA-seq reads that lack their orientations (known as unstranded reads) and certain boundary information. Methods to expand the usability of unstranded RNA-seq data by predetermining the orientation of the reads and precisely determining the boundaries of assembled transcripts could significantly benefit the quality of the resulting transcriptome maps. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing; Third-party reanalysis
Platform: GPL13112 2 Samples
FTP download: GEO (GTF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97212/
Series		Accession: GSE97212	ID: 200097212

3016. High-confidence Coding and Noncoding Transcriptome Maps
(Submitter supplied) The advent of high-throughput RNA sequencing (RNA-seq) has led to the discovery of unprecedentedly immense transcriptomes encoded by eukaryotic genomes. However, the transcriptome maps are still incomplete partly because they were mostly reconstructed based on RNA-seq reads that lack their orientations (known as unstranded reads) and certain boundary information. Methods to expand the usability of unstranded RNA-seq data by predetermining the orientation of the reads and precisely determining the boundaries of assembled transcripts could significantly benefit the quality of the resulting transcriptome maps. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Third-party reanalysis
FTP download: GEO (GTF, TXT, XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97211/
Series		Accession: GSE97211	ID: 200097211

3017. ChIPseq and RNAseq of ER mutant breast cancer cell lines
(Submitter supplied) We performed several extensive phenotypic, genomic, and transcriptomic analyses in an effort to discern the biological differences between normal breast cancer cell lines and breast cancer cells with a mutation in the ESR1 Ligand Binding Domain.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 97 Samples
FTP download: GEO (BED, CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94493/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA371468
Series		Accession: GSE94493	ID: 200094493

3018. Grainyhead-like 2 is essential for androgen receptor expression and activity in 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: GPL18573 10 Samples
FTP download: GEO (BIGWIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80452/
Series		Accession: GSE80452	ID: 200080452

3019. Grainyhead-like 2 is essential for androgen receptor expression and activity in prostate cancer (RNA-seq)
(Submitter supplied) The mainstay treatment for men with metastatic prostate cancer is androgen deprivation therapy (ADT), which inhibits androgen biosynthesis and/or binding of ligand to the androgen receptor (AR). Most men respond to ADT, but all subsequently develop resistance and progression to incurable and lethal castration-resistant prostate cancer (CRPC). CRPC generally remains driven by the AR: therefore, the development of novel AR-targeted therapies, as well as elucidating therapy-driven changes to the AR signalling axis that mediate resistance, remain priorities for the field. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80450/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA318925
Series		Accession: GSE80450	ID: 200080450

3020. Characterization of human Merkel cells and their response to Merkel cell polyomavirus
(Submitter supplied) Merkel cells are epidermal mechanoreceptor cells responsible for the perception of gentle touch. Merkel cell carcinoma (MCC) is a rare and highly aggressive skin cancer. Although MCC histologically resembles Merkel cells, the cell of origin for MCC is unknown. MCC frequently contains integrated Merkel cell polyomavirus (MCPyV), a small DNA tumor virus with widespread prevalence. Whether MCPyV can transform Merkel cells is unknown. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 3 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79657/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA316545
Series		Accession: GSE79657	ID: 200079657

3021. TRIM25
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 142 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79589/
Series		Accession: GSE79589	ID: 200079589

3022. Next generation sequencing facilitates quantitative analysis of changes in mRNA after knock-down of putative master regulators of the breast cancer metastasis transcriptome.
(Submitter supplied) Purpose:  To identify regulatory proteins that are potential drivers of a coordinated breast cancer metastasis gene expression signatures. Methods: Knockdown of target genes in breast cancer cell lines was achieved using scramble and/or gene-specific siRNA (ON-TARGET SMARTpool, Thermo Scientific) and Lipofectamine RNAiMAX.  48h post transfection, total RNA was isolated from cell lines using the RNeasy Plus mini prep kit (Qiagen). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 128 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79586/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA316332
Series		Accession: GSE79586	ID: 200079586

3023. Identification of long noncoding RNAs regulated by p53
(Submitter supplied) Analyize the transcriptpme regulated by p53 in 3 pairs of isogenic p53WT and p53KO colorectal cancer cell lines untreated or treated with Doxorubicin. The hypothsis of this study is that p53 can regulate the expression of subset of lncRNAs to mediate its biological functions.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 14 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79249/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA315294
Series		Accession: GSE79249	ID: 200079249

3024. Transcription elongation factors are in vivo-specific cancer dependencies in glioma
(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 26 Samples
FTP download: GEO (BED, BIGWIG, TDF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74529/
Series		Accession: GSE74529	ID: 200074529

3025. RNA-seq Profiles in Transcription elongation factors are in vivo-specific cancer dependencies in glioma
(Submitter supplied) Glioblastoma ranks as one of the most lethal human cancers, with no effective therapies.  To discover novel  therapeutic targets, here we performed parallel in vivo and in vitro RNA interference screens of epigenetic regulators and show that transcription elongation factors are essential for human glioblastoma cell survival in vivo, but not in vitro.  Context-specific dependency in vivo is driven by microenvironment-induced global changes in the cancer epigenome. more...
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/GSE74nnn/GSE74516/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA300648
Series		Accession: GSE74516	ID: 200074516

3026. Gene expression analysis of human hepatocellular cancers
(Submitter supplied) Gene expression profiling was carried out in 4 matched human hepatocellular cancer samples/normal liver smapls, and 4 human hepatocellular cancer samples to characterize the molecular mechanisms relevant to the etiology of human hepatocellular cancer development.
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/GSE73708/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA297700
Series		Accession: GSE73708	ID: 200073708

3027. Genome-wide multi-omics profiling reveals extensive genetic complexity in 8p11-p12 amplified breast carcinomas
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Genome variation profiling by genome tiling array; Expression profiling by high throughput sequencing
4 related Platforms 152 Samples
FTP download: GEO (GPR, IDAT, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97293/
Series		Accession: GSE97293	ID: 200097293

3028. Single cell RNA-seq analysis of IDH-mutant astrocytoma
(Submitter supplied) To understand the diversity of expression states within IDH-mutant astrocytoma tumors, we profiled 6341 cells from 10 tumors by single cell RNA-seq
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6341 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89567/
Series		Accession: GSE89567	ID: 200089567

3029. Conserved roles for murine mDUX and human DUX4 in activating cleavage stage genes and MERVL/HERVL retrotransposons
(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; Other
Platforms: GPL11154 GPL16791 GPL17021 57 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85632/
Series		Accession: GSE85632	ID: 200085632

3030. Next-generation sequencing analysis of transcriptom in gemcitabine resistant pancreatic cancer cells
(Submitter supplied) Next-generation sequencing was applied to compare the transcriptom of 1) SW1990 human pancreatic cancer cell lines and its gemcitabine-resistant derivative established with long-term exposure in medium containing 100 nM gemcitabine; 2) TRA-1-81+ cells and TRA-1-81- cells isolated from SW1990 human pancreatic cancer cell line.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79953/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA317483
Series		Accession: GSE79953	ID: 200079953

3031. Functional genomic analysis of the haploinsufficient tumor suppressor, CUX1
(Submitter supplied) CUX1 is a homeodomain-containing transcription factor that is conserved, ubiquitous, and essential in vertebrates and invertebrates. CUX1 is mutated or deleted in high-risk myeloid neoplasms and solid tumors, resulting in haploinsufficiency and tumor growth.  Here we provide the first analysis of endogenous, whole genome, CUX1 DNA binding.  We demonstrate that CUX1 binds with transcriptional activators and cohesin at distal enhancers across three different human cell types. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL20301 17 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE92nnn/GSE92882/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA358710
Series		Accession: GSE92882	ID: 200092882

3032. Argonaute CLIP defines a deregulated miR-122 bound transcriptome that correlates with patient survival in human liver cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL16791 GPL17021 46 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97061/
Series		Accession: GSE97061	ID: 200097061

3033. The m6A Demethylase ALKBH5 Maintains Tumorigenicity of Glioblastoma Stem-Like Cells by Sustaining FOXM1 Expression and Cell Proliferation Programing
(Submitter supplied) The dynamic and reversible N6-methyladenosine (m6A) RNA modification installed and erased by N6-methyltransferases and demethylases regulates gene expression and cell fate. Here, we show that the m6A demethylase ALKBH5 is highly expressed in glioblastoma stem-like cells (GSCs). Silencing ALKBH5 suppresses the proliferation of patient-derived GSCs in vitro and in vivo. Integrated transcriptome and m6A-seq analyses revealed altered expression of select ALKBH5 target genes, including FOXM1, a critical transcription factor for the ALKBH5-dependent cell cycle gene expression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL16791 8 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87515/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA345000
Series		Accession: GSE87515	ID: 200087515

3034. Cellular model of colon cancer progression reveals signatures of mRNAs, miRNA, lncRNAs and epigenetic modifications associated with metastasis.
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by genome tiling array; Non-coding RNA profiling by array
Platforms: GPL21576 GPL13534 GPL16791 18 Samples
FTP download: GEO (IDAT, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85688/
Series		Accession: GSE85688	ID: 200085688

3035. RNA profiling of four DLD1 colorectal cancer cell derivatives that recapitulate EMT/MET transitions during metastasis.
(Submitter supplied) RNA profiling of a cellular model of colorectal cancer progression, which is based on four defined derivates of a CRC cell line that resulted from EMT/MET transitions and phenotypically recapitulate the metastatic cascade: epithelial-like primary tumor, mesenchymal-like tumor cells growing in soft agar or as colonospheres, and mouse xenografts of the latter resulting in lung-metastasis comprised of epithelial-state cells.
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/GSE85nnn/GSE85685/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA339111
Series		Accession: GSE85685	ID: 200085685

3036. DHX9 suppresses spurious RNA processing defects originating from the Alu invasion of the human genome
(Submitter supplied) Transposable elements are viewed as ‘selfish genetic elements’, yet they contribute to gene regulation and genome evolution in diverse ways. More than half of the human genome consists of transposable elements. With over 1 million insertions, Alu elements belong to the short interspersed nuclear element (SINE) family of repetitive elements, and with over 1 million insertions they make up more than 10% of the human genome. more...
Organism:	Homo sapiens; Drosophila melanogaster; Mus musculus
Type:		Expression profiling by high throughput sequencing; Other
6 related Platforms 90 Samples
FTP download: GEO (BED, BIGWIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85164/
Series		Accession: GSE85164	ID: 200085164

3037. WT1 expression in breast cancer disrupts the epithelial/mesenchymal balance of tumour cells and correlates with the metabolic response to docetaxel
(Submitter supplied) The Wilms' Tumour gene 1 (WT1), encodes for a complex protein with transcription factor activity which is essential in mammals throughout life. We provide a complete study of WT1 expression across different breast cancer subtypes as well as isoform specific expression analysis. Using in vitro cell lines, clinical samples and publicly available gene expression datasets, we demonstrate that WT1 plays a role in regulating the epithelial-mesenchymal balance of breast cancer cells and that WT1-expressing tumours are mainly associated with a mesenchymal phenotype. 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/GSE93nnn/GSE93636/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA361398
Series		Accession: GSE93636	ID: 200093636

3038. Novel RNA biomarkers of prostate cancer revealed by RNA-seq analysis of formalin-fixed samples obtained from Russian patients
(Submitter supplied) Due to heterogeneous multifocal nature of prostate cancer (PCa), there is currently a lack of biomarkers that stably distinguish it from benign prostatic hyperplasia (BPH), predict clinical outcome and guide the choice of optimal treatment. In this study, RNA-seq analysis was applied to formalin-fixed paraffin-embedded (FFPE) tumor and matched normal tissue samples collected from Russian patients with PCa and BPH. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 32 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89223/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA350714
Series		Accession: GSE89223	ID: 200089223

3039. Utilizing single-cell variations to reveal environment-dependent tuning of network connectivity in human macrophages
(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; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL11154 GPL21782 1411 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81444/
Series		Accession: GSE81444	ID: 200081444

3040. Utilizing single-cell variations to reveal environment-dependent tuning of network connectivity in human macrophages (RNA-Seq, CAGE and ChIP-Seq)
(Submitter supplied) Through analysis of gene expression and chromatin state, this study examines human monocyte-derived macrophages activated in vitro by various stimuli such as cytokines or microbial products
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 29 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80727/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA315538
Series		Accession: GSE80727	ID: 200080727

3041. Global transcriptional analysis of different HT1080 cell phenotypes induced by cell proliferation and density
(Submitter supplied) Following uncontrolled proliferation, a subset of primary tumor cells acquires additional traits/mutations to trigger phenotypic changes that enhance migration and are hypothesized to be the initiations of metastasis. This study reveals a novel adaptive mechanism that harnesses synergistic paracrine signaling via IL-6/8, which is amplified by cell proliferation and cell density, to directly promote cell migration. 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/GSE96nnn/GSE96817/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA379815
Series		Accession: GSE96817	ID: 200096817

3042. Interaction between mitoNEET and NAF-1 in cancer cells
(Submitter supplied) The NEET proteins mitoNEET (mNT) and nutrient-deprivation autophagy factor-1 (NAF-1) are required for cancer cell proliferation and resistance to oxidative stress. MitoNEET and NAF-1 are also implicated in a number of other human pathologies including diabetes, neurodegeneration and heart disease, as well as in development, differentiation and aging. Previous studies suggested that mNT and NAF-1 could function in the same pathway in cancer cells, preventing the over-accumulation of iron and reactive oxygen species (ROS) in mitochondria. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87626/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA345431
Series		Accession: GSE87626	ID: 200087626

3043. siRNA RNA-seq from K562 (ENCSR287SHU)
(Submitter supplied) Control siRNA against no target in K562 cells followed by RNA-seq.  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/GSE97nnn/GSE97025/
Series		Accession: GSE97025	ID: 200097025

3044. Identification of genes induced by NOTCH1 in a chronic lymphocytic leukaemia (CLL) cell line and tracking of these genes in primary CLL patients
(Submitter supplied) NOTCH1 is mutationally activated in ~15% of cases of chronic lymphocytic leukaemia (CLL), but its role in B-cell development and leukemogenesis is not known. Here, we report that the active intracellular portion of NOTCH1 (ICN1) is detectable in ~50% of peripheral blood CLL cases lacking gene mutations. We identify a ‘NOTCH1 CLL gene expression signature’ in CLL cells, and show that this signature is significantly enriched in primary CLL cases expressing ICN1, independent of NOTCH1 mutation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 57 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE92nnn/GSE92626/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA358194
Series		Accession: GSE92626	ID: 200092626

3045. Systematic Functional Perturbations Uncover a Prognostic Genetic Network Driving Human 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
Platform: GPL11154 26 Samples
FTP download: GEO (BED, FPKM_TRACKING, TDF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95305/
Series		Accession: GSE95305	ID: 200095305

3046. Systematic Functional Perturbations Uncover a Prognostic Genetic Network Driving Human Breast Cancer [RNA-Seq]
(Submitter supplied) Gene-expression patterns of primary breast cancers aid clinicians in predicting the risk of metastatic disease. Some prognostic signatures have recently been prospectively validated, highlighting their clinical value. Such classifiers conceivably comprise biomarker genes that, in fact, functionally contribute to the oncogenic and metastatic properties of the tumors, but this has not been investigated systematically. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 20 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95304/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA376601
Series		Accession: GSE95304	ID: 200095304

3047. Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol 
(Submitter supplied) Most studies of responses to transcriptional stimuli measure changes in cellular mRNA concentrations.  By sequencing nascent RNA instead, it is possible to detect changes in transcription in minutes rather than hours, and thereby distinguish primary from secondary responses to regulatory signals.  Here, we describe the use of PRO-seq to characterize the immediate transcriptional response in human cells to celastrol, a compound derived from traditional Chinese medicine that has potent anti-inflammatory, tumor-inhibitory and obesity-controlling effects. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL18573 12 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE96nnn/GSE96869/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA379960
Series		Accession: GSE96869	ID: 200096869

3048. Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors
(Submitter supplied) Intratumoralmheterogeneity is a major obstacle to cancer treatment and a significant confounding factor in bulk-tumor profiling. We performed an unbiased analysis of transcriptional heterogeneity in colorectal tumors and their microenvironments using single-cell RNA–seq from 11 primary colorectal tumors and matched normal mucosa. To robustly cluster single-cell transcriptomes, we developed reference component analysis (RCA), an algorithm that substantially improves clustering accuracy. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 1220 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81861/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA323703
Series		Accession: GSE81861	ID: 200081861

3049. Transcriptional landscape of the human cell cycle
(Submitter supplied) Steady-state  gene  expression  across  the  cell  cycle  has  been  studied  extensively.  However, 2 transcriptional gene regulation and histone modification dynamics at different cell cycle stages is3 largely  unknown.  By  applying  a  combination  of  GRO-seq,  RNA-seq and  histone  modification 4 ChIP-seq, we depicted a comprehensive transcriptional landscape at G0/G1, G1/S and M phases 5 of  breast  cancer  MCF-7  cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platform: GPL11154 13 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94479/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA369803
Series		Accession: GSE94479	ID: 200094479

3050. CDK12 regulates alternative last exon mRNA splicing and promotes invasion of a breast cancer cell line
(Submitter supplied) We performed mRNA sequencing on 184-hTert and SK-BR-3 and MDA-MB-231 cell lines treated with siRNA directed to CDK12 (Cyclin dependent kinase 12) or a scrambled siRNA control. For each cell line, we generated 6 RNA-seq libraries (3 treatment replicates and 3 control replicates) to study the differential expression and the differential splicing patterns regulated by CDK12.
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/GSE80nnn/GSE80409/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA318813
Series		Accession: GSE80409	ID: 200080409

3051. Integrated analysis of MLL-AF9 AML patients and model leukemias highlights RET and other novel therapeutic targets (RNA-seq shRNA)
(Submitter supplied) Next generation DNA sequencing of acute myeloid leukemia (AML) patient samples has revealed novel recurrent mutations while at the same time highlighting the genetic heterogeneity of the disease. These observations suggest that an extraordinarily large number of combinations of mutations can contribute to leukemogenesis. In order to address the question of the contribution of patient genetic background to AML we have developed a model system to generate multiple human leukemias in a single donor’s genetic background. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72041/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA292831
Series		Accession: GSE72041	ID: 200072041

3052. Integrated analysis of MLL-AF9 AML patients and model leukemias highlights RET and other novel therapeutic targets (RNA-seq B-ALL)
(Submitter supplied) Next generation DNA sequencing of acute myeloid leukemia (AML) patient samples has revealed novel recurrent mutations while at the same time highlighting the genetic heterogeneity of the disease. These observations suggest that an extraordinarily large number of combinations of mutations can contribute to leukemogenesis. In order to address the question of the contribution of patient genetic background to AML we have developed a model system to generate multiple human leukemias in a single donor’s genetic background. 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/GSE71840/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA292311
Series		Accession: GSE71840	ID: 200071840

3053. Integrative epigenomic analysis in MLL-AF9 acute myeloid leukemia (AML) and B-acute lymphoblastic leukemia (B-ALL)
(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: GPL15520 GPL11154 55 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71691/
Series		Accession: GSE71691	ID: 200071691

3054. Microarray profiling and co-expression network analysis of lncRNAs and mRNAs associated with acute leukemia in adult
(Submitter supplied) To understand the distinct mechanisms in leukemogenesis between ALL and AML and to identify markers for diagnosis and treatment, lncRNA and mRNA expression profiles of AML and ALL patients and healthy controls were generated by using microarray analysis
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by array
Platform: GPL21242 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE96nnn/GSE96535/
Series		Accession: GSE96535	ID: 200096535

3055. m6A-seq in glioblastoma stem cells
(Submitter supplied) m6A RNA methylation plays an important role in regulating the self-renewal and tumorigenesis of glioblastoma stem cells. We performed m6A-seq analysis in glioblastoma stem cells with m6A levels modulated by knocking down METTL3 or METTL14 and identified m6A regulated genes in glioblastoma stem cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 8 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94808/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA374490
Series		Accession: GSE94808	ID: 200094808

3056. Reconstituting development of pancreatic intraepithelial neoplasia from primary human pancreas duct cells
(Submitter supplied) Development of systems that reconstitute hallmark features of human pancreatic intraepithelial neoplasia (PanINs), the precursor to pancreatic ductal adenocarcinoma, could generate new strategies for early diagnosis and intervention. However, human cell-based PanIN models with defined mutations are unavailable. Here, we report that genetic modification of primary human pancreatic cells leads to development of lesions resembling native human PanINs. more...
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/GSE88nnn/GSE88997/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA349475
Series		Accession: GSE88997	ID: 200088997

3057. KDM1A confers invasive and metastatic attributes in lung adenocarcinoma by modulating a non-canonical Integrin ß3-KRAS signaling pathway
(Submitter supplied) KRAS mutations occur in approximately 25% of non-small cell lung cancer (NSCLC). They account for the therapy resistance to EGFR inhibitors and are suggested to be difficult to target by specific drugs. Therefore, new therapies for KRAS mutant NSCLC are urgently needed. The histone H3K4 and H3K9 di/mono-demethylase KDM1A is a key epigenetic writer, aberrantly upregulated in many cancer types, including NSCLC. 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/GSE86nnn/GSE86874/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA342818
Series		Accession: GSE86874	ID: 200086874

3058. Messenger RNA expression after silencing or inhibition of MEN1in MCF-7 breast cancer cells
(Submitter supplied) We performed RNA-seq in MCF-7 cells after silencing of MEN1 using small hairpin RNA's directed at the MEN1 mRNA or chemical inhibition of the MEN1 gene product, menin. We demonstrate that a selected group of transcripts is affected by reduced menin function.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL18573 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86316/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA341401
Series		Accession: GSE86316	ID: 200086316

3059. Transcriptome-wide identification of transcripts regulated by MBNL3 in hepatocellular carcinoma cells
(Submitter supplied) Understanding the roles of splicing factors and splicing events during human tumorigenesis would open new avenues for targeted therapeutics. Here we identify an oncofetal splicing factor MBNL3, which indicates poor prognosis, and promotes hepatocellular carcinoma (HCC) tumorigenesis. Genetic MBNL3 inhibition almost completely abolishes HCC tumorigenesis. Transcriptomic analysis revealed that MBNL3 induces PXN antisense transcript 1 exon 4 inclusion. 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/GSE95nnn/GSE95778/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA378385
Series		Accession: GSE95778	ID: 200095778

3060. The antineoplastic drug, trastuzumab, dysregulates metabolism in iPSC derived cardiomyocytes.
(Submitter supplied) Background: The targeted ERBB2 therapy, trastuzumab, has had a tremendous impact on management of patients with HER2+ breast cancer, leading to development and increased use of further HER2 targeted therapies. The major clinical side effect is cardiotoxicity but the mechanism is largely unknown. On the basis that gene expression is known to be altered in multiple models of heart failure, we examined differential gene expression of iPSC derived cardiomyocytes treated at day 11 with the ERBB2 targeted monoclonal antibody, trastuzumab for 48 hours and the small molecule tyrosine kinase inhibitor of EGFR and ERBB2. 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/GSE91nnn/GSE91383/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA356882
Series		Accession: GSE91383	ID: 200091383

3061. Acriflavine inhibits the epithelial-to-mesenchymal transition in vitro in liver and pancreatic 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
Platforms: GPL18573 GPL15207 38 Samples
FTP download: GEO (CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE82nnn/GSE82299/
Series		Accession: GSE82299	ID: 200082299

3062. Acriflavine inhibits the epithelial-to-mesenchymal transition in vitro in liver and pancreatic cancer cells (part of study on HepG2)
(Submitter supplied) Background: Epithelial-to-mesenchymal transition (EMT) is considered an important driving mechanism behind aggressive cancer phenotype. This was recently challenged by the finding that cells can metastasize without undergoing EMT. However, the same studies confirmed the important role of the EMT program in drug resistance. The EMT program is largely dependent on the cell’s microenvironment. Acriflavine (ACF) is a heteroaromatic dye with antibacterial and antiviral effects. 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/GSE82110/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA324072
Series		Accession: GSE82110	ID: 200082110

3063. Acriflavine inhibits the epithelial-to-mesenchymal transition in vitro in liver and pancreatic cancer cells (part of study on PANC1 cells treated with CoCl2)
(Submitter supplied) Background: Epithelial-to-mesenchymal transition (EMT) is considered an important driving mechanism behind aggressive cancer phenotype. This was recently challenged by the finding that cells can metastasize without undergoing EMT. However, the same studies confirmed the important role of the EMT program in drug resistance. The EMT program is largely dependent on the cell’s microenvironment. Acriflavine (ACF) is a heteroaromatic dye with antibacterial and antiviral effects. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE82nnn/GSE82104/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA324011
Series		Accession: GSE82104	ID: 200082104

3064. Recurrent TRIO fusion in non-translocation-related sarcomas
(Submitter supplied) We used NGS on a cohort of complex genetics sarcomas to study their transcriptomes (RNA-seq technology), looking for recurrent and specific gene fusions. We identified multiple TRIO fusions with different partners in our cohort. No TRIO fusions were reported in negative-control cells (normal tissues) and in simple genetics sarcomas.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 117 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75885/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA305611
Series		Accession: GSE75885	ID: 200075885

3065. Integrin-b4 identifies cancer stem cell-enriched populations of partially mesenchymal carcinoma cells
(Submitter supplied) We report the gene expression profiles of normal epithelial and carcinoma cell populations that differ in their relative levels of integrin-beta 4 expression. ITGB4 high, mesenchymal subtype, triple-negative breast cancer cells were found to be more epithelial than related ITGB4 low cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 36 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95540/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA377346
Series		Accession: GSE95540	ID: 200095540

3066. A combinatorial screen of the CLOUD uncovers a synergy targeting the androgen receptor
(Submitter supplied) Approved drugs are invaluable tools to study biochemical pathways and further characterization of these compounds may lead to repurposing of single drugs or combinations. Here, we describe a collection of 308 small molecules representing the diversity of structures and molecular targets of all FDA-approved chemical entities. The CeMM Library of Unique Drugs (CLOUD) covers prodrugs and active forms at pharmacologically relevant concentrations and is ideally suited for combinatorial studies. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 8 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94783/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA374038
Series		Accession: GSE94783	ID: 200094783

3067. Effect of BCL11B overexpression on transcriptome of T-cell acute lymphoblastic leukemia (T-ALL) cells
(Submitter supplied) To investigate the effects of BCL11B on T-cell differentiation, we  performed gain of function studies in cells with a T-lineage differentiation arrest, namely T-ALL cells. Gene expression profiling by RNA-Seq demonstrated that BCL11B overexpression induced transcriptional changes consistent with T-cell differentiation as early as 72 hours after transduction, indicating a rapid regulatory effect of BCL11B on the T-lineage transcriptional program and supporting an important role for BCL11B in human T-cell differentiation.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84675/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA330819
Series		Accession: GSE84675	ID: 200084675

3068. SLC2525-AS1: a potential lncRNA biomarker for radiotherapy sensitivity of colorectal carcinoma
(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: GPL16791 GPL23146 10 Samples
FTP download: GEO (PAIR) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95652/
Series		Accession: GSE95652	ID: 200095652

3069. SLC25A25-AS1 knockdown data of two colorectal carcinoma cell lines (HT29 and SW480)
(Submitter supplied) We identified that SLC25A25-AS1 was a lncRNA influencing radiation response. Therefore, we aimed to explore more biological roles of SLC25A25-AS1 in this process. Towards this end, we used RNA interference (RNAi)-mediated knockdown of SLC25A25-AS1 in HT29 and SW480 to explore the changes of mRNA expression profiles and explore the phenotype outcomes.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95605/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA377628
Series		Accession: GSE95605	ID: 200095605

3070. Lipid degradation promotes prostate cancer cell survival
(Submitter supplied) Prostate cancer is the most common male cancer and androgen receptor (AR) is the major driver of the disease. Here we show that Enoyl-CoA delta isomerase 2 (ECI2) is a novel AR-target that promotes prostate cancer cell survival. Increased ECI2 expression predicts mortality in prostate cancer patients (p=0.0086). ECI2 encodes for an enzyme involved in lipid metabolism, and we use multiple metabolite profiling platforms and RNA-seq to show that inhibition of ECI2 expression leads to decreased glucose utilization, accumulation of fatty acids and down-regulation of cell cycle related genes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75035/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA302270
Series		Accession: GSE75035	ID: 200075035

3071. Gene signature driving invasive mucinous adenocarcinoma of the lung
(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 29 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86959/
Series		Accession: GSE86959	ID: 200086959

3072. Transcriptome of invasive mucinous adnocarcinoma of the lung and adjacent normal lung tissues from 6 patients based on RNA-seq method
(Submitter supplied) In order to identify genes that are highly expressed in human IMA, we performed mRNA-seq analysis using RNAs extracted from 6 human invasive mucinous adenocarcinoma of the lung (IMA) and adjacent normal lung tissues and determined genes differentially expressed in human IMA.
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/GSE86nnn/GSE86958/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA343087
Series		Accession: GSE86958	ID: 200086958

3073. Genes regulated by SPDEF or FOXA3 in A549 lung carcinoma cells [RNA-seq]
(Submitter supplied) To identify genes regulated by SPDEF or FOXA3 in A549 lung carcinoma cells, we analyzed the whole-transcriptomic mRNA profiles of A549 cells expressing SPDEF or FOXA3 based on RNA-seq.
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/GSE86nnn/GSE86956/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA343086
Series		Accession: GSE86956	ID: 200086956

3074. Genome-wide functional assessment of enhancer activities in the human genome
(Submitter supplied) We illustrate that modifications to the previously published STARR-seq protocols are capable of  assessing enhancer activity of  whole genomes on mammalian systems using the human prostate cancer cell line, LNCaP. Besides detecting accessible enhancers located in open chromatin regions, we are also able to discover active, inaccessible enhancers in closed chromatin regions. By applying histone deacetylase inhibitor, trichostatin A, genes nearby the previously inaccessible enhancers are up-regulated, indicating the potential for endogenous functionality of these regulatory elements. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL11154 18 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE82nnn/GSE82204/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA324294
Series		Accession: GSE82204	ID: 200082204

3075. RNA-Seq of Single Lung Circulating Tumor Cells (CTCs) and primary Tumor Cells from an orthotopic lung xenograft model
(Submitter supplied) An orthotopic lung xenograft model was used to identify differential expression of lung CTCs in comparison to primary lung tumor cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16288 16 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74639/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA301050
Series		Accession: GSE74639	ID: 200074639

3076. pSILAC mass spectrometry reveals ZFP91 as novel IMiD dependent substrate of the CRL4CRBN ligase
(Submitter supplied) Thalidomide and its derivatives lenalidomide and pomalidomide (IMiDs) are effective treatments of hematologic malignancies. It was shown that IMiDs impart gain of function properties to the CUL4-RBX1-DDB1-CRBN (CRL4CRBN) ubiquitin ligase that enable binding, ubiquitination and degradation of key therapeutic targets such as IKFZ1, IKZF3 and CSNK1A1. While these substrates have been implicated as efficacy targets in multiple myeloma (MM) and 5q deletion associated myelodysplastic syndrome (del(5q)-MDS), other targets likely exist. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94728/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA373859
Series		Accession: GSE94728	ID: 200094728

3077. PARP3 is a promoter of chromosomal rearrangements and limits G4 DNA
(Submitter supplied) Chromosomal rearrangements are essential events in the pathogenesis of both malignant and nonmalignant disorders, yet the factors affecting their formation are incompletely understood.  We developed a zinc finger nuclease translocation reporter (ZITR) and screened for factors that modulate rearrangements in human cells.  We identified UBC9 and RAD50 as suppressors and 53BP1, DDB1, and PARP3 as promoters of chromosomal rearrangements across human cell types. 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/GSE94nnn/GSE94588/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA371550
Series		Accession: GSE94588	ID: 200094588

3078. Zika virus infection reprograms global transcription of host cells to allow sustained infection
(Submitter supplied) Zika virus (ZIKV) is an emerging virus causally linked to neurological disorders, including congenital microcephaly and Guillain–Barré syndrome. There are currently no targeted therapies for ZIKV infection. To identify novel antiviral targets and to elucidate the mechanisms by which ZIKV exploits the host cell machinery to support sustained replication, we analyzed the transcriptomic landscape of human microglia, fibroblast, embryonic kidney, and monocyte-derived macrophage cell lines before and after ZIKV infection.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 8 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93870/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA362626
Series		Accession: GSE93870	ID: 200093870

3079. Gene Expression of Breast Cancer Cell Lines Across Biomaterial Platforms
(Submitter supplied) 2 Breast Cancer Cell lines were seeded onto TCPS, on 2D PEG-PC gels, and encapsulated in 3D PEG-Maleimide  gels as single cells or spheroids to determine transcript level changes based on culture platform
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93562/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA361122
Series		Accession: GSE93562	ID: 200093562

3080. Effect of drugs on transcriptomic profiles
(Submitter supplied) the goal of this project is to determine the impact on genome-wide RNA expression of two molecules with biomedical applications on cancer
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93206/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA360294
Series		Accession: GSE93206	ID: 200093206

3081. Transcriptome analysis for KDM6A mutated urothelial bladder carcinoma and EZH2 inhibitor treated KDM6A mutated urothelial bladder carcinoma
(Submitter supplied) Purpose:  The goals of this study are to compare 1. The transcription profile in KDM6A wildtype and KDM6A mutated urothelial bladder carcinoma. 2. The transcriptional changes in KDM6A mutated urothelial bladder carcinoma upon EZH2 inhibitor treatment.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 50 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE92nnn/GSE92723/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA358425
Series		Accession: GSE92723	ID: 200092723

3082. Calpain 2 is a Mechanosensitive Link Between Integrin α6 and EGFR
(Submitter supplied) RNA-Seq Transcriptome analysis of MDA-MB-231s cultured on 2D biomaterials
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 9 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE92nnn/GSE92653/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA358236
Series		Accession: GSE92653	ID: 200092653

3083. ChIP-seq of ER and RUNX2 in MCF7 breast cancer cell lines
(Submitter supplied) We performed ChIP-seq on MCF7 cells in an effort to discern differential binding patterns between wild type MCF7s and MCF7s that have acquired resistance to Tamoxifen and Estrogen deprivation. Furthermore, we also performed an HAtag ChIP on a DOX inducible RUNX2 overexpression MCF7 cell line. We also performed RNA-seq on MCF7 cells to determine transciptional changes after acquisition of Tamoxifen resistance, and also transciptional changes in a DOX inducible RUNX2 overexpression model.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL18573 18 Samples
FTP download: GEO (BED, CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86538/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA342148
Series		Accession: GSE86538	ID: 200086538

3084. Cell responses to dysregulated VZV-induced cell-cell fusion
(Submitter supplied) The highly conserved herpesvirus glycoprotein complex, gB/gH-gL, mediates membrane fusion during virion entry and cell-cell fusion.  Varicella-zoster virus (VZV) characteristically forms multi-nucleated cells, or syncytia, during the infection of human tissues but little is known about this process.  The cytoplasmic domain of VZV gB (gBcyt) has been implicated in cell-cell fusion regulation because a gB[Y881F] substitution causes hyperfusion. more...
Organism:	Homo sapiens; Human alphaherpesvirus 3
Type:		Expression profiling by high throughput sequencing
Platforms: GPL26132 GPL11154 30 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85493/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA338650
Series		Accession: GSE85493	ID: 200085493

3085. Identification of mesothelial-to-mesenchymal gene signature in ascitic fluid-isolated mesothelial cells through RNA-sequencing
(Submitter supplied) RNA-sequencing analysis was carried out on ascetic fluid-isolated mesothelial cells from ovarian cancer patients compared to control human peritoneal mesothelial cells to identify a mesothelial-mesenchymal gene signature.
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/GSE84nnn/GSE84829/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA335318
Series		Accession: GSE84829	ID: 200084829

3086. RNA-seq analysis of SLIRP knockdown with 1nM DHT in LNCaP cells
(Submitter supplied) The purpose of this study was to profile gene expression changes that could occur with the loss of co-repressor SLIRP. In addition, we wanted to investigate how DHT could further alter gene expression. Methods: LNCaP cells were transfected with custom nonsense control siRNA or a pool of SLIRP siRNA (HSS130109, HSS188666, HSS188667 Invitrogen, Carlsbad, CA) at 40nM for 24hrs. Cells were washed once with PBS and replaced with SFM containing EtOH or 1nM/ml DHT for another 24hrs. 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/GSE77nnn/GSE77829/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA311699
Series		Accession: GSE77829	ID: 200077829

3087. 3alpha-acetonyltabersonine induces glioblastoma apoptosis via the inhibition of DNA damage repair
(Submitter supplied) we report the antitumor activity of an indole alkaloid, 3alpha-acetonyltabersonine, which was isolated from Melodinus suaveolens. 3alpha-acetonyltabersonine was found to be cytotoxic to glioblastoma cell line and stem cells at low concentrations.
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/GSE95nnn/GSE95392/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA376875
Series		Accession: GSE95392	ID: 200095392

3088. Global transcriptome profiling of triple-negative breast cancer cell lines treated with small-molecules targeting Bromodomain and Extra Terminal (BET) proteins
(Submitter supplied) Triple negative breast cancer (TNBC) represents the most clinically challenging subtypes of breast cancer for which targeted therapeutics are still lacking. Bromodomain and Extra Terminal (BET) proteins, including ubiquitously expressed BRD2, BRD3, BRD4 and testis-specific BRDT, are epigenetic “readers” and play a major role in epigenetic regulation of gene transcription. BET proteins have emerged as new therapeutic targets for human cancer and other diseases. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 24 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95375/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA376804
Series		Accession: GSE95375	ID: 200095375

3089. EZH2 is a potential therapeutic target for H3K27M mutant paediatric gliomas
(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: GPL16791 GPL17021 38 Samples
FTP download: GEO (BED, BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85390/
Series		Accession: GSE85390	ID: 200085390

3090. Transcriptome analysis revealed that SMD regulates neuronal differentiation.
(Submitter supplied) Transcriptome analysis from Staufen-mediated mRNA (SMD) targets during differentiation confirmed that STAU1 was a key factor in neuronal differentiation.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 5 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94948/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA374890
Series		Accession: GSE94948	ID: 200094948

3091. Identification of a unique gene expression signature in mercury and 2,3,7,8-tetrachlorodibenzo-p-dioxin co-exposed cells
(Submitter supplied) Mercury (Hg) and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) are major environmental contaminants that commonly co-occur in the environment. Both Hg and TCDD are associated with a number of human diseases including cancers. While the individual toxicological effects of Hg and TCDD have been extensively investigated, studies on co-exposure are limited to a few genes and pathways. Therefore, a significant knowledge gap exists in the understanding of the deleterious effects of co-exposure to Hg and TCDD. 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/GSE83nnn/GSE83886/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA327259
Series		Accession: GSE83886	ID: 200083886

3092. Heterotypic nucleosomes and PRC2 drive DIPG oncogenesis
(Submitter supplied) Diffuse intrinsic pontine gliomas (DIPG) are characterized by a heterozygous lysine-to-methionine mutation of histone H3 (H3K27M) that potently reduces Polycomb Repressive Complex 2 (PRC2) methylation of wild-type histone H3K27 (H3K27wt). The role of H3K27M and reduced H3K27wt methylation in DIPG pathogenesis has yet to be determined. Here, we have performed epigenomic profiling of patient-derived H3K27M mutant DIPG cells and demonstrate that H3K27M resides in nucleosomes with H3K27wt acetylation (H3K27ac), and H3K27M-H3K27ac containing nucleosomes co-localize with bromodomain proteins at actively transcribed genes and that PRC2 is excluded from H3K27M occupied regions. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 100 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78801/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA313974
Series		Accession: GSE78801	ID: 200078801

3093. Cell Cycle Reprogramming for PI3K Inhibition Overrides Relapse-Specific C481S BTK Mutation Revealed by Longitudinal Functional Genomics in Mantle Cell Lymphoma
(Submitter supplied) The RNA-seq data presented in this study include libraries from Mantle Cell Lymphoma (MCL) tumor cells sequentially obtained from patients
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE55nnn/GSE55405/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA239521
Series		Accession: GSE55405	ID: 200055405

3094. Dynamics of HIV Latency and Reactivation in a Primary CD4+ T Cell Model
(Submitter supplied) HIV latency is a major obstacle to curing infection. Current strategies to eradicate HIV aim at increasing transcription of the latent provirus. In the present study we observed that latently infected CD4+ T cells from HIV-infected individuals failed to produce viral particles upon ex vivo exposure to SAHA (vorinostat), despite effective inhibition of histone deacetylases. To identify steps that were not susceptible to the action of SAHA or other latency reverting agents, we used a primary CD4+ T cell model, joint host and viral RNA sequencing, and a viral-encoded reporter. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 34 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95297/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA376596
Series		Accession: GSE95297	ID: 200095297

3095. RNA-sequencing of human AML cells expressing high and low levels of CD99
(Submitter supplied) We FACS purified human AML cells based on CD99 expression and performed RNA-sequencing, demonstrating in CD99 high expression AML cells significant enrichment for hematopoietic stem cell and leukemic stem cell gene expression signatures.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 28 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86506/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA342100
Series		Accession: GSE86506	ID: 200086506

3096. Whole transcriptome sequencing of the human thyroid primary cells with knock-down of the FOXE1 gene
(Submitter supplied) FOXE1 gene (also known as thyroid transcription factor 2) has been reported to be essential for thyroid gland development and the maintenance of thyroid differentiated status. Current knowledge of FOXE1 regulated genes is mostly based on the expression and functional studies using cell line models. Here we report gene expression profiles of human thyroid primary cells on Day 5 treated with FOXE1 siRNA or nontarget siRNA. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83919/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA326158
Series		Accession: GSE83919	ID: 200083919

3097. Cis-Regulatory Circuits Regulating NEK6 Kinase Overexpression in Transformed B Cells Are Super-Enhancer-Independent (RNA-seq)
(Submitter supplied) Alterations in distal regulatory elements that control gene expression underlie many diseases, including cancer. Epigenomic analyses of normal and diseased cells have produced correlative predictions for connections between dysregulated enhancers and target genes involved in pathogenesis. However, with few exceptions, these predicted cis-regulatory circuits remain untested. Here, we dissect cis-regulatory circuits that lead to overexpression of NEK6, a mitosis-associated kinase, in human B cell lymphoma. 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/GSE87nnn/GSE87320/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA344336
Series		Accession: GSE87320	ID: 200087320

3098. The LIM protein AJUBA promotes colorectal cancer cell survival through suppression of JAK1/STAT1/IFIT2 network
(Submitter supplied) Background and Aims: The LIM protein AJUBA participates in the regulation of cell adhesion, mitosis, DNA damage, cell differentiation, proliferation, migration and gene transcription, yet its roles in tumor development and progression are poorly defined. The aim is to determine the role of AJUBA in colorectal tumorigenesis. Methods:  We performed data mining in Oncomine databases and immunohistochemistry (IHC) assays on 67 paired colorectal cancer (CRC) samples; we manipulated the AJUBA expression in SW-1116 and Caco-2 cells using specific shRNA and overexpression plasmids and performed assays for cell viability, cell cycle and apoptosis; we performed RNA-seq and qRT-PCR assays to identify genes regulated by AJUBA; we performed western blot, co-immunoprecipitation assays to study the interaction of AJUBA and JAK/STAT; Results: We discovered that AJUBA is highly expressed in CRC and promotes CRC cell growth in culture and in xenograted mice via an inhibition of apoptosis by repression of the IFIT2 gene. 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/GSE84nnn/GSE84902/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA335606
Series		Accession: GSE84902	ID: 200084902

3099. Transcription control by the ENL YEATS domain in acute leukemia
(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 38 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE82nnn/GSE82118/
Series		Accession: GSE82118	ID: 200082118

3100. Transcription control by the ENL YEATS domain in acute leukemia [RNA-seq]
(Submitter supplied) Recurrent chromosomal translocations involving the mixed lineage leukemia gene (MLL) give rise to highly aggressive acute leukemia associated with poor clinical outcomes. The preferential involvement of chromatin-associated factors in MLL rearrangements belies a dependency on transcriptional control. To identify new targets for therapeutic development in MLL, we performed a genome-scale CRISPR-Cas9 knockout screen in MLL-AF4 leukemia. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE82nnn/GSE82117/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA324086
Series		Accession: GSE82117	ID: 200082117

3101. Next Generation Sequencing Facilitates Quantitative Analysis of colorectal cancer cells transfected with NC siRNA or RPL9 siRNA
(Submitter supplied) Ribosomal protein L9 (RPL9), a component of the 60S subunit, is up-regulated in human colorectal cancer (CRC). We thus hypothesized if targeting of RPL9 with small interfering (si) RNA could inhibit CRC progression. We also investigated molecular mechanism to mediate CRC cell death caused by RPL9 silencing. HCT116 and HT29 human CRC cells were transfected with RPL9 siRNA and tested for growth inhibition and apoptotic induction using MTS, FACS and microscopic analysis. 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/GSE78nnn/GSE78195/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA312903
Series		Accession: GSE78195	ID: 200078195

3102. OTX2 activity at distal regulatory elements shapes the chromatin landscape of Group 3 medulloblastoma
(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 107 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE92nnn/GSE92585/
Series		Accession: GSE92585	ID: 200092585

3103. OTX2 activity at distal regulatory elements shapes the chromatin landscape of Group 3 medulloblastoma [RNA-seq]
(Submitter supplied) Medulloblastoma is the most frequent malignant pediatric brain tumor and is divided into at least four subgroups known as Wnt, SHH, Group 3 and Group 4. Here we characterized gene regulation mechanisms in the most aggressive subtype, Group 3 tumors, through genome-wide chromatin and expression profiling. Our results show that most active distal sites in these tumors are occupied by the transcription factor OTX2. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE92nnn/GSE92583/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA358125
Series		Accession: GSE92583	ID: 200092583

3104. Inflammatory cytokines activate unliganded estrogen receptor and alter the sensitivity of breast cancer cells to tamoxifen
(Submitter supplied) Genome-wide analyses of the transcriptomes and transcription factor recruitment in estrogen receptor breast cancer cells in response to estradiol, IL1b, or TNFa treatments. Also, the role of inflammatory cytokines on affecting tamoxifen sensitivity is analyzed on a genome-wide scale.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 56 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67295/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA279424
Series		Accession: GSE67295	ID: 200067295

3105. Dissection of functionally relevant Wnt/beta-catenin target genes in an organ culture model of Wilms tumor
(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
Platforms: GPL571 GPL13112 GPL8321 32 Samples
FTP download: GEO (CEL, CHP, CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE65nnn/GSE65899/
Series		Accession: GSE65899	ID: 200065899

3106. Diffuse Large B Cell Lymphoma cell line with Acquired Resistance to PI3Kδ Inhibitor Idelalisib
(Submitter supplied) RNAseq profile of TMD8 cell lines resistant to Idelalisib treatment.  Idelalisib resistant TMD8 cells were generated by continuous passage in the presence of 1 μM idelalisib for 8 weeks until stable resistance to idelalisib was established. Parallel cultures were grown in the presence of 0.1% DMSO as passage-matched, drug-sensitive control lines. Sensitive and resistant TMD8 cells were clonally isolated through two rounds of single cell limiting dilution
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/GSE93nnn/GSE93156/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA360147
Series		Accession: GSE93156	ID: 200093156

3107. RNA-seq analysis of hepatocellular carcinoma with portal vein tumor thrombosis
(Submitter supplied) Portal vein tumor thrombosis is a strong poor indication of HCC. Characterizing the molecular alterations of these metastatic HCCs is important for understanding the molecular mechanisms during HCC progression and metastasis. Previous genomic studies mainly focus on single molecular layer, such as gene expressions or exonic mutations. In this study, we systematically examined the copy number variation (CNV), DNA methylation, miRNA and transcriptome of matched adjacent normal tissues, primary tumors and PVTTs from 19 HCC patients. 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/GSE77nnn/GSE77509/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA310654
Series		Accession: GSE77509	ID: 200077509

3108. The molecular landscape of hepatocellular carcinoma with portal vein tumor thrombosis
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Non-coding RNA profiling by high throughput sequencing; Methylation profiling by genome tiling array; Genome variation profiling by high throughput sequencing; Genome variation profiling by SNP array; Expression profiling by high throughput sequencing
Platforms: GPL13534 GPL16131 GPL16791 240 Samples
FTP download: GEO (CEL, CYCHP, IDAT, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77276/
Series		Accession: GSE77276	ID: 200077276

3109. Stage-specific human induced pluripotent stem cells map the progression of myeloid transformation to transplantable leukemia
(Submitter supplied) Comparison of disease stage transitions between a panel of iPSC clones derived  from different MDS patients
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 11 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE92nnn/GSE92494/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA357698
Series		Accession: GSE92494	ID: 200092494

3110. Transcriptome of iPSC-derived Cerebral Organoids with Heterozygous Knockout in CHD8
(Submitter supplied) CHD8 (chromodomain helicase DNA binding protein 8), which codes for a member of the CHD family of ATP-dependent chromatin-remodeling factors, is the most commonly mutated gene in autism spectrum disorders (ASD) identified in exome-sequencing studies. Loss of function mutations in the gene have also been found in schizophrenia (SZ) and intellectual disabilities, and affects cancer cell proliferation. 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/GSE85nnn/GSE85417/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA338401
Series		Accession: GSE85417	ID: 200085417

3111. Robust Stratification of Breast Cancer Subtypes
(Submitter supplied) Breast cancer, the second leading cause of cancer death of women worldwide, is a heterogenous disease with multiple different subtypes. These subtypes carry important implications for prognosis and therapy. Interestingly, it is known that these different subtypes not only have different biological behaviors, but also have distinct gene expression profiles. However, it has not been rigorously explored whether particular transcriptional isoforms are also differentially expressed among breast cancer subtypes, or whether transcript isoforms from the same sets of genes can be used to differentiate subtypes. 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/GSE94nnn/GSE94899/
Series		Accession: GSE94899	ID: 200094899

3112. RNA sequencing of Esophageal adenocarcinomas
(Submitter supplied) Identify EAC-relative fusion genes,differential genes  and mutations
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 80 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94869/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA374673
Series		Accession: GSE94869	ID: 200094869

3113. Histone deacetylase inhibition 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; Methylation profiling by genome tiling array; Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL13534 36 Samples
FTP download: GEO (BIGWIG, IDAT, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE92nnn/GSE92911/
Series		Accession: GSE92911	ID: 200092911

3114. Gene expression profiling of histone deacetylase inhibition in triple-negative breast cancer
(Submitter supplied) Analysis of changes in gene expression levels after after prolonged exposure of triple-negative breast cancer cell lines to low doses of Panobinostat (LBH589), a pan-histone deacetylase inhibitor.
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/GSE92nnn/GSE92910/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA358776
Series		Accession: GSE92910	ID: 200092910

3115. A Novel RNA Sequencing Data Analysis Method for Cell Line Authentication
(Submitter supplied) We have developed a novel analysis method that can interrogate the authenticity of biological samples used for generation of transcriptome profiles in public data repositories. The method uses RNA sequencing information to reveal mutations in expressed transcripts and subsequently confirms the identity of analysed cells by comparison with publicly available cell-specific mutational profiles. Cell lines constitute key model systems widely used within cancer research, but their identity needs to be confirmed in order to minimise the influence of cell contaminations and genetic drift on the analysis. 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/GSE81nnn/GSE81194/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA320872
Series		Accession: GSE81194	ID: 200081194

3116. Interaction between cyclooxygenase-2 and caspase-3 abolishes the cleavage of RNA-binding protein HuR and promotes drug resistance in oral squamous cell carcinoma
(Submitter supplied) Here, we show that HuR cleavage is dependent on active caspase-3 in oral cancer cells treated with ionizing radiation and the chemotherapeutic drug paclitaxel.  We determined that oral cancer cells overexpressing cyclooxygenase-2 (COX-2) limited the cleavage of both caspase-3 and HuR, which in turn, reduced the rate of apoptosis in paclitaxel treated cells. Specific inhibition of COX-2 by celecoxib promoted apoptosis through activation of caspase-3 and cleavage of HuR in paclitaxel-resistant oral cancer cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15456 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79477/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA315952
Series		Accession: GSE79477	ID: 200079477

3117. Next Generation Sequencing Facilitates Quantitative Analysis of HCC cells transfected with NCsiRNA or CDCA8siRNA
(Submitter supplied) We hypothesized if targeting of CDCA8 with small interfering (si) RNA could inhibit HCC progression. We also investigated molecular mechanism to mediate HCC cell death caused by CDCA8 silencing. To accomplish this, Huh1 and Huh7 human HCC cells were transfected with CDCA8 siRNA and tested for growth inhibition and apoptotic induction using MTS, FACS and microscopic analysis. To obtain insights into the molecular changes in response to CDCA8 knockdown, global changes in gene expression were examined using 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/GSE77nnn/GSE77992/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA312309
Series		Accession: GSE77992	ID: 200077992

3118. Effects of NSD2 depletion on gene expression and H3K36me2 in a lung cancer cell line
(Submitter supplied) The histone methyltransferase NSD2/WHSC1/MMSET is overexpressed in a number of solid tumors but its contribution to the biology of these tumors is not well understood. Here, we describe that NSD2 contributes to the proliferation of a subset of lung cancer cell lines by supporting oncogenic RAS transcriptional responses. Co-treatment with MEK and BRD4 inhibitors causes co-operative inhibitory responses on cell growth. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 30 Samples
FTP download: GEO (FPKM_TRACKING, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73696/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA297680
Series		Accession: GSE73696	ID: 200073696

3119. Interaction with ZMYND11 mediates opposing roles of Ras-responsive transcription factors ETS1 and ETS2
(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 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86240/
Series		Accession: GSE86240	ID: 200086240

3120. Interaction with ZMYND11 mediates opposing roles of Ras-responsive transcription factors ETS1 and ETS2
(Submitter supplied) Aberrant activation of RAS/MAPK signaling is a driver of over one third of all human carcinomas. The homologous transcription factors ETS1 and ETS2 mediate the activation of gene expression programs downstream of RAS/MAPK signaling. ETS1 is important for oncogenesis in many tumor types. However, ETS2 can act as an oncogene in some cellular backgrounds, and as a tumor suppressor in others, and the molecular mechanism responsible for this cell-type specific function remains unknown. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL18573 6 Samples
FTP download: GEO (DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86239/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA341062
Series		Accession: GSE86239	ID: 200086239

3121. Targeting the Creatine Kinase Pathway in EVI1-Positive Acute Myeloid Leukemia
(Submitter supplied) Purpose: Identify new targets in EVI1-Positive Acute Myeloid Leukemia Methods: Treatment with cyclocreatine  of EVI1-driven AML cell lines TF-1,  UT-7 and UCSD-AML1. Cyclocreatine was purchased from Sigma-Aldrich (Sigma). TF-1, UT-7 and UCSD-AML1 cells were treated in quadruplicate with either vehicle or 3 mM cyclocreatine for 24 hours. Total RNA was extracted and profiled by RNA sequencing (HiSeq, Illumina) at BioMicroCenter from Massachusetts Institute of Technology (Cambridge, MA, USA). 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/GSE86nnn/GSE86151/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA340369
Series		Accession: GSE86151	ID: 200086151

3122. Single Cell Transcriptome Conservation in Cryopreserved Cells and Tissues
(Submitter supplied) Sample preservation method that maintains transcripts in viable single cells and so allows to disconnect time and place of sampling from subsequent processing steps.
Organism:	Canis lupus familiaris; Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
4 related Platforms 1486 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85534/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA338759
Series		Accession: GSE85534	ID: 200085534

3123. RNA sequencing of MDA-MB231 and U2OS cancer cell lines exposed to the alkylating agent methyl methanesufonate (MMS) and classical chemotherapeutics 
(Submitter supplied) Understanding the mechanisms by which cells respond to chemotherapeutics is key to identifying means to improve therapy effiicacy while reducing systemic toxicity of these widely used classes of drugs. While determining the role of NRF2-GSH and ER stress in cells exposed to alkylating compounds such as methyl-methanesulfonate (MMS), we asked if these pathways could also be a general cell damage response relevant to other clinically used chemotherapeutics or if it is an alkylation specific response. 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/GSE84nnn/GSE84863/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA335388
Series		Accession: GSE84863	ID: 200084863

3124. A RUNX2-mediated Epigenetic Regulation of the Survival of p53 Defective Cancer Cells
(Submitter supplied) The goal is to identify transcripts that are regulated by RUNX2 in SAOS2 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77352/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA310114
Series		Accession: GSE77352	ID: 200077352

3125. Species-Specific Developmental Timing is Maintained by Pluripotent Stem Cells Ex Utero
(Submitter supplied) We performed whole transcriptome RNA sequencing experiments on two sets of differentiation time course starting from human ES cells (EGFP-H1) and mouse EGFP-EpiS cells: (1) in vitro neural differentiation, and (2) teratoma formation
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL17021 81 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90053/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA354394
Series		Accession: GSE90053	ID: 200090053

3126. Gene expression analysis of C4-2 cells treated with ACLY inhibitor and Enzalutamide
(Submitter supplied) This study examined the gene expression effects of treating androgen-deprived C4-2 prostate cancer cells with the ACLY inhibitor BMS-303141 and the AR antagonist enzalutamide.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81796/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA322550
Series		Accession: GSE81796	ID: 200081796

3127. Integrated Profiling of mRNAs and microRNAs to Identify Potential Biomarkers for Oral Malignant Transformation
(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 12 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70666/
Series		Accession: GSE70666	ID: 200070666

3128. Integrated Profiling of mRNAs and microRNAs to Identify Potential Biomarkers for Oral Malignant Transformation [mRNA-Seq]
(Submitter supplied) The purpose of this study was to systematically profile the expression of both mRNAs and miRNAs in OSCC and its premalignant disease to identify some novel potential biomarkers for the detection of malignant transformation.
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/GSE70nnn/GSE70665/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA289313
Series		Accession: GSE70665	ID: 200070665

3129. Illumina Total RNA-seq in HeLa
(Submitter supplied) Purpose: Examine the effect of the long non-coding RNA PARROT on the transcriptome in HeLa cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (BW, RPKM) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69842/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA286901
Series		Accession: GSE69842	ID: 200069842

3130. Gene expression of rhabdomyosarcoma cells infected with cytolytic and non-cytolytic variants of coxsackievirus B2 Ohio
(Submitter supplied) In this study the gene expression in cells infected with lytic and non-lytic variants of coxsackievirus B2 Ohio (CVB2O) were analyzed using next generation sequencing. This approach was selected with the purpose of elucidating the effects of lytic and non-lytic viruses on host cell transcription. Total RNA was extracted from infected cells, next generation sequencing was performed, and the reads were subsequently mapped against the human and CVB2O genomes. more...
Organism:	Coxsackievirus B2 (strain Ohio-1); Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20238 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69205/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA284884
Series		Accession: GSE69205	ID: 200069205

3131. Effects of LKB1/STK11 expression on MDA-MB-231 triple-negative breast cancer cells
(Submitter supplied) MDA-MB-231 cells transfected with pcDNA-vector or pcDNA-LKB1 were analyzed for changes in gene expression. Results provide insight into genes regulated by LKB1 signaling with implications in tumor and metastasis suppression in breast cancer.
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/GSE56882/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA244857
Series		Accession: GSE56882	ID: 200056882

3132. Morphological and molecular characterization of human dermal lymphatic collectors
(Submitter supplied) Millions of patients suffer from lymphedema worldwide. Supporting the contractility of lymphatic collectors is an attractive target for pharmacological therapy of lymphedema. However, lymphatics have mostly been studied in animals, while the cellular and molecular characteristics of human lymphatic collectors are largely unknown. We studied epifascial lymphatic collectors of the thigh, which were isolated for autologous transplantations. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 15 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87360/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA344487
Series		Accession: GSE87360	ID: 200087360

3133. Identification of transcriptomic drivers of squamous cell carcinoma development through a preneoplastic intermediate [human RNA-Seq]
(Submitter supplied) Cutaneous squamous cell carcinoma (cuSCC) comprises 15-20% of all skin cancers, accounting for over 700,000 cases in the U.S. annually. Most cuSCC arise in association with a distinct precancerous lesion, the actinic keratosis (AK). In order to identify potential targets for molecularly targeted chemoprevention, we performed integrated cross-species genomic analysis of cuSCC development through the preneoplastic AK stage using matched human samples and a solar UV-driven Hairless mouse model. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 26 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84293/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA328602
Series		Accession: GSE84293	ID: 200084293

3134. Identification of transcriptomic drivers of squamous cell carcinoma development through a preneoplastic intermediate
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL9115 GPL9250 45 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84194/
Series		Accession: GSE84194	ID: 200084194

3135. Carcinoma-astrocyte gap junctions promote brain metastasis by cytosolic dsDNA response transfer
(Submitter supplied) Brain metastasis represents a substantial source of morbidity and mortality in various cancers, and is characterized by high resistance to chemotherapy. Here we define the role of the most abundant cell type in the brain, the astrocyte, in brain metastasis. Cancer cells assemble of carcinoma-astrocyte gap junctions composed of connexin 43 (Cx43). Cx43 in cancer cells support brain metastatic colonization. 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/GSE79nnn/GSE79256/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA315285
Series		Accession: GSE79256	ID: 200079256

3136. HeLa transcriptome induction by IFN gamma and indoleamine 2,3-dioxygenase (IDO)
(Submitter supplied) We describe the modulation of gene expression by IDO induction in HeLa cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75956/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA305853
Series		Accession: GSE75956	ID: 200075956

3137. Genome-wide RNA-sequencing (RNA-seq) of benign and malignant prostate cell lines without and with androgen (R1881) stimulation.
(Submitter supplied) RNA-seq data were obtained from hTERT immortalized human prostate transit amplifying EP156T cells (+/- 10 nM R1881 for 48 hrs), progeny tumorigenic EPT3-M1 cells recovered from mouse metastatic tumor  (+/- 10 nM R1881 for 48 hrs) and the prostate cancer cell lines LNCaP  (+/- 10 nM R1881 for 48 hrs), VCaP (+/- 1 nM R1881 for 24 hrs) and 22Rv1 (+/- 1 nM R1881 for 24 hrs) (obtained from the American Type Culture Collection). 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/GSE71nnn/GSE71797/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA292095
Series		Accession: GSE71797	ID: 200071797

3138. Investigation about Monocytes in metastatic breast cancer patients under chemotherapy +/- Avastin
(Submitter supplied) The goal of this study was to determine if blood circulating monocytes of metastatic breast cancer patient would express a different activation profile compared to healthy donors, in order to use this specific changesas biomarkers to monitor then response to therapy
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/GSE70nnn/GSE70404/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA288542
Series		Accession: GSE70404	ID: 200070404

3139. RNA-Seq analysis of Head and Neck Squamous cell carcinoma cell-lines
(Submitter supplied) Analysis of gene-probe expression data (FPKM) for HNSCC cell-lines using single-end RNA-Seq
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (GTF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68872/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA283957
Series		Accession: GSE68872	ID: 200068872

3140. DLX3-dependent p53 signaling network controls keratinocyte cell cycle and squamous tumor growth
(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: GPL16791 GPL571 11 Samples
FTP download: GEO (CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67714/
Series		Accession: GSE67714	ID: 200067714

3141. DLX3 alters transcriptomic profile of adhesion, cell cycle, and cell death in Squamous Cell Carcinoma Cells
(Submitter supplied) Reinstatement of DLX3 into SCC13 cells upregulates genes involved with cell cycle exit, signaling, and adhesion whiles downregulates genes involved with cell death, proliferation, and movement.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67713/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA280746
Series		Accession: GSE67713	ID: 200067713

3142. The effect of HOXB13 CRISPR knockout on the transcriptome in G401 cells
(Submitter supplied) We report the expression profiles of G401 rhabdoid tumor of the kidney cell lines with and without the expression of the homeobox transcription factor HOXB13.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 2 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE65nnn/GSE65655/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA274620
Series		Accession: GSE65655	ID: 200065655

3143. Molecular Biomarkers Screened by Next-generation RNA Sequencing for non-sentinel lymph node status predicting in breast cancer patients with metastatic sentinel lymph node
(Submitter supplied) Six candidates (all ER/PR+, HER2−, Ki-67 <20 %) with metastatic SLNs selected from 305 patients were equally categorized as NSLN negative and positive. We identified 103 specifically expressed genes in the NSLN negative group and 47 in the NSLN positive group. Among them, FABP1 (negative group) and CYP2A13 (positive group) were the only 2 protein-encoding genes with expression levels in the 8th to 10th deciles. 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/GSE64nnn/GSE64850/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA272156
Series		Accession: GSE64850	ID: 200064850

3144. Quantitative analysis of CD133+ liver cancer stem cells vs CD133- non cancer stem cell by RNA-Seq profiling
(Submitter supplied) Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goal of this study is to compare the differentially expressed transcriptomes between CD133+ liver cancer stem cells versus CD133- non cancer stem cells by RNA-Seq profiling
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/GSE62nnn/GSE62905/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA266017
Series		Accession: GSE62905	ID: 200062905

3145. The epigenetic reader protein SPIN1 controls proliferation and survival of liposarcoma by modulating the RET signaling pathway
(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 11 Samples
FTP download: GEO (BED, TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57502/
Series		Accession: GSE57502	ID: 200057502

3146. The epigenetic reader protein SPIN1 controls proliferation and survival of liposarcoma by modulating the RET signaling pathway [RNA-Seq]
(Submitter supplied) The aim of this study is to identify the SPIN1 target genes in liposarcoma cells
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/GSE57nnn/GSE57501/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA246555
Series		Accession: GSE57501	ID: 200057501

3147. Abraxane, the Nanoparticle Formulation of Paclitaxel can Induce Drug Resistance by Up-regulation of P-gp
(Submitter supplied) Abraxane, a nanoparticle (NP) formulation of paclitaxel (PTX), has been demonstrated to be more effective than Taxol, the small molecule formulation, for the treatment of breast cancer and non-small cell lung cancer (NSCLC). It was reported that Abraxane existed in plasma as particles with the size of ~10 nm. NPs get in and out of the cells by endocytosis and exocytosis, whereas small molecules by diffusion and efflux. 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/GSE56nnn/GSE56742/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA244412
Series		Accession: GSE56742	ID: 200056742

3148. Impact of laminin α1 chain on colorectal cancer progression
(Submitter supplied) Expression analysis of control HT29 or Laminin α1 expressing HT29 xenografts in nude mice
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platform: GPL16061 6 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84296/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA328768
Series		Accession: GSE84296	ID: 200084296

3149. Integrated Systems Biology Analysis of KSHV Latent Infection Reveals Viral Induction and Reliance on Peroxisome Mediated Lipid Metabolism
(Submitter supplied) Kaposi’s Sarcoma herpesvirus (KSHV), an oncogenic virus, modulates host cell signaling and metabolism to maintain latent infection. To unravel the underlying cellular mechanisms modulated by KSHV, we identified changes in the host proteome, phosphoproteome and transcriptome landscape upon KSHV infection of endothelial cells. A Steiner Forest algorithm was used to integrate proteomic, phosphoproteomic and transcriptomic data with transcriptome based predicted transcription factor activity to identify cellular networks altered by latent KSHV.
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/GSE84nnn/GSE84237/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA328457
Series		Accession: GSE84237	ID: 200084237

3150. Target Specificity of Epigenetic Therapy
(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: GPL16791 31 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78110/
Series		Accession: GSE78110	ID: 200078110

3151. RNA-seq of HL60 cells treated with epigenetic therapy
(Submitter supplied) RNA-seq was performed after HL60 cells were treated with S2101, UNC0638, GSK343, depsipeptide alone or in combination with decitabine
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 30 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78102/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA312611
Series		Accession: GSE78102	ID: 200078102

3152. Hotspots of aberrant enhancer activity punctuate the colorectal cancer epigenome
(Submitter supplied) We sought to identify hotspots of aberrant enhancer activity in colorectal cancer (CRC) through interrogation of the enhancer epigenomes of a large cohort of genetically diverse CRC samples and normal colonic crypts, representing the cell type of origin for CRC. Through characterization of loci that exhibit differential enhancer activity, we identified sets of enhancers that are recurrently commissioned and decommissioned in CRC relative to normal crypts. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL9052 GPL15456 GPL16791 139 Samples
FTP download: GEO (BED, BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77737/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA311329
Series		Accession: GSE77737	ID: 200077737

3153. Genomic Profiling of Neuroblastoma Cell Lines
(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; SNP genotyping by SNP array
Platforms: GPL18573 GPL21168 68 Samples
FTP download: GEO (IDAT, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89969/
Series		Accession: GSE89969	ID: 200089969

3154. Transcriptomic Profiling of 39 Neuroblastoma Cell Lines
(Submitter supplied) Neuroblastoma cell lines are an important and cost-effective model used to study oncogenic drivers of the disease. While many of these cell lines have been previously characterized with SNP, methylation, and/or expression microarrays, there has not been an effort to comprehensively sequence these cell lines. Here, we present raw whole transcriptome data generated by RNA sequencing of 39 commonly-used neuroblastoma cell lines. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 41 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89413/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA352080
Series		Accession: GSE89413	ID: 200089413

3155. Effect of SF3B1 suppression in cancer cells with different SF3B1 copy-number levels
(Submitter supplied) Breast cancer cell lines containing stable dox inducible shRNAs targeting SF3B1 were profiled by RNA sequencing. We determined the effect of gene expression and splicing changes before and after knocking down SF3B1 in cell lines with normal copy number (SF3B1neutral) or partial copy loss (SF3B1loss) cell lines
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 16 Samples
FTP download: GEO (GCT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81978/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA323711
Series		Accession: GSE81978	ID: 200081978

3156. Recurrent rearrangements of the Myb/SANT-like DNA-binding domain containing 3 gene (MSANTD3) in salivary gland acinic cell carcinoma
(Submitter supplied) By transcriptome (RNAseq) analysis of 3 human acinic cell carcimoma (AcCC) cases, we discovered two novel gene fusions, and further validated recurrent rearrangement of the MSANTD3 gene. By RNAseq of engineered MSANTD3 overexpression in rat salivary epithelial cells (compared to vector control), we identifed elevated expression of genes involved in protein synthesis.
Organism:	Homo sapiens; Rattus norvegicus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL14844 GPL11154 5 Samples
FTP download: GEO (HTML, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76354/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA307084
Series		Accession: GSE76354	ID: 200076354

3157. Genetic analysis of Ikaros target genes and tumor suppressor function in BCR-ABL1+ pre-B ALL
(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 (BED, BEDGRAPH, BIGWIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90670/
Series		Accession: GSE90670	ID: 200090670

3158. Genetic analysis of Ikaros target genes and tumor suppressor function in BCR-ABL1+ pre-B ALL [RNA-seq]
(Submitter supplied) RNA-seq was performed in human Ph+ pre-B ALL cells that harbor a deletion of the Ikaros DNA binding domain (Ik6) after doxycycline induction of exogenous expression of wild-type Ikaros (Ik1) or control empty vector over 0, 12, 24 and 48 hours. Biological replicates (n=2) using independent cultures and inductions were performed.
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/GSE90nnn/GSE90659/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA355295
Series		Accession: GSE90659	ID: 200090659

3159. Inhibition of BET protein BRD4 activity synergizes with cisplatin in ovarian cancer by targeting ALDH activity through an ALDH1A1 super-enhancer and the associated enhancer RNA
(Submitter supplied) The emergence of tumor cells with certain stem-like characteristics such as high aldehyde dehydrogenase (ALDH) activity contributes to chemotherapy resistance.  Here we report that inhibition of the BET protein BRD4 potentiates the tumor suppressive effects of cisplatin by targeting ALDH activity.  The clinically applicable small molecule BET inhibitor JQ1 synergized with cisplatin by suppressing the growth of epithelial ovarian cancer cells both in vitro and in vivo. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL11154 5 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77568/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA310832
Series		Accession: GSE77568	ID: 200077568

3160. The effect of PPARG inhibition on human angiomyolipoma cells
(Submitter supplied) Angiomyolipoma (AML), the most common benign renal tumor, can result in severe morbidity from hemorrhage and renal failure. While mTORC1 activation is involved in its growth, mTORC1 inhibitors fail to eradicate AML, highlighting the need for new therapies. Moreover, the identity of the AML cell of origin is obscure. AML research, however, is hampered by the lack of in-vivo models. Here, we establish a human AML-xenograft (Xn) model in mice, recapitulating AML at the histological and molecular levels. more...
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/GSE94nnn/GSE94461/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA369759
Series		Accession: GSE94461	ID: 200094461

3161. Interrogation of functional cell surface markers identifies CD151 dependency in high-grade serous ovarian cancer
(Submitter supplied) The high degree of genetic aberrations characteristic of high-grade serous ovarian cancer (HGSC) makes identification of the molecular features that drive tumor progression difficult. Here, we perform genome-wide RNAi screens and comprehensive expression analysis of cell surface markers in a panel of HGSC cell lines to identify genes that are critical to their survival. We report that the tetraspanin CD151 contributes to survival of a subset of HGSC cell lines associated with a ZEB transcriptional program and supports the growth of HGSC tumors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 41 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94304/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA369618
Series		Accession: GSE94304	ID: 200094304

3162. polyA mRNA RNA-seq from K562 (ENCSR000BZV)
(Submitter supplied) RNA-seq on human K562 cytosol long polyadenalated RNA  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: GPL18723 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94234/
Series		Accession: GSE94234	ID: 200094234

3163. polyA mRNA RNA-seq from PFSK-1 (ENCSR000BYN)
(Submitter supplied) RNA-seq on PFSK-1 greater than 200bp polyA+  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: GPL10999 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93451/
Series		Accession: GSE93451	ID: 200093451

3164. polyA mRNA RNA-seq from Panc1 (ENCSR000BYM)
(Submitter supplied) RNA-seq on Panc-1 greater than 200bp polyA+  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: GPL10999 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93450/
Series		Accession: GSE93450	ID: 200093450

3165. polyA mRNA RNA-seq from SK-N-SH (ENCSR000BYL)
(Submitter supplied) RNA-seq on SK-N-SH greater than 200bp polyA+  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: GPL10999 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93449/
Series		Accession: GSE93449	ID: 200093449

3166. polyA mRNA RNA-seq from BE2C (ENCSR000BYK)
(Submitter supplied) RNA-seq on BEC-C greater than 200bp polyA+  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: GPL10999 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93448/
Series		Accession: GSE93448	ID: 200093448

3167. polyA mRNA RNA-seq from A549 (ENCSR000BYJ)
(Submitter supplied) RNA-seq on A549 greater than 200bp polyA+ treated with dexamethasone at 5nM  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: GPL10999 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93447/
Series		Accession: GSE93447	ID: 200093447

3168. polyA mRNA RNA-seq from A549 (ENCSR000BYI)
(Submitter supplied) RNA-seq on A549 greater than 200bp polyA+ treated with dexamethasone at 500pM  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: GPL10999 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93446/
Series		Accession: GSE93446	ID: 200093446

3169. polyA mRNA RNA-seq from A549 (ENCSR000BYH)
(Submitter supplied) RNA-seq on A549 greater than 200bp polyA+ treated with dexamethasone at 1nM  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: GPL10999 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93445/
Series		Accession: GSE93445	ID: 200093445

3170. polyA mRNA RNA-seq from T47D (ENCSR000BYG)
(Submitter supplied) RNA-seq on T-47D greater than 200bp polyA+ treated with genistein at 100nM for 4 hours  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: GPL10999 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93444/
Series		Accession: GSE93444	ID: 200093444

3171. polyA mRNA RNA-seq from T47D (ENCSR000BYF)
(Submitter supplied) RNA-seq on T-47D greater than 200bp polyA+ treated with estradiol at 10nM for 4 hours  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: GPL10999 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93443/
Series		Accession: GSE93443	ID: 200093443

3172. polyA mRNA RNA-seq from T47D (ENCSR000BYE)
(Submitter supplied) RNA-seq on T-47D greater than 200bp polyA+ treated with dimethylsulfoxide for 4 hours  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: GPL10999 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93442/
Series		Accession: GSE93442	ID: 200093442

3173. polyA mRNA RNA-seq from T47D (ENCSR000BYD)
(Submitter supplied) RNA-seq on T-47D greater than 200bp polyA+ treated with bisphenol A at 100nM for 4 hours  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: GPL10999 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93441/
Series		Accession: GSE93441	ID: 200093441

3174. polyA mRNA RNA-seq from Ishikawa (ENCSR000BYC)
(Submitter supplied) RNA-seq on ECC-1 greater than 200bp polyA+ treated with genistein at 100nM for 4 hours. Note- This experiment previously referred to its biosample as ECC-1, however it has been found that all currently available ECC-1 are actually Ishikawa cells.  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: GPL10999 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93440/
Series		Accession: GSE93440	ID: 200093440

3175. polyA mRNA RNA-seq from Ishikawa (ENCSR000BYB)
(Submitter supplied) RNA-seq on ECC-1 greater than 200bp polyA+ treated with estradiol at 10nM for 4 hours. Note- This experiment previously referred to its biosample as ECC-1, however it has been found that all currently available ECC-1 are actually Ishikawa cells.  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: GPL10999 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93439/
Series		Accession: GSE93439	ID: 200093439

3176. polyA mRNA RNA-seq from Ishikawa (ENCSR000BYA)
(Submitter supplied) RNA-seq on ECC-1 greater than 200bp polyA+ treated with dimethylsulfoxide for 4 hours. Note- This experiment previously referred to its biosample as ECC-1, however it has been found that all currently available ECC-1 are actually Ishikawa cells.  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: GPL10999 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93438/
Series		Accession: GSE93438	ID: 200093438

3177. polyA mRNA RNA-seq from Ishikawa (ENCSR000BXZ)
(Submitter supplied) RNA-seq on ECC-1 greater than 200bp polyA+ treated with bisphenol A at 100nM for 4 hours. Note- This experiment previously referred to its biosample as ECC-1, however it has been found that all currently available ECC-1 are actually Ishikawa cells.  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: GPL10999 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93437/
Series		Accession: GSE93437	ID: 200093437

3178. polyA mRNA RNA-seq from A549 (ENCSR000BXY)
(Submitter supplied) RNA-seq on A549 greater than 200bp polyA+ treated with dexamethasone at 100pM  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: GPL10999 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93436/
Series		Accession: GSE93436	ID: 200093436

3179. polyA mRNA RNA-seq from Jurkat clone E61 (ENCSR000BXX)
(Submitter supplied) RNA-seq on Jurkat greater than 200bp polyA+  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: GPL10999 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93435/
Series		Accession: GSE93435	ID: 200093435

3180. Oncogenic ZEB2 activation drives sensitivity towards LSD1 inhibition in T-cell acute lymphoblastic leukemia
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18480 GPL18573 48 Samples
FTP download: GEO (TAB, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83128/
Series		Accession: GSE83128	ID: 200083128

3181. downregulation of DDX5 and DDX17
(Submitter supplied) RNAseq : MCF-7 cells were transfected with siRNA targeting both DDX5 and DDX17 RNA helicases, and total RNA were extracted as described previously (Dardenne Cell Rep 2014).
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/GSE94nnn/GSE94372/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA369520
Series		Accession: GSE94372	ID: 200094372

3182. Potential of epigenetic therapy of acute myeloid leukemia using 5-aza-2'-deoxycytidine (decitabine) and 3-deazaneplanocin-A
(Submitter supplied) Background:Aberrant DNA methylation that silences tumor suppressor genes occurs frequently in patients with acute myeloid leukemia (AML). Treatment of AML patients with the inhibitor of DNA methylation, 5-aza-2'-deoxycytidine (5-AZA-CdR) can induce complete remissions, but most patients will relapse. The clinical efficacy of 5-AZA-CdR may be influenced by its limited capacity to activate tumor suppressor genes silenced by methylation of lysine 27 histone H3 (H3K27) by EZH2. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94344/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA316529
Series		Accession: GSE94344	ID: 200094344

3183. BET-Bromodomain Inhibitors Engage The Host Immune System And Regulate Expression Of The Immune Checkpoint Ligand PD-L1
(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: GPL16791 GPL19057 GPL17021 53 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94134/
Series		Accession: GSE94134	ID: 200094134

3184. BET-Bromodomain Inhibitors Engage The Host Immune System And Regulate Expression Of The Immune Checkpoint Ligand PD-L1 [3mRNA-seq]
(Submitter supplied) BET inhibitors (BETi) target bromodomain-containing proteins and are currently being evaluated as anti-cancer agents. We discovered that the maximal therapeutic effects of BETi in a Myc-driven B cell lymphoma model required an intact host immune system. Genome-wide analysis of the BETi induced transcriptional response identified the immune checkpoint ligand Cd274 (Pd-l1) as a Myc-independent, BETi target-gene. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL17021 GPL16791 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94057/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA368684
Series		Accession: GSE94057	ID: 200094057

3185. Expression data from control and WHSC1 siRNA treated PC3 cells
(Submitter supplied) We conduct transcriptome comparison of control and WHSC1 depleted PC3 cells to gain genomic insights on the biological processes that WHSC1 is involved in prostate cancer cells. More than 2000 known genes were found changed in the WHSC1 depleted cells. Ingenuity Pathway Analysis (IPA) and Gene Set Enrichment Analysis (GSEA) show that the most prominent altered pathways in the WHSC1 depleted cells are related to regulation of actin-based motility, mTOR signaling pathway.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84868/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA335397
Series		Accession: GSE84868	ID: 200084868

3186. RNA-Seq Analysis of Anacardic Acid Treated MCF7 and MDA-MB-231 Breast Cancer Cell Lines
(Submitter supplied) Anacardic acid (AnAc) is a mixture of 6-alkylbenzoic acid congeners that are produced in a number of plants. Previously, we showed a specific congener AnAc 24:1n5 acts as a nuclear receptor alternate site modulator (NRAM) to inhibit breast cancer cells in an estrogen receptor (ER)-dependent manner by interfering with ER-DNA binding. AnAc 24:1n5 also inhibited the growth of a triple negative breast cancer (TNBC) cell line, through an undefined mechanism. 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/GSE78nnn/GSE78011/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA312354
Series		Accession: GSE78011	ID: 200078011

3187. The significance of different algorithms in transcriptome analysis of leukemic cells with rearranged MLL
(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: GPL6244 GPL11154 8 Samples
FTP download: GEO (CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE54nnn/GSE54654/
Series		Accession: GSE54654	ID: 200054654

3188. The significance of different algorithms in transcriptome analysis of leukemic cells with rearranged MLL (RNA-seq)
(Submitter supplied) This study shows how the way by which the RNA-Seq data is analyzed affects the resulting gene expression profile. Three parameters were explored: the RNA-Seq analysis algorithm pipeline (cufflinks – Cuffdiff 2 or HTSeq & DESeq), sequencing depth and sequencing protocol: single or paired end, 100 or 50 bases. For comparison, the same samples were processed by gene microarrays.
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/GSE54nnn/GSE54641/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA237246
Series		Accession: GSE54641	ID: 200054641

3189. RNA-Seq analysis facilitates quantitative analysis to identify DEGs in lung cancer cell lines regulated by S100A7A introduction in comparison with Cl1-0 control and S100A7A knockdown in comparison with CL1-5 control.
(Submitter supplied) Methods: The cDNA libraries from 3 pooled samples of cultured cells for each group were sequenced to generate RNA profiles using Illumina Miseq platform Results: The sequencing runs yielded a total of 95.01 M reads with an average length of 73-74 bp. The high-throughput sequencing performed for liver samples with different treatments showed similar numbers of yielded reads ranged from 5.57 to 5.74 M and the same average length. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86344/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA341495
Series		Accession: GSE86344	ID: 200086344

3190. Phosphatidylinositol 3-Kinase (PI3K) delta blockade increases genomic instability in B cells
(Submitter supplied) Activation-induced cytidine deaminase (AID) is a B-cell specific enzyme that targets immunoglobulin (Ig) genes to initiate class switch recombination (CSR) and somatic hypermutation (SHM). Through off-target activity, however, AID has a much broader impact on genomic instability by initiating oncogenic chromosomal translocations and mutations involved in lymphoma development and progression. AID expression is tightly regulated in B cells and its overexpression leads to enhanced genomic instability and lymphoma formation. more...
Organism:	Mus musculus; Homo sapiens
Type:		Other; Expression profiling by high throughput sequencing
Platforms: GPL15520 GPL16417 GPL13112 162 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77788/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA311552
Series		Accession: GSE77788	ID: 200077788

3191. RNA-seq of normal breast epithelial cells
(Submitter supplied) RNA-seq was performed on primary normal breast epithelial cells that were grown briefly in culture
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 3 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74417/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA300315
Series		Accession: GSE74417	ID: 200074417

3192. RNA-seq of YB5 and MCF7 treated with different doses of decitabine
(Submitter supplied) RNA-seq was performed after YB5 cells were treated with 1uM decitabine, and MCF7 cells were treated with 100nM decitabine
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/GSE74nnn/GSE74251/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA299580
Series		Accession: GSE74251	ID: 200074251

3193. Transcriptome of EMT induced MCF10A cells by TGFb treatment or SNAIL S6A expression.
(Submitter supplied) EMT, Epithelial to mesenchymal transition is a developmental biology process associated with migration, known to be involved in cancer metastasis. To study this process, we used the breast epithelial cell line MCF10A that enter in EMT after treatment with the cytokine TGFB or by expression of EMT transcriptor factor SNAIL.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89152/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA350495
Series		Accession: GSE89152	ID: 200089152

3194. Specific expression of novel long non-coding RNAs in high-hyperdiploid childhood ALL
(Submitter supplied) Pre-B cell childhood acute lymphoblastic leukemia (pre-B cALL) is a heterogeneous disease involving many subtypes typically stratified using a combination of cytogenetic and molecular-based assays. These methods, although widely used rely on the presence of known chromosomal translocations, which is a limiting factor. There is therefore a need for robust, sensitive, and specific molecular biomarkers unaffected by such limitations that would allow better risk stratification and consequently better clinical outcome. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16558 56 Samples
FTP download: GEO (GTF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89071/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA350700
Series		Accession: GSE89071	ID: 200089071

3195. ZBTB33 (Kaiso) Differentially Regulates Cell Cycle Through cyclin D1 and cyclin E1 in a Cell Specific Manner [RNA-seq]
(Submitter supplied) The emerging correlation between aberrant DNA methylation patterns leading to transcriptional responses that promote and progress many cancers has prompted an interest in discerning the associated regulatory mechanisms. ZBTB33 (also known as Kaiso) is a specialized transcription factor that selectively recognizes mCpG-containing sites as well as a sequence-specific DNA target (termed the KBS) utilizing three Cys2His2 zinc fingers. 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/GSE81nnn/GSE81781/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA322534
Series		Accession: GSE81781	ID: 200081781

3196. Gene expression profiles in 786-O cells in response to glucose starvation
(Submitter supplied) To understand gene expression profiling in glucose starvation, we treated 786-O cells with and without glucose, and then subjected to next generation sequencing.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9520 2 Samples
FTP download: GEO (TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77415/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA310239
Series		Accession: GSE77415	ID: 200077415

3197. The effect of Abl kinases on non-small cell carcinoma global transcriptome
(Submitter supplied) To gain insight into the signaling pathway(s) required for ABL1/ABL2-dependent non-small cell carcinoma cells metastasis
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/GSE77nnn/GSE77422/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA310252
Series		Accession: GSE77422	ID: 200077422

3198. Systematic mapping of RNA-chromatin interactions in vivo
(Submitter supplied) RNA molecules can attach to chromatin and thus provide a type of epigenomic information. It remains difficult to know what RNAs are associated with chromatin and where are the genomic target loci of these RNAs. Here, we present MARGI (Mapping RNA-genome interactions), a technology to massively reveal native RNA-chromatin interactions from unperturbed cells. The gist of this technology is to ligate chromatin-associated RNA (caRNA) with their target genomic sequence by proximity ligation, forming RNA-DNA chimeric sequences, which are converted to sequencing library for paired-end sequencing. more...
Organism:	Homo sapiens; Drosophila melanogaster
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL22791 GPL16791 GPL22790 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE92nnn/GSE92345/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA357269
Series		Accession: GSE92345	ID: 200092345

3199. RNA Sequencing Reveals Immunosuppressive Role of Anthrax Lethal Toxin in Human Lung Epithelial and Monocytic Cells
(Submitter supplied) Using RNA-seq, we report here that anthrax lethal toxin (LeTx) induces immunosuppression in human lung epithelial cell line A549 and monocytic cell line U937.
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/GSE77nnn/GSE77219/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA309769
Series		Accession: GSE77219	ID: 200077219

3200. Transcriptome Profiling of Influenza A Virus-infected Lung Epithelial (A549) Cells with Lariciresinol-4-β-D-glucopyranoside Treatment
(Submitter supplied) The influenza A virus is an acute contagious pathogen that affects the human respiratory system and can cause severe lung disease and even death. Lariciresinol-4-β-D-glucopyranoside is a lignan that is extracted from Isatis indigotica, which is a medicinal herb plant that was commonly applied to treat infections, the common cold, fever and inflammatory diseases. Our previous study demonstrated that lariciresinol-4-β-D-glucopyranoside possesses anti-viral and anti-inflammatory properties. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93999/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA363033
Series		Accession: GSE93999	ID: 200093999

3201. PANC-1 and AsPC-1 human pancreatic carcinoma cells under hypoxia, nutrient starvation and low pH culture condition
(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: GPL10999 GPL16791 GPL570 30 Samples
FTP download: GEO (BIGWIG, CEL, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93989/
Series		Accession: GSE93989	ID: 200093989

3202. Gene expression in PANC-1 and AsPC-1 human pancreatic carcinoma cells under hypoxia, nutrient starvation and low pH culture condition.
(Submitter supplied) The conditions of the tumor microenvironment, such as hypoxia and nutrient starvation, play critical roles in cancer progression. However, the role of acidic extracellular pH in cancer progression is not studied as extensively as that of hypoxia. Here, we show that extracellular acidic pH (pH 6.8) triggered activation of sterol regulatory element-binding protein 2 (SREBP2) by stimulating nuclear translocation and promoter binding to its targets along with intracellular acidification. 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/GSE93nnn/GSE93988/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA363011
Series		Accession: GSE93988	ID: 200093988

3203. eIF1 modulates the recognition of sub-optimal translation start sites and steers gene expression control mediated by uORFs
(Submitter supplied) Alternative translation initiation mechanisms such as leaky scanning and reinitiation potentiate the polycistronic nature of transcripts. By allowing for reprogrammed translation, these mechanisms can mediate biological responses to stress stimuli. We combined proteomics with ribosome profiling and mRNA sequencing to identify the biological targets of translation control triggered by eukaryotic translation initiation factor 1 (eIF1), a protein implicated in the stringency of start codon selection. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL18573 6 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87328/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA344393
Series		Accession: GSE87328	ID: 200087328

3204. Adaptive chromatin remodeling in glioblastoma stem cell plasticity and drug tolerance
(Submitter supplied) Many cancers are postulated to harbor developmental hierarchies in which cells display variability in stem-like character, tumor propagating ability, and proliferation. In glioblastoma (GBM), glioma stem cells (GSCs) reside atop such a tumor cellular hierarchy, and are thought to resist current therapies and thus underlie inevitable relapse. Here we show that GSCs can evade RTK inhibition by reversibly regressing to a slow-cycling state reminiscent of quiescent neural stem cells. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL18573 44 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74557/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA300725
Series		Accession: GSE74557	ID: 200074557

3205. RNA-Seq data from ZR75-1 cells
(Submitter supplied) We report the transcription factor Six1 directly increases the expression of many glycolytic genes by performing RNA sequencing using Six1 stable knockdown ZR75-1 breast cancer cell line and control cell line.
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/GSE93nnn/GSE93925/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA362845
Series		Accession: GSE93925	ID: 200093925

3206. The MLL-AF9 and MLL-AF4 oncofusion proteins bind a distinct enhancer repertoire and target the RUNX1 program in MLLr AML
(Submitter supplied) In MLL-rearranged (MLLr) leukemias the N terminal part of the MLL gene can be fused to over 60 different partner genes. Here, we investigate the genome wide binding of the MLL-AF9 and MLL-AF4 fusion proteins and their epigenetic signatures in order to define a core set of MLLr targets. We uncover both common as well as specific MLL-AF9 and MLL-AF4 target genes, which are all marked by H3K79me2, H3K27ac, and H3K4me3. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms: GPL10999 GPL11154 24 Samples
FTP download: GEO (BEDGRAPH, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79899/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA317349
Series		Accession: GSE79899	ID: 200079899

3207. Activation of a SOX2-dependent transcriptional regulatory circuit drives glioblastoma.
(Submitter supplied) Overexpression of the transcription factor SRY-related box 2 (SOX2) is characteristic of Glioblastoma (GBM), yet its regulatory network in vivo is poorly understood. Using a human orthotopic tumor model of GBM for ChIP-Seq analysis, we mapped the SOX2 cistrome. Integrative analysis of SOX2 cistrome and GBM transcriptome data identified two transcription factors, oligodendrocyte lineage transcription factor 2 (OLIG2) and zinc finger E-box binding homeobox 1 (ZEB1) as critical SOX2 targets. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL16558 10 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58345/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA252047
Series		Accession: GSE58345	ID: 200058345

3208. RNA-Seq and ATAC-Seq in SMARCD2 k/d NB4 cells with/without ATRA differentiation
(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 ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93878/
Series		Accession: GSE93878	ID: 200093878

3209. RNA-Seq in SMARCD2 k/d NB4 cells with/without ATRA differentiation
(Submitter supplied) We report differential gene expression in the human AML cell line NB4 that can be partially differentiated into neutrophil granulocytes by 1µM ATRA for 2d or the vehicle DMSO only ((mock))
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93877/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA362639
Series		Accession: GSE93877	ID: 200093877

3210. Enhancer Remodeling During Adaptive Bypass to MEK Inhibition Is Attenuated by Pharmacological Targeting of the P-TEFb Complex
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Methylation profiling by genome tiling array; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing
5 related Platforms 167 Samples
FTP download: GEO (BED, CSV, IDAT, TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87424/
Series		Accession: GSE87424	ID: 200087424

3211. Enhancer Remodeling During Adaptive Bypass to MEK Inhibition Is Attenuated by Pharmacological Targeting of the P-TEFb Complex (RNA-seq)
(Submitter supplied) Targeting the dysregulated BRaf-MEK-ERK pathway in cancer has increasingly emerged in clinical trial design. Despite clinical responses in specific cancers using inhibitors targeting BRaf and MEK, resistance develops often involving non-genomic adaptive bypass mechanisms.   Inhibition of MEK1/2 by trametinib in triple negative breast cancer (TNBC) patients induced dramatic transcriptional responses, including upregulation of receptor tyrosine kinases (RTKs) comparing tumor samples before and after one week of treatment. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL13112 GPL11154 GPL18573 64 Samples
FTP download: GEO (CSV, TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87419/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA344725
Series		Accession: GSE87419	ID: 200087419

3212. Profiling in vivo Bone Lesion and ex vivo Bone-In-Culture Array Samples by Next-Generation Sequencing
(Submitter supplied) Based on RNA-seq, we performed transcriptomic profiling to examine the similarities or differences between BICA (bone-in-culture array) and IVBL (in vivo bone lesion). CIBERSORT analysis reveals that the major local cellular components are comparable between BICA and IVBL, but differ dramatically in orthotopic tumors. Principle component analysis of human RNAs indicated that the transcriptomic profiles of cancer cells in BICA are more closely mimicking IVBL, as compared to cancer cells in 2D and in orthotopic tumors. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL19415 GPL18573 17 Samples
FTP download: GEO (RDATA) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84114/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA328044
Series		Accession: GSE84114	ID: 200084114

3213. An Argonaute phosphorylation cycle promotes microRNA-mediated silencing
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL11154 GPL18573 80 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89946/
Series		Accession: GSE89946	ID: 200089946

3214. An Argonaute phosphorylation cycle promotes microRNA-mediated silencing [whole transcriptome RNA-seq]
(Submitter supplied) MicroRNAs (miRNAs) perform critical functions in normal physiology and disease by associating with Argonaute proteins and downregulating partially complementary messenger RNAs (mRNAs).  To identify new regulators of the miRNA pathway, we employed CRISPR-Cas9 genome-wide loss-of-function screening coupled with a fluorescent reporter of miRNA activity.  Iterative rounds of screening revealed a novel mechanism whereby target engagement by Argonaute 2 (AGO2) triggers its hierarchical, multi-site phosphorylation by CSNK1A1 on a set of highly conserved residues (S824-S834), followed by rapid dephosphorylation by the ANKRD52-PPP6C phosphatase complex. 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/GSE89nnn/GSE89942/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA354540
Series		Accession: GSE89942	ID: 200089942

3215. An Argonaute phosphorylation cycle promotes microRNA-mediated silencing [polyA RNA-seq]
(Submitter supplied) MicroRNAs (miRNAs) perform critical functions in normal physiology and disease by associating with Argonaute proteins and downregulating partially complementary messenger RNAs (mRNAs).  To identify new regulators of the miRNA pathway, we employed CRISPR-Cas9 genome-wide loss-of-function screening coupled with a fluorescent reporter of miRNA activity.  Iterative rounds of screening revealed a novel mechanism whereby target engagement by Argonaute 2 (AGO2) triggers its hierarchical, multi-site phosphorylation by CSNK1A1 on a set of highly conserved residues (S824-S834), followed by rapid dephosphorylation by the ANKRD52-PPP6C phosphatase complex. 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/GSE89nnn/GSE89940/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA354539
Series		Accession: GSE89940	ID: 200089940

3216. Next Generation Sequencing Analysis of control and SRSF2-/- Huh7 cells Transcriptomes
(Submitter supplied) We generated the SRSF2-/- Huh7 cells,and collected the cells at 2 days after transfected with siRNA. Then, we extracted RNAs and performed next generation sequencing. By comparing sequencing data from control and SRSF2 -/- samples, we profiled the alternative splicing events and gene expression regulated by SRSF2 in HCC.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78705/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA313267
Series		Accession: GSE78705	ID: 200078705

3217. Gene expression in HT-29-MTX intestinal epithelial cells treated with Ancylostoma ceylanicum hookworm larvae
(Submitter supplied) HT-29-MTX cells were treated with Ancylostoma ceylanicum hookworm larvae or left untreated.  The differences in gene expression between treated and untreated samples was observed.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (DIFF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93620/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA361298
Series		Accession: GSE93620	ID: 200093620

3218. Epigenetic alterations affecting transcription factors and signaling pathways in stromal cells of endometriosis: Expression data (RNA-seq)
(Submitter supplied) Endometriosis is characterized by growth of endometrial-like tissue outside the uterine cavity. Since its pathogenesis may involve epigenetic changes, we used Illumina 450K Methylation Beadchips to profile CpG methylation in endometriosis stromal cells compared to stromal cells from normal endometrium. We validated and extended the Beadchip data using bisulfite sequencing (bis-seq), and analyzed differential methylation (DM) at the CpG-level and by an element-level classification for groups of CpGs in chromatin domains. 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/GSE87nnn/GSE87809/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA347653
Series		Accession: GSE87809	ID: 200087809

3219. KANK1 inhibits cell growth by inducing apoptosis though regulating CXXC5 in human malignant peripheral nerve sheath tumors
(Submitter supplied) The purpose of this study is to identify expression differences between untreated and Doxycycline treated human malignant peripheral nerve sheathing tumors (MPNST) cell lines. We sequenced mRNA from 6 lentiviral infected MPNST human stable cell lines(STS26T-pLIX405-KANK1 using Illumina Hiseq 2500 sequencing platform. Three control samples are untreated stable cells and three samples are Doxycycline treated (1 ug/ml).
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/GSE85nnn/GSE85271/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA338007
Series		Accession: GSE85271	ID: 200085271

3220. MLL-AF4 Spreading Identifies Binding Sites that Are Distinct from Super-Enhancers and that Govern Sensitivity to DOT1L Inhibition in Leukemia.
(Submitter supplied) Understanding the underlying molecular mechanisms of defined cancers is crucial for effective personalized therapies. Translocations of the Mixed Lineage Leukemia (MLL) gene produce fusion proteins such as MLL-AF4 that disrupt epigenetic pathways and cause poor prognosis leukemias. Here we find that MLL-AF4 occupies a subset of unmethylated CG-enriched genes in combination with its cofactors Menin/LEDGF and ENL. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL16791 GPL18573 59 Samples
FTP download: GEO (BED, BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83671/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA326673
Series		Accession: GSE83671	ID: 200083671

3221. Mapping heterogeneity in a patient-derived melanoma culture by single-cell RNA-seq
(Submitter supplied) Recent technological advances in single-cell genomics make it possible to analyze cellular heterogeneity of tumor samples. Here, we applied single-cell RNA-seq to measure the transcriptomes of 307 single cells cultured from three biopsies of three different patients with a BRAF/NRAS wild type, BRAF mutant/NRAS wild type and BRAF wild type/NRAS mutant melanoma metastasis, respectively. Analysis based on self-organizing maps identified sub-populations defined by multiple gene expression modules involved in proliferation, oxidative phosphorylation, pigmentation and cellular stroma. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 307 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81383/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA321420
Series		Accession: GSE81383	ID: 200081383

3222. Gene expression profile of T-DM1 resistant and parental cell lines
(Submitter supplied) The esophageal cancer cell line OE-19 was used to select resistant cells to T-DM1. They were selected by prolonged exposure to increasing concentrations of T-DM1 in the absence or presence of ciclosporin A (CsA). Two cell lines resulted from these experimental conditions: OE-19 TR in the absence of CsA and OE-19 TCR in the presence of CsA. The parental cell line was named OE-19 S. The present study aims to detect the transcriptomic changes between OE-19 S, OE-19 TR and OE-19 TCR cell lines to identify the deregulated pathways involved in acquired resistance to T-DM1.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Expression profiling by array
Platform: GPL10558 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93352/
Series		Accession: GSE93352	ID: 200093352

3223. The role of miR-17-92 in the miRegulatory landscape of Ewing Sarcoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL11154 13 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80494/
Series		Accession: GSE80494	ID: 200080494

3224. The role of miR-17-92 in the miRegulatory landscape of Ewing Sarcoma (RNA-Seq)
(Submitter supplied) MicroRNAs serve to fine-tune gene expression and play an important regulatory role in tissue specific gene networks. The identification and validation of miRNA target genes in a tissue still poses a significant problem since the presence of a seed sequence in the 3´UTR of an mRNA and its expression modulation upon ectopic expression of the miRNA do not reliably predict regulation under physiological conditions. 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/GSE80nnn/GSE80492/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA319050
Series		Accession: GSE80492	ID: 200080492

3225. Epigenetic siRNA and chemical screens identify SETD8 inhibition as a new therapeutic strategy of p53 reactivation in high-risk Neuroblastoma.
(Submitter supplied) Purpose: The intergration of genetic and chemical screens identified SETD8 as a new druggable target in neuroblastoma tumor. The goal of this study is to evaluate the transcriptome profiling (RNA-seq) of Neuroblastoma cell lines after genetic and pharmacological inhibition of SETD8. Methods: mRNA profiles of NB cells after genetic and pharmacological inhibition of SETD8 were generated by deep sequencing in duplicate with Ilumina HiSeq2500 using Illumina TruSeq V4. 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/GSE81nnn/GSE81626/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA322142
Series		Accession: GSE81626	ID: 200081626

3226. Therapeutic targeting MLL degradation pathways in MLL-rearranged leukemia
(Submitter supplied) Chromosomal translocations of the mixed-lineage leukemia (MLL) gene with various partner genes result in aggressive leukemia with dismal outcomes. Despite similar expression at the mRNA level from the wild-type and chimeric MLL alleles, the chimeric protein is more stable. We report that UBE2O functions in regulating the stability of wild-type MLL in response to interleukin-1 signaling. Targeting wild-type MLL degradation impedes MLL leukemia cell proliferation, and it downregulates a specific group of target genes of the MLL chimeras and their oncogenic cofactor, the super elongation complex. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms: GPL11154 GPL13112 GPL18573 64 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89485/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA352353
Series		Accession: GSE89485	ID: 200089485

3227. Analysis of gene expression (RNAseq) from shTP53:RB1 LNCaP/AR cell lines
(Submitter supplied) Some cancers evade targeted therapies through a mechanism known as lineage plasticity, whereby tumor cells acquire phenotypic characteristics of a cell lineage whose survival no longer depends on the drug target. Here we show, using in vitro and in vivo prostate cancer models, that these tumors can develop resistance to the antiandrogen drug enzalutamide by a phenotypic shift from androgen receptor (AR) dependent luminal epithelial cells to AR independent basal-like 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/GSE89nnn/GSE89226/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA350780
Series		Accession: GSE89226	ID: 200089226

3228. MYC Mediates mRNA Cap Methylation of Canonical Wnt/beta-catenin Signaling Transcripts by Recruiting CDK7 and RNA Methyltransferase
(Submitter supplied) We performed an RNA pulldown against a methyl group on the mRNA cap using a fusion protein, GST-eIF4E, highly specific for a m7G-mRNA cap. We performed RNA-seq on both the pulldowns and inputs and normalized our pulldown to input in order to determine which genes MYC targets for mRNA cap methylation above and beyond any affect at the transcriptional level. We found that MYC targets approximately 30% of transcripts for enhanced mRNA cap methylation above 1.2 fold on a global scale following 24 h of MYC induction, specifically transcripts involved in the canonical Wnt/β-catenin signaling pathway. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76614/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA308140
Series		Accession: GSE76614	ID: 200076614

3229. Patient-derived luminal breast cancer xenografts with progestins
(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 GPL11532 48 Samples
FTP download: GEO (CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93109/
Series		Accession: GSE93109	ID: 200093109

3230. RNAseq analysis of patient-derived luminal breast cancer xenografts treated with progestins
(Submitter supplied) Primary breast cancer xenografts
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93057/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA359750
Series		Accession: GSE93057	ID: 200093057

3231. siRNA RNA-seq from K562 (ENCSR942MUW)
(Submitter supplied) Control siRNA against no target in K562 cells followed by RNA-seq.  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/GSE92nnn/GSE92179/
Series		Accession: GSE92179	ID: 200092179

3232. siRNA RNA-seq from K562 (ENCSR644GSV)
(Submitter supplied) Control siRNA against no target in K562 cells followed by RNA-seq.  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/GSE91nnn/GSE91947/
Series		Accession: GSE91947	ID: 200091947

3233. siRNA RNA-seq from K562 (ENCSR641CMW)
(Submitter supplied) Control siRNA against no target in K562 cells followed by RNA-seq.  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/GSE91nnn/GSE91943/
Series		Accession: GSE91943	ID: 200091943

3234. siRNA RNA-seq from K562 (ENCSR626SFM)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting BHLHE40.  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/GSE91nnn/GSE91927/
Series		Accession: GSE91927	ID: 200091927

3235. siRNA RNA-seq from K562 (ENCSR561NXJ)
(Submitter supplied) Control siRNA (3x Buffer,1x siRNA) against no target in K562 cells followed by RNA-seq.  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/GSE91nnn/GSE91874/
Series		Accession: GSE91874	ID: 200091874

3236. siRNA RNA-seq from K562 (ENCSR336ZWX)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting TAL1.  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/GSE91nnn/GSE91677/
Series		Accession: GSE91677	ID: 200091677

3237. siRNA RNA-seq from K562 (ENCSR261IHP)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting CHD2.  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/GSE91nnn/GSE91613/
Series		Accession: GSE91613	ID: 200091613

3238. siRNA RNA-seq from K562 (ENCSR205BWT)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting BRCA1.  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/GSE91nnn/GSE91571/
Series		Accession: GSE91571	ID: 200091571

3239. siRNA RNA-seq from K562 (ENCSR128HAQ)
(Submitter supplied) Control siRNA against no target in K562 cells followed by RNA-seq.  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/GSE91nnn/GSE91515/
Series		Accession: GSE91515	ID: 200091515

3240. Transcriptome profile of HepG2-expressing ATP7B-H1069Q (liver hepatocellular cells) exposed to JNK or p38 Inhibitor
(Submitter supplied) In order to identify the effects of JNK inhibitor or p38 Inhibitor on the transcriptome of ATP7B H1069Q-overexpressing liver cells, we performed RNAseq experiments
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80361/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA318738
Series		Accession: GSE80361	ID: 200080361

3241. RNA Sequencing Reveals the Snail-Regulated Transcriptome in Head-and-Neck Squamous Cell Carcinoma.
(Submitter supplied) The epithelial-to-mesenchymal transition (EMT) is a critical biological process in normal development and tumor progression. One of the EMT regulator, Snail is shown to suppress or activate its downstream genes to sustain migratory capacities while remodeling the tumor microenvironment. Identification of the Snail-regulated transcriptome through a robust sequencing technique will give a global direction for targeting Snail-driven malignancy.
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/GSE65nnn/GSE65131/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA273188
Series		Accession: GSE65131	ID: 200065131

3242. siRNA RNA-seq from K562 (ENCSR100ODO)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting NFE2L2.  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/GSE91nnn/GSE91484/
Series		Accession: GSE91484	ID: 200091484

3243. siRNA RNA-seq from K562 (ENCSR047MQO)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting VEZF1.  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 3 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE91nnn/GSE91435/
Series		Accession: GSE91435	ID: 200091435

3244. CD86 regulates a pro-survival signal in myeloma cells
(Submitter supplied) While multiple myeloma patient prognosis has improved over the past decade, research towards discovery of new therapeutic avenues is important, and could lead to a cure for this chronic plasma cell malignancy. Data analysis from a myeloma patient database shows that the CD28-CD86 signaling module may provide a survival advantage in myeloma cells that negatively impacts patient outcome. Here we show that blocking the CD28-CD86 pathway, by silencing or with CTLA-4-Ig, leads to myeloma cell death. 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/GSE89nnn/GSE89511/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA352410
Series		Accession: GSE89511	ID: 200089511

3245. Analysis of germline modifiers of aggressive prostate cancer using cross-species variation and systems genetics
(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
Platforms: GPL13112 GPL16686 299 Samples
FTP download: GEO (CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87491/
Series		Accession: GSE87491	ID: 200087491

3246. ILF2 Regulates RNA Splicing of DNA Damage Response Genes to Confer Poor Prognosis in 1q21-Amplified Multiple Myeloma
(Submitter supplied) To understand whether ILF2 is required to ensure the alternative splicing and processing of specific pre-mRNAs in Multiple Myeloma (MM), both in physiological and DNA damage conditions, we performed RNA sequencing (RNA-Seq) analysis of untreated or melphalan-treated ILF2-depleted JJN3 cells. Non-silencing or ILF2 shRNA transduced JJN3 cells were treated with melphalan for 10 hours.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83712/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA326776
Series		Accession: GSE83712	ID: 200083712

3247. Genome-wide expression change by SHARPIN knockdown in MCF-7 cells
(Submitter supplied) We aim to investigate the role of SHARPIN in breast cancer progression. MCF-7 cells were used as the model and SHARPIN was silenced by siRNA.SHARPIN (SHANK-Associated RH Domain Interactor) is also named as SIPL1 and HSIPL1. The  gene is located in Chr 8. SHARPIN protein is shown to regulate cell adhesion and migration. Besides, SHARPIN is proved to the component of the LUBAC complex and is necessary for NKFB function, while SHARPIN KO mice will lead to chronic dermatitis and immune deficiency in B cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77261/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA309884
Series		Accession: GSE77261	ID: 200077261

3248. Nucleotide stress induction of HEXIM1 suppresses melanoma by modulating cancer cell-specific gene transcription
(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: GPL18573 GPL16791 38 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68053/
Series		Accession: GSE68053	ID: 200068053

3249. Nucleotide stress induction of HEXIM1 suppresses melanoma by modulating cancer cell-specific gene transcription [RNA-Seq2]
(Submitter supplied) Cancer metabolism has been actively studied to gain insights into tumorigenic survival mechanisms and susceptibilities. In melanoma, we identify HEXIM1, a transcription elongation regulator, as a novel melanoma suppressor that participates in nucleotide stress regulation. HEXIM1 expression is low in melanoma. Its overexpression suppresses melanoma while its inactivation accelerates tumor onset in vivo. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68040/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA281631
Series		Accession: GSE68040	ID: 200068040

3250. Nucleotide stress induction of HEXIM1 suppresses melanoma by modulating cancer cell-specific gene transcription [RNA-Seq1]
(Submitter supplied) Cancer metabolism has been actively studied to gain insights into tumorigenic survival mechanisms and susceptibilities. In melanoma, we identify HEXIM1, a transcription elongation regulator, as a novel melanoma suppressor that participates in nucleotide stress regulation. HEXIM1 expression is low in melanoma. Its overexpression suppresses melanoma while its inactivation accelerates tumor onset in vivo. 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/GSE68nnn/GSE68039/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA281632
Series		Accession: GSE68039	ID: 200068039

3251. Conversion of Human Fibroblasts to Stably Self-Renewing Neural Stem Cells with a Single Zinc-Finger Transcription Factor
(Submitter supplied) Direct conversion of somatic cells into neural stem cells (NSCs) by defined factors holds great promise for mechanistic studies, drug screening, and potential cell therapies for different neurodegenerative diseases. Here, we report that a single zinc-finger transcription factor, Zfp521, is sufficient for direct conversion of human fibroblasts into long-term self-renewable and multipotent NSCs. In vitro, Zfp521-induced NSCs maintained their characteristics in the absence of exogenous factor expression and exhibited morphological, molecular, developmental, and functional properties that were similar to control NSCs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 9 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64882/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA272398
Series		Accession: GSE64882	ID: 200064882

3252. Harnessing RNA sequencing for global, unbiased evaluation of two new adjuvants for dendritic-cell immunotherapy
(Submitter supplied) Effective stimulation of immune cells is crucial for the success of cancer immunotherapies. Current approaches to evaluate the efficiency of stimuli activating immune cells are mainly defined by known flow cytometry-based cell activation or cell maturation markers. This method however does not give a complete overview of the achieved activation state and may leave important side effects unnoticed. Here, we used an unbiased RNA sequencing (RNA-seq)-based approach to compare the capacity of four clinical-grade dendritic cell (DC) activation stimuli used to prepare DC-vaccines composed of various types of DC subsets; the already clinically applied GM-CSF and Frühsommer meningoencephalitis (FSME) prophylactic vaccine and the novel clinical grade adjuvants protamine-RNA (pRNA) complexes and CpG-P. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 23 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89442/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA352224
Series		Accession: GSE89442	ID: 200089442

3253. DUX4-induced dsRNA and MYC mRNA Stabilization Activate Apoptotic Pathways in Human Cell Models of Facioscapulohumeral Dystrophy
(Submitter supplied) Facioscapulohumeral muscular dystophy (FSHD) is caused by the mis-expression of DUX4 in skeletal muscle cells. DUX4 is a transcription factor that activates genes normally associated with stem cell biology and its mis-expression in FSHD cells results in apoptosis. To identify genes and pathways necessary for DUX4-mediated apoptosis, we performed an siRNA screen in an RD rhabdomyosarcoma cell line with an inducible DUX4 transgene. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (CSV, RDA) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87495/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA344913
Series		Accession: GSE87495	ID: 200087495

3254. RNA-seq analysis in Jurkat cells
(Submitter supplied) RNA-seq analysis was performed in Jurkat cells (T-cell lymphoblastic leukemia cell line).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 1 Sample
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81712/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA322342
Series		Accession: GSE81712	ID: 200081712

3255. Bladder tumor sequencing
(Submitter supplied) Prospective sequencing of a patient's bladder tumor
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/GSE81nnn/GSE81201/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA320879
Series		Accession: GSE81201	ID: 200081201

3256. LSD1 mediates MYCN control of epithelial-mesenchymal transition through silencing of metastatic suppressor NDRG1 gene
(Submitter supplied) Neuroblastoma (NB) with MYCN amplification is a highly metastatic tumor in children, and unraveling the key players involved in MYCN-induced invasion may identify new targets for therapy. Epithelial-mesenchymal transition (EMT) plays a critical role in promoting metastasis and we have recently determined that MYCN interacts with LSD1, a histone de-methylase flavin oxidase, which has been found to promote EMT. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80753/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA319931
Series		Accession: GSE80753	ID: 200080753

3257. RNA-seq of MCF7 cells treated with epigenetic therapy
(Submitter supplied) RNA-seq was performed after MCF7 cells were treated with S2101, UNC0638, GSK343, depsipeptide alone or in combination with decitabine
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 30 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74036/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA298835
Series		Accession: GSE74036	ID: 200074036

3258. RNA-seq of YB5 cells treated with epigenetic therapy
(Submitter supplied) RNA-seq was performed after YB5 cells were treated with S2101, UNC0638, GSK343, depsipeptide alone or in combination with decitabine
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 30 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73966/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA298594
Series		Accession: GSE73966	ID: 200073966

3259. Next Generation Sequencing Facilitates Quantitative Analysis of HCC cells transfected with NCsiRNA or ODC1siRNA
(Submitter supplied) We investigated if targeting of ODC1 with siRNA could inhibit HCC progression. To accomplish this, Huh1 and Huh7 human HCC cells were transfected with ODC1 siRNA and tested for growth inhibition and apoptotic induction using MTS, FACS and microscopic analysis. To obtain insights into the molecular changes in response to ODC1 knockdown, global changes in gene expression were examined using 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/GSE73nnn/GSE73268/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA296492
Series		Accession: GSE73268	ID: 200073268

3260. HNRNPL and its RNA Targets in Prostate Cancer
(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; Other
Platform: GPL11154 22 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72844/
Series		Accession: GSE72844	ID: 200072844

3261. Identifying lincRNA as prognostic biomarker for clear cell renal cell carcinoma
(Submitter supplied) RNA sequencing libraries were made for A-498 and 786-O to detect the transcripts regulated by the lincRNA comparing knockdown and the non-targeting control.
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/GSE70nnn/GSE70602/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA289133
Series		Accession: GSE70602	ID: 200070602

3262. Transcriptome analysis of Jurkat T-ALL clones from control and CBAP-knockdown/knockout sets
(Submitter supplied) We sequenced whole-genome mRNA from 8 different single stable clones of Jurkat cells modified with CBAP gene expression usng shRNA knockdown or CRISPR/Cas9-mediated knockout and their controls.
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/GSE69511/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA285770
Series		Accession: GSE69511	ID: 200069511

3263. mRNA expression in human DAOY cells
(Submitter supplied) We generate ZNF423 knockdown and control DAOY cells with lentivirus that co-expressed the fluorescent protein mCherry. We performed whole genome RNA sequencing (RNA-seq) of three batched of cultured ZNF423 KD or control KD cells. The sequence reads were analyzed by Homer followed by edgeR. The analyzed RNA-seq results showed  differential expression profile including 12 known cilia genes, and 3 of these were validated with qRT-PCR on mouse granule cell precursors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59598/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA255674
Series		Accession: GSE59598	ID: 200059598

3264. The flightless I protein is involved in the genome-wide mRNA post-transcriptional regulation in lung carcinoma cells
(Submitter supplied) We report the function of Flightless I involved in the overall nuclear export, and genome-wide translation of mRNAs in H1299 cells. By using high-throughput transcriptome and translatome sequencing combined with cell fractionation, we generated genome-wide transcriptome and translatome maps of lung carcinoma cells and normal cells. We find that flightless I protein could modulate the genome-wide translation and mRNA traffiking, suggesting that the post-transcriptional regulation of mRNA might be a major mechanism of action for Flightless I.
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/GSE92nnn/GSE92979/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA359205
Series		Accession: GSE92979	ID: 200092979

3265. CD74 role in transcription regulation
(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 38 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88957/
Series		Accession: GSE88957	ID: 200088957

3266. CD74 role in transcription regulation [RNA-seq]
(Submitter supplied) CD74 activation was previously shown to affect gene transcription. The goal of this study was to reasarch its role as a transcriptor regulator. CD74 was activated in primary CLL cells obtained from patients for 2 and 8 h. mRNA was then extracted, and mRNA-seq was conducted.
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/GSE88nnn/GSE88956/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA349182
Series		Accession: GSE88956	ID: 200088956

3267. HNRNPL RIP-seq in LNCaP prostate cancer cells
(Submitter supplied) RNA immunoprecipitation coupled with next generation sequencing (RIP-seq)  was used to map the HNRNPL-RNA interactome in LNCaP cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72841/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA295188
Series		Accession: GSE72841	ID: 200072841

3268. Deptor transcriptionally regulates Endoplasmic Reticulum homeostasis in Multiple Myeloma cells.
(Submitter supplied) We performed a RNA-seq analysis by using mRNA from KMS27 cells transfected with siRNA Deptor or siRNA negative control.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 2 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79820/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA315795
Series		Accession: GSE79820	ID: 200079820

3269. Genome models integrating chromatin contacts and nuclear lamin-genome interactions reveal implications of laminopathy-causing lamin mutations on genome architecture
(Submitter supplied) Processes shaping the 3-dimensional (3D) human genome remain elusive. We present Chrom3D, a user-friendly 3D whole-genome modeling software that dynamically simulates the radial positioning of topological domains (TADs) in the nucleus. We integrate Hi-C and lamin-associated domain (LAD) information to generate high-resolution ensembles of models that recapitulate single-cell TAD distribution. Chrom3D reveals dynamic TADs and TADs constitutively placed at the nuclear periphery or nuclear interior. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 25 Samples
FTP download: GEO (BED, FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81671/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA322286
Series		Accession: GSE81671	ID: 200081671

3270. MRTF activates TEAD-YAP target gene expression
(Submitter supplied) Yes Associated Protein (YAP) and Myocardin Related Transcription Factor (MRTF) play similar roles and crosstalk in directing the transcriptional responses to chemical and physical extracellular cues. However the mechanism by which the two proteins crosstalk has been unclear. Here, we show MRTF family proteins bind YAP via a conserved PPXY motif that interacts with the YAP WW domain. This interaction allows MRTF to recruit NcoA3 to the TEAD-YAP transcriptional complex and potentiate its transcriptional activity. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89182/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA350532
Series		Accession: GSE89182	ID: 200089182

3271.  RNA Sequencing Reveals that Kaposi Sarcoma-Associated Herpesvirus Infection Mimics Hypoxia Gene Expression Signature
(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 12 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79032/
Series		Accession: GSE79032	ID: 200079032

3272. KSHV Infection Mimics the Hypoxic Response Based on Next-Generation Sequencing [mRNA-Seq]
(Submitter supplied) Purpose: Kaposi’s sarcoma associated-herpesvirus (KSHV) causes several hyperproliferative disorders, including Kaposi’s sarcoma, primary effusion lymphoma and multicentric Castleman’s disease. KSHV encodes for a number of microRNAs (miRNAs), and KSHV infection can affect the expression of cellular miRNAs. Hypoxia has been shown to induce KSHV reactivation, directly induce several KSHV lytic genes, and also induce the most abundant latent viral protein, LANA. more...
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/GSE79nnn/GSE79029/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA314765
Series		Accession: GSE79029	ID: 200079029

3273. Mapping of DHT-responsive or -independent AR-binding sites induced by activated Src in prostate 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
Platform: GPL11154 25 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE92nnn/GSE92576/
Series		Accession: GSE92576	ID: 200092576

3274. Mapping of DHT-responsive or -independent AR-binding sites induced by activated Src in prostate cancer cell lines [RNA-seq]
(Submitter supplied) Building on the observation that metastatic, castration-resistant prostate cancer (CRPC) correlates with activation of Src-family tyrosine kinases, we showed that the expression of activated Src renders LNCaP androgen-independent.  Here, we report on RNA-seq and/or AR ChIP-seq analyses of LNCaP, LNCaP[Src], VCaP, 22Rv1 cells grown in the presence or absence of 10 nM DHT for 16h, or LuCaP35.1 tumors grown in androgen-supplemented vs. 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/GSE92nnn/GSE92574/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA358067
Series		Accession: GSE92574	ID: 200092574

3275. The Human Initiator Is a Distinct and Abundant Element That Is Precisely Positioned in Focused Core Promoters
(Submitter supplied) DNA sequence signals in the core promoter, such as the initiator (Inr), direct transcription initiation by RNA polymerase II. Here we show that the human Inr has the consensus of BBCA+1BW at focused promoters in which transcription initiates at a single site or a narrow cluster of sites. The analysis of 7,678 focused transcription start sites revealed 40% with a perfect match to the Inr and 16% with a single mismatch outside of the CA+1 core. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL18573 3 Samples
FTP download: GEO (BED, BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90035/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA354379
Series		Accession: GSE90035	ID: 200090035

3276. mRNA sequencing in acute myeloid leukemia (AML) cells with and without knockdown of FTO
(Submitter supplied) To identify the expression of mRNAs after knockdown of FTO, we performed RNA-Seq in MA9.3ITD cells with or without knockdown of FTO.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 2 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85008/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA335858
Series		Accession: GSE85008	ID: 200085008

3277. N6-methyladenosine (m6A) sequencing of messenger RNAs in acute myeloid leukemia (AML) cells with and without knockdown of FTO
(Submitter supplied) To identify potential mRNA targets of FTO whose m6A levels are influenced in acute myeloid leukemia (AML) cells, we conducted m6A-seq for mRNA isolated from MA9.3ITD cells with and without knockdown of FTO
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL16791 2 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84944/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA335722
Series		Accession: GSE84944	ID: 200084944

3278. Fusion Negative Rhabdomyosarcoma Cell Lines
(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 7 Samples
FTP download: GEO (BED, FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84630/
Series		Accession: GSE84630	ID: 200084630

3279. Gene Expression Profiling of Fusion Negative Rhabdomyosarcoma Cell Lines
(Submitter supplied) We analyzed the expression of two fusion-negative established Rhabdomyosarcoma cell lines. Together with Chip-seq, we were able to identify transcribed loci bound by myogenic regulatory transcription factors (MYF5 and MYOD) that pertain to embryonic muscle development and cell cycle regulation pathways.  Keywords: rhabdomyosarcoma, gene expression profiling, RD, Rh18
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/GSE84nnn/GSE84629/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA330703
Series		Accession: GSE84629	ID: 200084629

3280. NKX2.2
(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, CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79725/
Series		Accession: GSE79725	ID: 200079725

3281. Nucleosome dynamics in human colorectal cancer specimens reveal activation of a CNOT3-regulated pathway of embryonic stem cell self-renewal
(Submitter supplied) Temporal chromatin dynamics can reveal transcriptional determinants of cell differentiation, and we reasoned that dynamic changes in nucleosome configuration might similarly disclose transcriptional regulators in cancer. To this end, we identified thousands of cis-regulatory sites where chromatin marks and configuration in human CRCs differed from those in their respective precursor adenomas. (based on H3K4me2 mark). more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL11154 45 Samples
FTP download: GEO (BED, FPKM_TRACKING, TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66216/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA276129
Series		Accession: GSE66216	ID: 200066216

3282. Perturb-seq: Dissecting molecular circuits with scalable single cell RNA profiling of pooled genetic screens
(Submitter supplied) Methods: We create a CRISPR vector containing a polyadenylated RNA barcode and couple it with droplet scRNA-seq to get a large scale transcriptional measurements of perturbations Results: We were able to perform regulatory inference of gene function, observe nonlinear interactions, and perform downsampling analysis to show that gene signature effects can be seen with as few as 10's of cells while gene level phenotypes, depending on effects size would require 100's of cells Conclusion: Perturb-seq presents a scalable paradigm for obtaining rich genomic profiles of perturbations
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL19057 GPL18573 6 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90063/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA354362
Series		Accession: GSE90063	ID: 200090063

3283. Molecular liver cancer prevention in cirrhosis by organ transcriptome analysis and lysophosphatidic acid pathway inhibition
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus; Rattus norvegicus
Type:		Expression profiling by array; Expression profiling by high throughput sequencing
4 related Platforms 298 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64520/
Series		Accession: GSE64520	ID: 200064520

3284. THZ1 targeting CDK7 suppresses STAT transcriptional activity and sensitizes T-cell lymphomas to BCL2 inhibitors
(Submitter supplied) Peripheral T-cell lymphomas (PTCL) are aggressive diseases with poor response to chemotherapy and dismal survival. Identification of effective strategies to target PTCL biology represents an urgent need. Here we report that PTCL are sensitive to transcription-targeting drugs, and, in particular, to THZ1, a covalent inhibitor of cyclin-dependent kinase 7 (CDK7). The STAT-signaling pathway is highly vulnerable to THZ1 even in PTCL cells that carry the activating STAT3 mutation Y640F. 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/GSE79955/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA317489
Series		Accession: GSE79955	ID: 200079955

3285. Integrated analyses identify phenotype specific BMP4 signaling 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 10 Samples
FTP download: GEO (BED, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84579/
Series		Accession: GSE84579	ID: 200084579

3286. Integrated analyses identify phenotype specific BMP4 signaling in breast cancer [RNA-seq]
(Submitter supplied) Bone morphogenetic protein 4 (BMP4) plays an important role in cancer pathogenesis. In breast cancer, it reduces proliferation and increases migration in a cell line-dependent manner. To characterize the transcriptional mediators of these phenotypes, we performed RNA-seq and DNase-seq analyses after BMP4 treatment in MDA-MB-231 and T-47D breast cancer cells that respond to BMP4 with enhanced migration and decreased cell growth, respectively.
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/GSE84nnn/GSE84577/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA329672
Series		Accession: GSE84577	ID: 200084577

3287. CTCF modulates Estrogen Receptor function through specific chromatin and nuclear matrix interactions
(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, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85108/
Series		Accession: GSE85108	ID: 200085108

3288. CTCF modulates Estrogen Receptor function through specific chromatin and nuclear matrix interactions [RNA-seq]
(Submitter supplied) In our work we used high-throughput sequencing methods to get insight in the role of CTCF in ER-mediated gene regulation in luminal breast cancer cells. After assessing genome-wide binding of CTCF, ER, FOXA1 and Lamin B in MCF7 cells treated with estrogen for different time points, we could correlate the interaction to the chromatin with estrogen-induced de novo transcription (from GRO-seq data) and loop formation (from ChIA-PET, Fullwood et al., 2009). 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/GSE85nnn/GSE85088/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA336120
Series		Accession: GSE85088	ID: 200085088

3289. Single cell RNA sequencing of primary breast cancer.
(Submitter supplied) We performed single cell RNA sequencing (RNA-seq) for 549 primary breast cancer cells and lymph node metastases from 11 patients with distinct molecular subtypes (BC01-BC02, estrogen receptor positive (ER+); BC03, double positive (ER+ and HER2+); BC03LN, lymph node metastasis of BC03; BC04-BC06, human epidermal growth factor receptor 2 positive (HER2+); BC07-BC11, triple-negative breast cancer (TNBC); BC07LN, lymph node metastasis of BC07) and matched bulk tumors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 563 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75688/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA305054
Series		Accession: GSE75688	ID: 200075688

3290. Global transcriptional profiling changes upon knockdown of LKB1 in human glioblastoma cell lines
(Submitter supplied) The experiment was designed to display differential gene expression profiling changes in two human glioblastoma cells upon knockdow of LKB1 tumor suppressor, by using RNAseq technology.
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/GSE91nnn/GSE91016/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA356645
Series		Accession: GSE91016	ID: 200091016

3291. Transcriptomic profiling discloses molecular and cellular events related to neuronal differentiation in SH-SY5Y cells
(Submitter supplied) Human SH-SY5Y neuroblastoma cells are widely utilized in in vitro studies to dissect out pathogenetic mechanisms of neurodegenerative disorders. These cells are considered as neuronal precursors and differentiate into more mature neuronal phenotypes under selected growth conditions. In this study, we performed systematic transcriptomic (RNA-seq) and bioinformatic analysis to pinpoint pathways and cellular processes underlying neuronal differentiation of SH-SY5Y cells according to a two-step paradigm: retinoic acid treatment followed by enriched neurobasal medium. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77383/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA310195
Series		Accession: GSE77383	ID: 200077383

3292. polyA mRNA RNA-seq from HepG2 (ENCSR329MHM)
(Submitter supplied) RNA-seq on human HepG2 (paired-ended)  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: GPL9115 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90322/
Series		Accession: GSE90322	ID: 200090322

3293. polyA mRNA RNA-seq from MCF-7 (ENCSR000CTU)
(Submitter supplied) The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line MCF-7. 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 (BED, BIGBED, BIGWIG, GTF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90267/
Series		Accession: GSE90267	ID: 200090267

3294. polyA mRNA RNA-seq from SK-N-SH (ENCSR000CTT)
(Submitter supplied) The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line SK-N-SH. 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 (BED, BIGBED, BIGWIG, GTF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90266/
Series		Accession: GSE90266	ID: 200090266

3295. polyA mRNA RNA-seq from SK-N-SH (ENCSR000CTS)
(Submitter supplied) The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line SK-N-SH. 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 (BED, BIGBED, BIGWIG, GTF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90265/
Series		Accession: GSE90265	ID: 200090265

3296. polyA mRNA RNA-seq from SK-N-SH (ENCSR000CTR)
(Submitter supplied) The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line SK-N-SH. 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 (BED, BIGBED, BIGWIG, GTF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90264/
Series		Accession: GSE90264	ID: 200090264

3297. polyA mRNA RNA-seq from MCF-7 (ENCSR000CTO)
(Submitter supplied) The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line MCF-7. 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 (BED, BIGBED, BIGWIG, GTF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90261/
Series		Accession: GSE90261	ID: 200090261

3298. polyA mRNA RNA-seq from A549 (ENCSR000CTM)
(Submitter supplied) The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line A549. They are stranded PE76 Illumina GAIIx 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 (BED, BIGBED, BIGWIG, GTF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90259/
Series		Accession: GSE90259	ID: 200090259

3299. polyA mRNA RNA-seq from A549 (ENCSR000CTL)
(Submitter supplied) The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line A549. They are stranded PE76 Illumina GAIIx 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 (BED, BIGBED, BIGWIG, GTF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90258/
Series		Accession: GSE90258	ID: 200090258

3300. polyA depleted RNA-seq from HepG2 (ENCSR000CQU)
(Submitter supplied) The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line HepG2. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized 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: GPL10999 2 Samples
FTP download: GEO (BED, BIGBED, BIGWIG, GTF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90256/
Series		Accession: GSE90256	ID: 200090256

3301. polyA depleted RNA-seq from HeLa-S3 (ENCSR000CQT)
(Submitter supplied) The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line HeLa-S3. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized 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: GPL10999 1 Sample
FTP download: GEO (BED, BIGBED, BIGWIG, GTF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90255/
Series		Accession: GSE90255	ID: 200090255

3302. polyA depleted RNA-seq from SK-N-SH (ENCSR000CQP)
(Submitter supplied) The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line SK-N-SH that has been treated with retinoic acid. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized 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: GPL10999 2 Samples
FTP download: GEO (BED, BIGBED, BIGWIG, GTF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90251/
Series		Accession: GSE90251	ID: 200090251

3303. polyA depleted RNA-seq from K562 (ENCSR000CQM)
(Submitter supplied) The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line K562. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized 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: GPL10999 2 Samples
FTP download: GEO (BED, BIGBED, BIGWIG, GTF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90250/
Series		Accession: GSE90250	ID: 200090250

3304. polyA depleted RNA-seq from K562 (ENCSR000CQL)
(Submitter supplied) The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line K562. They are stranded PE76 Illumina GaIIx RNA-Seq libraries from rRNA-depleted and DSN normalized 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: GPL10999 2 Samples
FTP download: GEO (BED, BIGBED, BIGWIG, GTF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90249/
Series		Accession: GSE90249	ID: 200090249

3305. polyA depleted RNA-seq from HepG2 (ENCSR000CQK)
(Submitter supplied) The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line HepG2. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized 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: GPL10999 2 Samples
FTP download: GEO (BED, BIGBED, BIGWIG, GTF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90248/
Series		Accession: GSE90248	ID: 200090248

3306. polyA depleted RNA-seq from HeLa-S3 (ENCSR000CQJ)
(Submitter supplied) The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line HeLa-S3. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized 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: GPL10999 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90247/
Series		Accession: GSE90247	ID: 200090247

3307. polyA depleted RNA-seq from HeLa-S3 (ENCSR000CQI)
(Submitter supplied) The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line HeLa-S3. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized 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: GPL10999 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90246/
Series		Accession: GSE90246	ID: 200090246

3308. polyA depleted RNA-seq from A549 (ENCSR000CQC)
(Submitter supplied) The libraries contained in this experiment come from whole cell fractions of independent growths of cell line A549. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized 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: GPL10999 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90242/
Series		Accession: GSE90242	ID: 200090242

3309. polyA depleted RNA-seq from MCF-7 (ENCSR000CQB)
(Submitter supplied) The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line MCF-7. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized 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: GPL10999 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90241/
Series		Accession: GSE90241	ID: 200090241

3310. total RNA-seq from K562 (ENCSR000CQA)
(Submitter supplied) The libraries contained in this experiment come from the nucleoplasm fraction of independent growths of cell line K562. They are stranded PE76 Illumina GAIIx 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: GPL10999 2 Samples
FTP download: GEO (BED, BIGBED, BIGWIG, GTF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90240/
Series		Accession: GSE90240	ID: 200090240

3311. total RNA-seq from K562 (ENCSR000CPZ)
(Submitter supplied) The libraries contained in this experiment come from the nucleolar fraction of independent growths of cell line K562. They are stranded PE76 Illumina GAIIx 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: GPL10999 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90239/
Series		Accession: GSE90239	ID: 200090239

3312. total RNA-seq from K562 (ENCSR000CPY)
(Submitter supplied) The libraries contained in this experiment come from the chromatin fraction of independent growths of cell line K562. They are stranded PE76 Illumina GAIIx 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: GPL10999 2 Samples
FTP download: GEO (BED, BIGBED, BIGWIG, GTF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90238/
Series		Accession: GSE90238	ID: 200090238

3313. polyA mRNA RNA-seq from MCF-7 (ENCSR000CPT)
(Submitter supplied) The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line MCF-7. They are stranded PE76 Illumina GAIIx 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: GPL10999 2 Samples
FTP download: GEO (BED, BIGBED, BIGWIG, GTF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90237/
Series		Accession: GSE90237	ID: 200090237

3314. polyA mRNA RNA-seq from K562 (ENCSR000CPS)
(Submitter supplied) The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line K562. They are stranded PE76 Illumina GAIIx 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: GPL10999 2 Samples
FTP download: GEO (BED, BIGBED, BIGWIG, GTF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90236/
Series		Accession: GSE90236	ID: 200090236

3315. polyA mRNA RNA-seq from HeLa-S3 (ENCSR000CPQ)
(Submitter supplied) The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line HeLa-S3. They are stranded PE76 Illumina GAIIx 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: GPL10999 2 Samples
FTP download: GEO (BED, BIGBED, BIGWIG, GTF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90235/
Series		Accession: GSE90235	ID: 200090235

3316. polyA mRNA RNA-seq from HeLa-S3 (ENCSR000CPP)
(Submitter supplied) The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line HeLa-S3. They are stranded PE76 Illumina GAIIx 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: GPL10999 2 Samples
FTP download: GEO (BED, BIGBED, BIGWIG, GTF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90234/
Series		Accession: GSE90234	ID: 200090234

3317. polyA mRNA RNA-seq from SK-N-SH (ENCSR000CPN)
(Submitter supplied) The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line SK-N-SH that has been treated with retinoic acid. They are stranded PE76 Illumina GAIIx 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: GPL10999 2 Samples
FTP download: GEO (BED, BIGBED, BIGWIG, GTF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90232/
Series		Accession: GSE90232	ID: 200090232

3318. polyA depleted RNA-seq from K562 (ENCSR000CPG)
(Submitter supplied) The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line K562. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized 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: GPL10999 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90231/
Series		Accession: GSE90231	ID: 200090231

3319. polyA mRNA RNA-seq from HepG2 (ENCSR000CPF)
(Submitter supplied) The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line HepG2. They are stranded PE76 Illumina GAIIx 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: GPL10999 2 Samples
FTP download: GEO (BED, BIGBED, BIGWIG, GTF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90230/
Series		Accession: GSE90230	ID: 200090230

3320. polyA depleted RNA-seq from HepG2 (ENCSR000CPD)
(Submitter supplied) The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line HepG2. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized 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: GPL10999 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90229/
Series		Accession: GSE90229	ID: 200090229

3321. polyA mRNA RNA-seq from HepG2 (ENCSR000CPC)
(Submitter supplied) The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line HepG2. They are stranded PE76 Illumina GAIIx 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: GPL10999 2 Samples
FTP download: GEO (BED, BIGBED, BIGWIG, GTF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90228/
Series		Accession: GSE90228	ID: 200090228

3322. polyA mRNA RNA-seq from K562 (ENCSR000COK)
(Submitter supplied) The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line K562. They are stranded PE76 Illumina GAIIx 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: GPL10999 2 Samples
FTP download: GEO (BED, BIGBED, BIGWIG, GTF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90220/
Series		Accession: GSE90220	ID: 200090220

3323. polyA mRNA RNA-seq from U-87 MG (ENCSR000BYO)
(Submitter supplied) RNA-seq on U87 greater than 200bp polyA+  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/GSE90nnn/GSE90176/
Series		Accession: GSE90176	ID: 200090176

3324. Identification of rare, dormant and therapy resistant stem cells in acute lymphoblastic leukemia
(Submitter supplied) Tumor relapse is associated with dismal prognosis, but responsible biological principles remain incompletely understood. To isolate and characterize relapse-inducing cells, we used genetic engineering and proliferation-sensitive dyes in patient-derived xenografts of acute lymphoblastic leukemia (ALL). We identified a rare subpopulation that resembled relapse-inducing cells with combined properties of long-term dormancy, treatment resistance, and stemness. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 228 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83142/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA325123
Series		Accession: GSE83142	ID: 200083142

3325. Heterogeneous nuclear ribonucleoprotein C1/C2 links transcriptional and splicing actions of 1,25-dihydroxyvitamin D
(Submitter supplied) Heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNPC1/C2) functions as an RNA splicing regulator through co-transcriptional association with nascent mRNA. HnRNPC1/C2 can also bind to double-stranded DNA as a vitamin D response element-binding protein (VDRE-BP), thereby regulating transcriptional activity of the vitamin D receptor (VDR) bound to 1,25-dihydroxyvitamin D (1,25(OH)2D). In this way hnRNPC1/C2 may act as a coupling factor for 1,25(OH)2D-directed transcription and RNA splicing. 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/GSE63nnn/GSE63086/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA266575
Series		Accession: GSE63086	ID: 200063086

3326. Functional genomics of artificial transcription factor-induced iPS cells
(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: GPL17021 GPL16791 65 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89221/
Series		Accession: GSE89221	ID: 200089221

3327. Global transcriptional profiling of HEK293 cells transfected with ATFs, mouse embryonic fibroblasts, and mouse iPS cells derived with artificial transcription factors
(Submitter supplied) We tested various architectures of artificial transcription factors (ATFs) in HEK293 cells to test the contribution of the interaction domain, nuclear localization domain, size of DNA-binding domain, and activation domain. Then we made a genome-scale ATF library and tested it in reprogramming mouse embryonic fibroblasts to induced pluripotent stem (iPS) cells. Three combinations of ATFs (C2, C3, and C4) could induce pluripotency when expressed with Sox2, Klf4, and c-Myc. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL17021 GPL16791 43 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89219/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA350708
Series		Accession: GSE89219	ID: 200089219

3328. Anaylsis of the effect of down-regulation of the EWS-FLI1 fusion protein in Ewing Sarcoma cells by RNA-seq.
(Submitter supplied) We generated A673 Ewing Sarcoma cell lines which stably express shRNA targeting the EWS-FLI1 fuison protein or Luciferase as a control to study the effect of EWS-FLI1 on the transcriptome. The vectors used to generate the cell lines were a gift from Stephen Lessnick and were first published in PMID 16697960
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/GSE53nnn/GSE53066/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA230789
Series		Accession: GSE53066	ID: 200053066

3329. Conserved recurrent gene mutations correlate with pathway deregulation and clinical outcomes of lung adenocarcinoma in never-smokers
(Submitter supplied) Background. Novel and targetable mutations are needed for improved understanding and treatment of lung cancer in never-smokers. Methods. Twenty-seven lung adenocarcinomas from never-smokers were sequenced by both exome and mRNA-seq with respective normal tissues. Somatic mutations were detected and compared with pathway deregulation, tumor phenotypes and clinical outcomes. Results. Although somatic mutations in DNA or mRNA ranged from hundreds to thousands in each tumor, the overlap mutations between the two were only a few to a couple of hundreds. 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/GSE87nnn/GSE87340/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA344450
Series		Accession: GSE87340	ID: 200087340

3330. Proteomics and transcriptomics of peripheral nerve tissue and cells unravel new aspects of the human Schwann cell repair phenotype
(Submitter supplied) The remarkable feature of Schwann cells (SCs) to transform into a repair phenotype turned the spotlight on this powerful cell type. SCs provide the regenerative environment for axonal re-growth after peripheral nerve injury (PNI) and play a vital role in differentiation of neuroblastic tumors into a benign subtype of neuroblastoma, a tumor originating from neural crest-derived neuroblasts. Hence, understanding their mode-of-action is of utmost interest for new approaches in regenerative medicine, but also for neuroblastoma therapy. 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/GSE90nnn/GSE90711/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA355561
Series		Accession: GSE90711	ID: 200090711

3331. Quantitative Analysis of PPARD Transcriptomes  in Colon Cancer Cells by Next Generation Sequencing (NGS)
(Submitter supplied) Purpose: NGS has revolutionized systems-based analysis of cell signaling pathways. The goal of this study is to determine the effects of PPARD in colon cancer cell transcriptomes in relation to the metastatic potential. Methods: NGS-derived colon cancer cell mRNA transcriptome profiles of HCT116 WT (HCT116) and HCT116 with genetic PPARD-knockout (KO1) cells were generated by deep sequencing, in quadruplicate, using Illumina  HiSeq2000 .The transcriptomes of HCT116 and KO1 cells will be compared to determine the differentially expressed genes between HCT116  and KO1 cells. 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/GSE89nnn/GSE89729/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA353014
Series		Accession: GSE89729	ID: 200089729

3332. Adaptive resistance of melanoma cells to RAF inhibition via reversible induction of a slowly-dividing de-differentiated state
(Submitter supplied) Treatment of BRAF-mutant melanomas with MAP-kinase pathway inhibitors is paradigmatic of the promise of precision cancer therapy but also highlights problems with drug resistance that limit patient benefit. We use live-cell imaging, single-cell analysis and molecular profiling to show that exposure of tumor cells to RAF/MEK inhibitors elicits a heterogeneous response in which some cells die, some arrest and a remaining fraction adapts to drug. 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/GSE87nnn/GSE87641/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA345487
Series		Accession: GSE87641	ID: 200087641

3333. CRISPRi-based genome-scale identification of functional long non-coding RNA loci in human cells
(Submitter supplied) The human genome produces thousands of long non-coding RNAs (lncRNAs) – transcripts >200 nucleotides long that do not encode proteins. While critical roles in normal biology and disease have been revealed for a subset of lncRNAs, the function of the vast majority remains untested. Here, we developed a CRISPR interference (CRISPRi) platform targeting 16,401 lncRNA loci in 7 diverse cell lines including 6 transformed cell lines and human induced pluripotent stem cells (iPSCs). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platform: GPL20301 112 Samples
FTP download: GEO (TXT, ZIP) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85011/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA335860
Series		Accession: GSE85011	ID: 200085011

3334. Whole transcriptome analysis of lung squamouse cell carcinoma
(Submitter supplied) Discovery of novel diagnostic and/or prognostic biomarkers of lung squamous cell carcinoma based on a whole transcriptome analysis using RNA sequencing (RNA-seq). Transcriptomic profiles of 12 available samples, out of 87 recruited patients with lung squamous cell carcinoma (SCC) were generated using Ion Proton system.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84339/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA328932
Series		Accession: GSE84339	ID: 200084339

3335. Transcriptional changes in breast cancer cell lines associated with vascular mimicry
(Submitter supplied) The goal of this study was to determine the transcriptional changes associated with breast cancer cells undergoing vascular mimicry in a 3D assay.  Two breast cancer cell lines were plated on matrigel in the presence or absence of serum.  MDA-MB-231 cells undergo vascular mimicry on matrigel in the absence of serum, MDA-MB-453 cells do not.
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/GSE77nnn/GSE77179/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA309666
Series		Accession: GSE77179	ID: 200077179

3336. Next generation sequencing to elucidate the novel function of RORC (RORgamma) in breast cancer
(Submitter supplied) Exploring the novel role of RORC (RORgamma) in breast cancer, utilizing NEXTseq with genetic gain and loss of function and pharmacological treatment.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 30 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74981/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA302118
Series		Accession: GSE74981	ID: 200074981

3337. Functional Genomic Analyses of Hep-G2 Cell Line after FTO knockdown
(Submitter supplied) To explore the molecular mechanism underlying glucose regulation by hepatic FTO, we used the human hepatocyte Hep-G2 cell line as an experimental platform and analyzed transcriptome changes following FTO knock-down.
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/GSE74nnn/GSE74791/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA301528
Series		Accession: GSE74791	ID: 200074791

3338. Age-Related Gene Expression Changes in Prostate Cancer Patients [RNA-Seq]
(Submitter supplied) Formalin-fixed, paraffin-embedded (FFPE) from prostate cancer patients
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 11 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90463/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA354708
Series		Accession: GSE90463	ID: 200090463

3339. Ailanthone targets p23 to overcome MDV3100 resistance in castration-resistant prostate cancer
(Submitter supplied) Anti-androgen therapies including the new androgen receptor (AR) antagonist MDV3100 are the first therapeutic approach in treating prostate cancer (PCa). However, tumors frequently become castration resistant through multiple mechanisms including alternative expression of AR splice variants. To identify new inhibitors which block both full-length AR (AR-FL) and constitutively-active truncated AR splice variants (AR-Vs), a library of natural compounds was screened for molecules that could inhibit AR-driven transcription in PCa cells expressing AR-FL or AR-Vs. 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/GSE85nnn/GSE85541/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA338761
Series		Accession: GSE85541	ID: 200085541

3340. Activation of Wnt/beta-catenin in Ewing sarcoma cells antagonizes EWS/ETS function and promotes phenotypic transition to more metastatic cell states
(Submitter supplied) Ewing sarcomas are characterized by the presence of EWS/ETS fusion genes in the absence of other recurrent genetic alterations and mechanisms of tumor heterogeneity that contribute to disease progression remain unclear. Mutations in the Wnt/beta-catenin pathway are rare in Ewing sarcoma but the Wnt pathway modulator LGR5 is often highly expressed, suggesting a potential role for the axis in tumor pathogenesis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75859/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA305534
Series		Accession: GSE75859	ID: 200075859

3341. RNA-seq of YB5 cells treated with Proscillaridin A
(Submitter supplied) RNA-seq was performed after YB5 cells were treated with DAC, Proscillaridin A, or the combinatino of the two
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/GSE89nnn/GSE89154/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA350500
Series		Accession: GSE89154	ID: 200089154

3342. The long non-coding RNA GAS5 differentially regulates cell cycle arrest and apoptosis in human neuroblastoma
(Submitter supplied) Comparison of the global transcriptional profiles of the neurblastoma cell line IMR-32 48 hours after transfection with a Negative Control siRNA compared to an siRNA for the lncRNA GAS5.
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/GSE90nnn/GSE90523/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA354960
Series		Accession: GSE90523	ID: 200090523

3343. Lowered H3K27me3 and DNA hypomethylation define poorly prognostic pediatric posterior fossa ependymomas
(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 35 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89452/
Series		Accession: GSE89452	ID: 200089452

3344. Global reduction in H3K27me3 and DNA hypomethylation define poorly prognostic pediatric posterior fossa ependymomas
(Submitter supplied) A subgroup of  Posterior fossa ependymomas show reduced H3K27me3, global DNA hypomethylation, are more invasive, exhibit poor prognosis and epigenetically deregulated genes converge on radial glial factors, suggesting developing cerebellar radial glia as candidate cells-of-origin.
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/GSE89nnn/GSE89448/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA352240
Series		Accession: GSE89448	ID: 200089448

3345. Low H3K27me3 and DNA hypomethylation define poorly prognostic pediatric posterior fossa ependymomas
(Submitter supplied) A subgroup of  Posterior fossa ependymomas show reduced H3K27me3, global DNA hypomethylation, are more invasive, exhibit poor prognosis and epigenetically deregulated genes converge on radial glial factors, suggesting developing cerebellar radial glia as candidate cells-of-origin.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 15 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89446/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA352234
Series		Accession: GSE89446	ID: 200089446

3346. RNA-sequencing analysis in human glioma stem cell
(Submitter supplied) Glioblastomas show heterogeneous histological features. These distinct phenotypic states are thought to be associated with the presence of glioma stem cells (GSCs), which are highly tumorigenic and self-renewing sub-population of tumor cells that have different functional characteristics. To investigate Glioblastomas (GBMs) show heterogeneous histological features. These distinct phenotypic states are thought to be originated by the glioma stem cells (GSCs), which are highly tumorigenic and self-renewing sub-population of tumor cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL15520 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86348/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA341490
Series		Accession: GSE86348	ID: 200086348

3347. MLL-AF4 binds directly to a BCL-2 specific enhancer and impacts H3K27 acetylation
(Submitter supplied) Survival rates for children diagnosed with acute lymphoblastic leukemia (ALL) have drastically improved, but those carrying mutations in the Mixed Lineage Leukemia (MLL) gene continue to have a very poor prognosis. The most common MLL mutation in ALL is the t(4;11)(q21;q23) chromosome translocation that fuses MLL in frame with the AF4 gene producing MLL-AF4 and AF4-MLL fusion proteins. Previously, we showed that MLL-AF4 binds to the BCL-2 gene and directly activates it through DOT1L recruitment and increased H3K79me2/3 levels. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL18573 GPL16791 21 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85988/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA339938
Series		Accession: GSE85988	ID: 200085988

3348. Knockdown of ADNP in HCT116 colon cancer cells
(Submitter supplied) RNASeq data from replicates after siRNA mediated knockdown of human ADNP in HCT116 colon cancer cells
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/GSE79nnn/GSE79395/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA315693
Series		Accession: GSE79395	ID: 200079395

3349. A faithful in vivo model of human MLL-AF4 proB acute lymphoblastic leukemia
(Submitter supplied) Transcriptome analysis by RNAseq of leukemia model promoted by MLL-Af4 or MLL-AF9 fusion proteins. We find each fusion protein promotes a specific gene signature correlating to those identified in patients
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 20 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76978/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA309171
Series		Accession: GSE76978	ID: 200076978

3350. High-throughput RNA-sequencing analysis in human glioma stem cell
(Submitter supplied) Glioblastomas show heterogeneous histological features. These distinct phenotypic states are thought to be associated with the presence of glioma stem cells (GSCs), which are highly tumorigenic and self-renewing sub-population of tumor cells that have different functional characteristics. To investigate gene expression including lncRNA (long non-coding RNA) in GSC, we have performed high-throughput RNA-sequencing (RNA-seq) experiment using Illumina GAIIx.
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/GSE66nnn/GSE66200/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA276100
Series		Accession: GSE66200	ID: 200066200

3351. Confirmation dataset of Transcriptome Sequencing (RNAseq) data utilizing Formalin-Fixed, Paraffin-Embedded Biopsies with Clear Cell Renal Cell Carcinoma for Exploration of Disease Biology and Biomarker Development
(Submitter supplied) This dataset complements GSE76207. 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 (Eikrem et al., PLoS One. 2016 Feb 22;11(2):e0149743. doi: 10.1371/journal.pone.0149743. eCollection 2016. PMID: 26901863) with FFPE confirmation dataset from clear cell renal cell carcinoma (ccRCC) patients. 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/GSE82nnn/GSE82122/
Series		Accession: GSE82122	ID: 200082122

3352. ARID1A loss impairs enhancer-mediated gene regulation and drives colon cancer in mice
(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: GPL11154 GPL13112 34 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71514/
Series		Accession: GSE71514	ID: 200071514

3353. ARID1A loss impairs enhancer-mediated gene regulation and drives colon cancer in mice [HCT116_RNA-seq]
(Submitter supplied) Genes encoding subunits of SWI/SNF chromatin remodeling complexes are collectively mutated in ~20% of all human cancers. Although ARID1A is the most frequent target of mutations, the mechanism by which its inactivation promotes tumorigenesis is unclear. Here, we demonstrate that Arid1a functions as a tumor suppressor in the mouse colon, but not the small intestine, and that invasive ARID1A-deficient adenocarcinomas resemble human colorectal cancer (CRC). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71511/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA291422
Series		Accession: GSE71511	ID: 200071511

3354. SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation
(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: GPL15520 GPL16791 GPL11154 116 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71506/
Series		Accession: GSE71506	ID: 200071506

3355. SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation [cell line_RNA-seq]
(Submitter supplied) SMARCB1 (SNF5/INI1/BAF47), a core subunit of the SWI/SNF (BAF) chromatin remodeling complex, is inactivated in nearly all pediatric rhabdoid tumors. These aggressive cancers are among the most genomically stable, suggesting an epigenetic mechanism by which SMARCB1 loss drives transformation. Here, we show that despite indistinguishable mutational landscapes, human RTs show distinct enhancer H3K27ac signatures, which reveal remnants of differentiation programs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 34 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71505/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA291409
Series		Accession: GSE71505	ID: 200071505

3356. SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation [primary tissue_RNA-seq]
(Submitter supplied) SMARCB1 (SNF5/INI1/BAF47), a core subunit of the SWI/SNF (BAF) chromatin remodeling complex, is inactivated in nearly all pediatric rhabdoid tumors. These aggressive cancers are among the most genomically stable, suggesting an epigenetic mechanism by which SMARCB1 loss drives transformation. Here, we show that despite indistinguishable mutational landscapes, human RTs show distinct enhancer H3K27ac signatures, which reveal remnants of differentiation programs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 3 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71503/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA291411
Series		Accession: GSE71503	ID: 200071503

3357. RNA-Seq expression profiling of hepatocellular carcinoma and adjacent non-tumor liver tissues
(Submitter supplied) Three pairs of hepatocellular carcinoma and adjacent non-tumor tissues were from 3 male patients suffering from stage I or II HCC with hepatitis C virus background. RNA-Seq libraries were prepared from total RNA using polyA enrichment strategy. The libraries were sequenced on Illumina HiSeq2000 instruments.
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/GSE81550/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA321974
Series		Accession: GSE81550	ID: 200081550

3358. Exosomal short RNA sequencing experiments
(Submitter supplied) The characterization of extracellular vesicular RNA (EV RNA) derived from nine cell types demonstrated the diversity of cell type specific RNA biotypes. A large proportion of these cell type specific RNAs are denoted by their processing into shorter versions of their full length structures as they function with the cells of origin.   specific portions of annotated pre-miRNA, tRNA, YRNA and other RNAs within EVs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 58 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89926/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA354289
Series		Accession: GSE89926	ID: 200089926

3359. EPOP interacts with Elongin BC and USP7 to modulate the chromatin landscape (EPOP KO)
(Submitter supplied) Gene regulatory networks are pivotal for many biological processes. In mouse embryonic stem cells (mESCs) the transcriptional network can be divided into three functionally distinct modules: Polycomb, Core and Myc. The Polycomb module represses developmental genes, while the Myc module is associated with proliferative functions and its mis-regulation is linked to cancer development. Here, we show that in mESCs the Polycomb Repressive Complex 2 (PRC2) associated protein EPOP (a.k.a C17orf96, esPRC2p48, E130012A19Rik) co-localizes at chromatin with members of the Myc and Polycomb module. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL9185 GPL9052 29 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76536/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA307667
Series		Accession: GSE76536	ID: 200076536

3360. Transcriptome profiling (RNA-seq) of CREBBP+/+ and CREBBP+/- clones of U2932 DLBCL cell line
(Submitter supplied) Purpose: Diffuse large B cell lymphomas (DLBCL) frequently harbor mutations in the histone acetyltransferase CREBBP, however their functional contribution to lymphomagenesis remains largely unknown. This study aims at elucidating and characterizing the molecular pathways affected by mutations in CREBBP. Methods: U2932, a DLBCL cell line that has wild type expression of CREBBP was manipulated by CRISPR-Cas9 strategy to mutate one allele of CREBBP and examine the pathways affected. 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/GSE89nnn/GSE89879/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA353640
Series		Accession: GSE89879	ID: 200089879

3361. Resetting cancer stem cell regulatory nodes upon MYC inhibition
(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 50 Samples
FTP download: GEO (BIGWIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86519/
Series		Accession: GSE86519	ID: 200086519

3362. Genome-wide mRNA expression in human glioblastoma cells and glioblastoma stem cells expressing or not Omomyc
(Submitter supplied) MYC deregulation is common in human cancer and has a role in sustaining the aggressive cancer stem cell populations. MYC mediates a broad transcriptional response controlling normal biological programs but its activity is not clearly understood. We address MYC function in cancer stem  cells through the inducible expression of Omomyc – a MYC derived polypeptide interfering with MYC activity – taking as model the most lethal brain tumour, glioblastoma. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL11154 29 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86518/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA342117
Series		Accession: GSE86518	ID: 200086518

3363. Regulatory T cells exhibit distinct features in human breast cancer
(Submitter supplied) The goal of this study is to compare transcriptional profiles of regulatory T cells and conventional CD4 T cells in human breast cancer to regulatory T cells and conventional CD4 T cells in normal breast parenchyma and in peripheral blood.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL17303 54 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89225/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA350777
Series		Accession: GSE89225	ID: 200089225

3364. A Druggable TCF4- and BRD4-dependent Transcriptional Network Sustains Malignancy in Blastic Plasmacytoid Dendritic Cell Neoplasm (RNA-Seq)
(Submitter supplied) Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is an aggressive and largely incurable hematologic malignancy originating from plasmacytoid dendritic cells (pDCs). Using RNA interference screening, we identified the E-box transcription factor TCF4 as a master regulator of the BPDCN oncogenic program. TCF4 served as a faithful diagnostic marker of BPDCN, and its downregulation caused the loss of the BPDCN-specific expression program and apoptosis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL18573 14 Samples
FTP download: GEO (XLS, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84471/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA329312
Series		Accession: GSE84471	ID: 200084471

3365. Gene expression profile of regenerated CD8αα T cells and CD8αβ T cells from LMP2 T-iPSCs
(Submitter supplied) Whereas cytotoxic T lymphocytes (CTLs) represent the most promising therapeutic avenue in cancer immunotherapy, adaptive transfer of antigen-specific CTLs has faced difficulty in efficient expansion of CTLs from patients in ex vivo culture. To solve this issue, several groups have proposed that the induced pluripotent stem cell (iPSC) technology can be applied for the expansion of antigen-specific CTLs: when iPSCs are produced from antigen-specific CTLs and CTLs are induced from these iPSCs, all regenerated CTLs express the same TCR as original CTLs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81975/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA323549
Series		Accession: GSE81975	ID: 200081975

3366. Epigenetic regulation of the apoptosis program in t(8;21) AMLs by an AML1-ETO, ERG and RUNX1 triad
(Submitter supplied) The t(8;21) acute myeloid leukemia associated oncoprotein AML1-ETO is a transcription factor that aberrantly regulates the pathways that lead to myeloid differentiation. Here, we set out to investigate the effects of AML1-ETO on gene expression and the epigenome in patient blast cells. We identify two modules, one in which AML1-ETO binds promoter regions of active genes and one represented by non-promoter binding to accessible, yet inactive chromatin regions. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL10999 GPL11154 16 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76464/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA307457
Series		Accession: GSE76464	ID: 200076464

3367. Pluripotent Reprogramming of Human AML Resets Leukemic Behavior and Models Therapeutic Targeting of Subclones
(Submitter supplied) Understanding the contribution of abnormal genetic and epigenetic programs to acute myeloid leukemia (AML) is necessary for the integrated design of targeted therapies. To investigate this, we determined the effect of epigenetic reprogramming on leukemic behavior by generating induced pluripotent stem cells (iPSCs) from AML patient samples harboring MLL rearrangements. AML-derived iPSCs (AML-iPSCs) retained leukemic mutations, but reset leukemic DNA methylation/gene expression patterns and lacked leukemic potential. more...
Organism:	Homo sapiens
Type:		Methylation profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL13534 GPL20301 87 Samples
FTP download: GEO (IDAT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89778/
Series		Accession: GSE89778	ID: 200089778

3368. Pluripotent Reprogramming of Human AML Resets Leukemic Behavior and Models Therapeutic Targeting of Subclones [RNA-seq]
(Submitter supplied) Understanding the contribution of abnormal genetic and epigenetic programs to acute myeloid leukemia (AML) is necessary for the integrated design of targeted therapies. To investigate this, we determined the effect of epigenetic reprogramming on leukemic behavior by generating induced pluripotent stem cells (iPSCs) from AML patient samples harboring MLL rearrangements. AML-derived iPSCs (AML-iPSCs) retained leukemic mutations, but reset leukemic DNA methylation/gene expression patterns and lacked leukemic potential. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 39 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89777/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA353508
Series		Accession: GSE89777	ID: 200089777

3369. Digitalis-like compounds facilitate redifferentiation of non-medullary thyroid cancer through intracellular Ca2+, cFOS and autophagy dependent pathways
(Submitter supplied) About 20-30% of patients with metastatic non-medullary thyroid cancer (TC) have persistent or recurrent disease resulting from tumor dedifferentiation. Tumor redifferentiation to restore sensitivity to radioactive iodine therapy is considered a promising strategy to overcome RAI resistance. Autophagy has emerged as an important mechanism in cancer dedifferentiation. Here, we demonstrate the therapeutic potential of autophagy activation for redifferentiation in thyroid cancer cell lines. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 27 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79400/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA315704
Series		Accession: GSE79400	ID: 200079400

3370. Development of diagnostic exosomal biomarkers for the detection of invasive non-functional pituitary adenomas (NFPAs)
(Submitter supplied) The incomplete surgical resection of invasive non-functional pituitary adenomas (iNFPAs) carries the increased risk of complications and requires adjuvant radiotherapy and medications. Thus, the molecular mechanisms and markers of invasiveness must be identified to guide the management of NFPA patients. This study explores the proteomic and transcriptomic variations of invasive and non-invasive NFPAs and other types of pituitary adenomas and evaluates the genetic markers in the exosome related to iNFPAs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 2 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89779/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA353245
Series		Accession: GSE89779	ID: 200089779

3371. Genetic and Epigenetic Landscapes of Laterally Spreading Tumors of the Colorectum
(Submitter supplied) Laterally spreading tumors (LSTs) are colorectal adenomas that develop into extremely large lesions but rarely become malignant. Elucidating their molecular profiles, and how these contrast with colorectal cancer (CRC), offers the opportunity to understand their biology and how they are able to grow to such large lesions without progressing to cancer. Profiling of 11 LSTs with multiple genome-wide approaches showed mutation rates comparable with microsatellite stable CRCs at 2.4 versus 2.6 mutations per megabase respectively, however copy number alterations are infrequent (averaging 1.5 per LST). more...
Organism:	Homo sapiens
Type:		Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL10999 GPL11154 39 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77635/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA311063
Series		Accession: GSE77635	ID: 200077635

3372. Loss of EGFR-DDEF1 signaling in metastatic and unresectable hepatoblastoma
(Submitter supplied) We report that the application of PE sequencing of mRNA in hepatoblastoma patient biopsies effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. 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/GSE89nnn/GSE89775/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA353132
Series		Accession: GSE89775	ID: 200089775

3373. Verification of the quality of the retroviral cDNA library composed of 176 proto-oncogenes and HOX genes
(Submitter supplied) We constructed retroviral cDNA library of 176 proto-oncogenes and HOX genes to screen for the leukemia initiating gene combinations. The present submission is the NGS data of the PCR products of the whole inserts from the library itself and the bone marrow cells infected with retroviral library
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/GSE74nnn/GSE74806/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA301591
Series		Accession: GSE74806	ID: 200074806

3374. Small molecules modulate chromatin accessibility to promote NEUROG2-mediated fibroblast-to-neuron reprogramming [RNA-seq]
(Submitter supplied) Pro-neural transcription factors and small molecules can induce the transdifferentiation of fibroblasts into functional neurons; however, a molecular mechanism detailing the immediate-early events that catalyze this conversion has not been well defined. We previously demonstrated that NEUROG2, forskolin (F), and dorsomorphin (D) can induce functional neurons with high-efficiency. Here, we used this model to define the genetic and epigenetic events that initiate an acquisition of neuronal identity. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 36 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75906/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA305689
Series		Accession: GSE75906	ID: 200075906

3375. shRNA RNA-seq from HepG2 (ENCSR998MZP)
(Submitter supplied) shRNA knockdown against PRPF8 in HepG2 cells followed by RNA-seq. (PRPF8_BGHLV17)  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/GSE88nnn/GSE88696/
Series		Accession: GSE88696	ID: 200088696

3376. shRNA RNA-seq from HepG2 (ENCSR995RPB)
(Submitter supplied) shRNA knockdown against SUPV3L1 in HepG2 cells followed by RNA-seq. (SUPV3L1_BGHLV17)  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/GSE88nnn/GSE88693/
Series		Accession: GSE88693	ID: 200088693

3377. shRNA RNA-seq from HepG2 (ENCSR995JMS)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPM. (HNRNPM_BGHLV30)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88692/
Series		Accession: GSE88692	ID: 200088692

3378. shRNA RNA-seq from HepG2 (ENCSR992JGE)
(Submitter supplied) shRNA knockdown against METAP2 in HepG2 cells followed by RNA-seq. (METAP2_BGHLV16)  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/GSE88nnn/GSE88691/
Series		Accession: GSE88691	ID: 200088691

3379. siRNA RNA-seq from K562 (ENCSR989NEA)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting TBL1XR1.  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/GSE88nnn/GSE88689/
Series		Accession: GSE88689	ID: 200088689

3380. shRNA RNA-seq from K562 (ENCSR984CLJ)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against KIAA1967. (KIAA1967_BGKLV25)  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/GSE88nnn/GSE88687/
Series		Accession: GSE88687	ID: 200088687

3381. shRNA RNA-seq from K562 (ENCSR978CSQ)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against PKM2. (PKM2_BGKLV21-B)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88685/
Series		Accession: GSE88685	ID: 200088685

3382. siRNA RNA-seq from K562 (ENCSR977SOT)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting CEBPZ.  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/GSE88nnn/GSE88684/
Series		Accession: GSE88684	ID: 200088684

3383. shRNA RNA-seq from K562 (ENCSR973QSV)
(Submitter supplied) shRNA knockdown against AATF in K562 cells followed by RNA-seq. (AATF BGKLV13)  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/GSE88nnn/GSE88683/
Series		Accession: GSE88683	ID: 200088683

3384. shRNA RNA-seq from HepG2 (ENCSR968YWY)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against GPKOW. (GPKOW_BGHLV35)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88681/
Series		Accession: GSE88681	ID: 200088681

3385. shRNA RNA-seq from HepG2 (ENCSR968BBQ)
(Submitter supplied) Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV22B)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88678/
Series		Accession: GSE88678	ID: 200088678

3386. siRNA RNA-seq from K562 (ENCSR965CCM)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting ZNF384.  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/GSE88nnn/GSE88676/
Series		Accession: GSE88676	ID: 200088676

3387. shRNA RNA-seq from HepG2 (ENCSR964YTW)
(Submitter supplied) shRNA knockdown against DDX55 in HepG2 cells followed by RNA-seq. (DDX55_BGHLV17)  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/GSE88nnn/GSE88675/
Series		Accession: GSE88675	ID: 200088675

3388. shRNA RNA-seq from K562 (ENCSR963RLK)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against APOBEC3C. (APOBEC3C_BGKLV25)  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/GSE88nnn/GSE88674/
Series		Accession: GSE88674	ID: 200088674

3389. shRNA RNA-seq from HepG2 (ENCSR960MSV)
(Submitter supplied) Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV27B)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88672/
Series		Accession: GSE88672	ID: 200088672

3390. shRNA RNA-seq from K562 (ENCSR958NDU)
(Submitter supplied) shRNA knockdown against HLTF in K562 cells followed by RNA-seq. (HLTF BGKLV13)  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/GSE88nnn/GSE88671/
Series		Accession: GSE88671	ID: 200088671

3391. shRNA RNA-seq from HepG2 (ENCSR958KSY)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against AKAP8. (AKAP8_BGHLV27)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88670/
Series		Accession: GSE88670	ID: 200088670

3392. shRNA RNA-seq from K562 (ENCSR954HAY)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against SART3. (SART3_BGKLV24_B)  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/GSE88nnn/GSE88667/
Series		Accession: GSE88667	ID: 200088667

3393. shRNA RNA-seq from HepG2 (ENCSR946OFN)
(Submitter supplied) shRNA knockdown against TROVE2 in HepG2 cells followed by RNA-seq. (TROVE2_BGHLV16)  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/GSE88nnn/GSE88665/
Series		Accession: GSE88665	ID: 200088665

3394. shRNA RNA-seq from HepG2 (ENCSR945XKW)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against PUM1. (PUM1-BGHLV23)  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/GSE88nnn/GSE88664/
Series		Accession: GSE88664	ID: 200088664

3395. shRNA RNA-seq from K562 (ENCSR945GUR)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against NAA15. (NAA15_BGKLV32)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88663/
Series		Accession: GSE88663	ID: 200088663

3396. shRNA RNA-seq from K562 (ENCSR943LIB)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against SNRNP200. (SNRNP200_BGKLV28)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88661/
Series		Accession: GSE88661	ID: 200088661

3397. shRNA RNA-seq from K562 (ENCSR942UNX)
(Submitter supplied) RNA-seq on K562 cells treated with a control shRNA against no target. (K-NT-30B)  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/GSE88nnn/GSE88660/
Series		Accession: GSE88660	ID: 200088660

3398. shRNA RNA-seq from HepG2 (ENCSR942MBU)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against ILF3. (ILF3-BGHLV22)  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/GSE88nnn/GSE88659/
Series		Accession: GSE88659	ID: 200088659

3399. shRNA RNA-seq from K562 (ENCSR936VPP)
(Submitter supplied) RNA-seq on K562 cells treated with a control shRNA against no target. (k562-shC)  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/GSE88nnn/GSE88657/
Series		Accession: GSE88657	ID: 200088657

3400. shRNA RNA-seq from K562 (ENCSR936TED)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against POLR2G. (K-POLR2G-30B)  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/GSE88nnn/GSE88655/
Series		Accession: GSE88655	ID: 200088655

3401. polyA mRNA RNA-seq from HepG2 (ENCSR931WGT)
(Submitter supplied) Initial cytosolic fractions on HepG2 Long Poly-A+ from Lecuyer  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/GSE88nnn/GSE88654/
Series		Accession: GSE88654	ID: 200088654

3402. shRNA RNA-seq from HepG2 (ENCSR929PXS)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against CEBPZ. (CEBPZ_BGHLV30)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88651/
Series		Accession: GSE88651	ID: 200088651

3403. shRNA RNA-seq from K562 (ENCSR927XBT)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against NUSAP1. (NUSAP1_BGKLV21)  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/GSE88nnn/GSE88650/
Series		Accession: GSE88650	ID: 200088650

3404. shRNA RNA-seq from K562 (ENCSR927TSP)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against TIAL1. (TIAL1_BGKLV21)  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/GSE88nnn/GSE88649/
Series		Accession: GSE88649	ID: 200088649

3405. shRNA RNA-seq from HepG2 (ENCSR927SLP)
(Submitter supplied) shRNA knockdown against LIN28B in HepG2 cells followed by RNA-seq. (LIN28B_BGHLV18)  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/GSE88nnn/GSE88648/
Series		Accession: GSE88648	ID: 200088648

3406. shRNA RNA-seq from HepG2 (ENCSR925SYZ)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against BOP1. (BOP1_BGHLV35)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88647/
Series		Accession: GSE88647	ID: 200088647

3407. shRNA RNA-seq from K562 (ENCSR925RNE)
(Submitter supplied) shRNA knockdown against SERBP1 in K562 cells followed by RNA-seq. (SERBP1_BGKLV19)  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/GSE88nnn/GSE88646/
Series		Accession: GSE88646	ID: 200088646

3408. shRNA RNA-seq from K562 (ENCSR921KDS)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against RCC2. (RCC2_BGKLV21)  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/GSE88nnn/GSE88645/
Series		Accession: GSE88645	ID: 200088645

3409. shRNA RNA-seq from HepG2 (ENCSR913ZWR)
(Submitter supplied) shRNA knockdown against DDX52 in HepG2 cells followed by RNA-seq. (DDX52_BGHLV16)  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/GSE88nnn/GSE88642/
Series		Accession: GSE88642	ID: 200088642

3410. shRNA RNA-seq from HepG2 (ENCSR912EHP)
(Submitter supplied) shRNA knockdown against PES1 in HepG2 cells followed by RNA-seq. (PES1_BGHLV17)  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/GSE88nnn/GSE88641/
Series		Accession: GSE88641	ID: 200088641

3411. shRNA RNA-seq from K562 (ENCSR911DGK)
(Submitter supplied) shRNA knockdown against TFIP11 in K562 cells followed by RNA-seq. (TFIP11_BGKLV19)  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/GSE88nnn/GSE88640/
Series		Accession: GSE88640	ID: 200088640

3412. shRNA RNA-seq from HepG2 (ENCSR910YNJ)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against PABPC1. (PABPC1-BGHLV22)  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/GSE88nnn/GSE88639/
Series		Accession: GSE88639	ID: 200088639

3413. shRNA RNA-seq from HepG2 (ENCSR910ECL)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against UTP3. (UTP3_BGHLV33)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88638/
Series		Accession: GSE88638	ID: 200088638

3414. shRNA RNA-seq from K562 (ENCSR907UTB)
(Submitter supplied) shRNA knockdown against DAZAP1 in K562 cells followed by RNA-seq. (DAZAP1 BGKLV13)  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/GSE88nnn/GSE88637/
Series		Accession: GSE88637	ID: 200088637

3415. shRNA RNA-seq from HepG2 (ENCSR905HID)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against FMR1. (FMR1-BGHLV23)  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/GSE88nnn/GSE88636/
Series		Accession: GSE88636	ID: 200088636

3416. shRNA RNA-seq from K562 (ENCSR902WSK)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against SSRP1. (SSRP1_BGKLV29)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88635/
Series		Accession: GSE88635	ID: 200088635

3417. shRNA RNA-seq from K562 (ENCSR898OPN)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against RBM17. (RBM17_BGKLV29-B)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88633/
Series		Accession: GSE88633	ID: 200088633

3418. shRNA RNA-seq from K562 (ENCSR898NWE)
(Submitter supplied) Control shRNA against no target in K562 cells followed by RNA-seq  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/GSE88nnn/GSE88632/
Series		Accession: GSE88632	ID: 200088632

3419. shRNA RNA-seq from HepG2 (ENCSR896MMU)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against MSI2. (MSI2_BGHLV30)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88631/
Series		Accession: GSE88631	ID: 200088631

3420. shRNA RNA-seq from HepG2 (ENCSR896CFV)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against SF3B1. (SF3B1_BGHLV35)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88630/
Series		Accession: GSE88630	ID: 200088630

3421. shRNA RNA-seq from K562 (ENCSR891DYO)
(Submitter supplied) shRNA knockdown against PES1 in K562 cells followed by RNA-seq. (PES1_BGKLV19)  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/GSE88nnn/GSE88629/
Series		Accession: GSE88629	ID: 200088629

3422. shRNA RNA-seq from K562 (ENCSR891AXF)
(Submitter supplied) shRNA knockdown against SSB in K562 cells followed by RNA-seq. (SSB BGKLV13)  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/GSE88nnn/GSE88628/
Series		Accession: GSE88628	ID: 200088628

3423. total RNA-seq from HepG2 (ENCSR887ZSY)
(Submitter supplied) Initial membrane fractions on HepG2 Long Total from Lecuyer  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/GSE88nnn/GSE88626/
Series		Accession: GSE88626	ID: 200088626

3424. shRNA RNA-seq from K562 (ENCSR885YOI)
(Submitter supplied) shRNA knockdown against CSTF2 in K562 cells followed by RNA-seq. (CSTF2_BGKLV19)  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/GSE88nnn/GSE88623/
Series		Accession: GSE88623	ID: 200088623

3425. total RNA-seq from K562 (ENCSR885DVH)
(Submitter supplied) Initial total fractions on K562 Long Total from Lecuyer  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/GSE88nnn/GSE88622/
Series		Accession: GSE88622	ID: 200088622

3426. shRNA RNA-seq from HepG2 (ENCSR883BXR)
(Submitter supplied) shRNA knockdown against LSM11 in HepG2 cells followed by RNA-seq. (LSM11_BGHLV18)  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/GSE88nnn/GSE88620/
Series		Accession: GSE88620	ID: 200088620

3427. shRNA RNA-seq from HepG2 (ENCSR880DEH)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against PNPT1. (PNPT1-BGHLV22)  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/GSE88nnn/GSE88617/
Series		Accession: GSE88617	ID: 200088617

3428. siRNA RNA-seq from K562 (ENCSR874ZXG)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting E2F4.  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/GSE88nnn/GSE88612/
Series		Accession: GSE88612	ID: 200088612

3429. shRNA RNA-seq from K562 (ENCSR874ZLI)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against CCDC124. (CCDC124_BGKLV32)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88611/
Series		Accession: GSE88611	ID: 200088611

3430. shRNA RNA-seq from K562 (ENCSR874DVZ)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against GLRX3. (GLRX3_BGKLV34)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88610/
Series		Accession: GSE88610	ID: 200088610

3431. shRNA RNA-seq from HepG2 (ENCSR871BXO)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against STIP1. (STIP1-BGHLV22)  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/GSE88nnn/GSE88609/
Series		Accession: GSE88609	ID: 200088609

3432. shRNA RNA-seq from K562 (ENCSR866XLI)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against LARP4. (LARP4_BGKLV28)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88607/
Series		Accession: GSE88607	ID: 200088607

3433. total RNA-seq from HepG2 (ENCSR862HPO)
(Submitter supplied) Initial cytosolic fractions on HepG2 Long Total from Lecuyer  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/GSE88nnn/GSE88604/
Series		Accession: GSE88604	ID: 200088604

3434. total RNA-seq from K562 (ENCSR860DWK)
(Submitter supplied) Initial cytosolic fractions on K562 Long Total from Lecuyer  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/GSE88nnn/GSE88602/
Series		Accession: GSE88602	ID: 200088602

3435. shRNA RNA-seq from HepG2 (ENCSR856ZRV)
(Submitter supplied) Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV17)  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/GSE88nnn/GSE88598/
Series		Accession: GSE88598	ID: 200088598

3436. shRNA RNA-seq from K562 (ENCSR856CJK)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against DDX55. (DDX55_BGKLV21)  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/GSE88nnn/GSE88597/
Series		Accession: GSE88597	ID: 200088597

3437. RAMPAGE from OCI-LY7 (ENCSR855LXJ)
(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 RAMPAGE 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 (BED, BIGBED, BIGWIG, GFF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88596/
Series		Accession: GSE88596	ID: 200088596

3438. shRNA RNA-seq from HepG2 (ENCSR853PBF)
(Submitter supplied) shRNA knockdown against DHX30 in HepG2 cells followed by RNA-seq. (DHX30-32-BGHLV20)  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/GSE88nnn/GSE88593/
Series		Accession: GSE88593	ID: 200088593

3439. RAMPAGE from SK-N-DZ (ENCSR852KOV)
(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 PE101 Illumina Hi-Seq RAMPAGE 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 (BED, BIGBED, BIGWIG, GFF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88591/
Series		Accession: GSE88591	ID: 200088591

3440. shRNA RNA-seq from HepG2 (ENCSR851KEX)
(Submitter supplied) shRNA knockdown against PPIL4 in HepG2 cells followed by RNA-seq. (PPIL4-BGHLV20)  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/GSE88nnn/GSE88590/
Series		Accession: GSE88590	ID: 200088590

3441. shRNA RNA-seq from K562 (ENCSR850PWM)
(Submitter supplied) shRNA knockdown against ZRANB2 in K562 cells followed by RNA-seq. (ZRANB2 BGKLV13)  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/GSE88nnn/GSE88589/
Series		Accession: GSE88589	ID: 200088589

3442. shRNA RNA-seq from HepG2 (ENCSR850FEH)
(Submitter supplied) shRNA knockdown against GRWD1 in HepG2 cells followed by RNA-seq. (GRWD1_BGHLV18)  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/GSE88nnn/GSE88587/
Series		Accession: GSE88587	ID: 200088587

3443. shRNA RNA-seq from K562 (ENCSR844QNT)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against PPP1R8. (PPP1R8_BGKLV28)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88584/
Series		Accession: GSE88584	ID: 200088584

3444. shRNA RNA-seq from K562 (ENCSR843LYF)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against YTHDC2. (YTHDC2_BGKLV28)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88582/
Series		Accession: GSE88582	ID: 200088582

3445. shRNA RNA-seq from HepG2 (ENCSR838SMC)
(Submitter supplied) shRNA knockdown against RPS5 in HepG2 cells followed by RNA-seq. (RPS5_BGHLV18)  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/GSE88nnn/GSE88578/
Series		Accession: GSE88578	ID: 200088578

3446. shRNA RNA-seq from HepG2 (ENCSR837QDN)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against SUGP2. (SUGP2_BGHLV27)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88576/
Series		Accession: GSE88576	ID: 200088576

3447. RAMPAGE from Karpas-422 (ENCSR836WAX)
(Submitter supplied) The libraries contained in this experiment come from independent growths of cell line Karpas-422. They are stranded PE101 Illumina Hi-Seq RAMPAGE 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 (BED, BIGBED, BIGWIG, GFF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88575/
Series		Accession: GSE88575	ID: 200088575

3448. shRNA RNA-seq from K562 (ENCSR835RMN)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against GRSF1. (GRSF1_BGKLV29-B)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88574/
Series		Accession: GSE88574	ID: 200088574

3449. shRNA RNA-seq from K562 (ENCSR829EFL)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against NSUN2. (NSUN2_BGKLV34)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88572/
Series		Accession: GSE88572	ID: 200088572

3450. shRNA RNA-seq from HepG2 (ENCSR825QXH)
(Submitter supplied) shRNA knockdown against PARN in HepG2 cells followed by RNA-seq. (PARN-BGHLV20)  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/GSE88nnn/GSE88570/
Series		Accession: GSE88570	ID: 200088570

3451. RAMPAGE from NCI-H460 (ENCSR824YLV)
(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 RAMPAGE 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 (BED, BIGBED, BIGWIG, GFF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88569/
Series		Accession: GSE88569	ID: 200088569

3452. shRNA RNA-seq from K562 (ENCSR823WTA)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against KIF1C. (KIF1C_BGKLV32)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88568/
Series		Accession: GSE88568	ID: 200088568

3453. shRNA RNA-seq from HepG2 (ENCSR820ROH)
(Submitter supplied) shRNA knockdown against SERBP1 in HepG2 cells followed by RNA-seq. (SERBP1_BGHLV16)  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/GSE88nnn/GSE88566/
Series		Accession: GSE88566	ID: 200088566

3454. shRNA RNA-seq from HepG2 (ENCSR815JDY)
(Submitter supplied) shRNA knockdown against CSTF2 in HepG2 cells followed by RNA-seq. (CSTF2_BGHLV17)  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/GSE88nnn/GSE88564/
Series		Accession: GSE88564	ID: 200088564

3455. shRNA RNA-seq from K562 (ENCSR815CVQ)
(Submitter supplied) Control shRNA against no target in K562 cells followed by RNA-seq. (NT BGKLV13)  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/GSE88nnn/GSE88563/
Series		Accession: GSE88563	ID: 200088563

3456. shRNA RNA-seq from K562 (ENCSR813NZP)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against SRFBP1. (SRFBP1_BGKLV21)  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/GSE88nnn/GSE88562/
Series		Accession: GSE88562	ID: 200088562

3457. total RNA-seq from HepG2 (ENCSR813BDU)
(Submitter supplied) Initial insoluble cytoplasmic fractions on HepG2 Long Total from Lecuyer  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/GSE88nnn/GSE88561/
Series		Accession: GSE88561	ID: 200088561

3458. shRNA RNA-seq from K562 (ENCSR812TLY)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against AGGF1. (AGGF1_BGKLV32)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88560/
Series		Accession: GSE88560	ID: 200088560

3459. shRNA RNA-seq from K562 (ENCSR812EIA)
(Submitter supplied) shRNA knockdown against EXOSC9 in K562 cells followed by RNA-seq. (EXOSC9 BGKLV13)  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/GSE88nnn/GSE88558/
Series		Accession: GSE88558	ID: 200088558

3460. shRNA RNA-seq from HepG2 (ENCSR810JYX)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against SUCLG1. (SUCLG1-BGHLV23)  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/GSE88nnn/GSE88556/
Series		Accession: GSE88556	ID: 200088556

3461. shRNA RNA-seq from K562 (ENCSR810FHY)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against UPF2. (UPF2_BGKLV21-B)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88555/
Series		Accession: GSE88555	ID: 200088555

3462. shRNA RNA-seq from K562 (ENCSR809ISU)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against AKAP8L. (AKAP8L_BGKLV32)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88553/
Series		Accession: GSE88553	ID: 200088553

3463. shRNA RNA-seq from HepG2 (ENCSR808FBR)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX5. (DDX5_BGHLV30)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88552/
Series		Accession: GSE88552	ID: 200088552

3464. shRNA RNA-seq from HepG2 (ENCSR807ODB)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against AKAP8L. (AKAP8L_BGHLV31)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88551/
Series		Accession: GSE88551	ID: 200088551

3465. shRNA RNA-seq from K562 (ENCSR795VAK)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against CPEB4. (CPEB4_BGKLV25)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88545/
Series		Accession: GSE88545	ID: 200088545

3466. shRNA RNA-seq from K562 (ENCSR794NUE)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPA2B1. (HNRNPA2B1_BGKLV28)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88544/
Series		Accession: GSE88544	ID: 200088544

3467. siRNA RNA-seq from K562 (ENCSR793ISR)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting BACH1.  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/GSE88nnn/GSE88543/
Series		Accession: GSE88543	ID: 200088543

3468. shRNA RNA-seq from K562 (ENCSR788YGG)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against RPS3A. (RPS3A_BGKLV24_B)  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/GSE88nnn/GSE88541/
Series		Accession: GSE88541	ID: 200088541

3469. shRNA RNA-seq from HepG2 (ENCSR788HVK)
(Submitter supplied) shRNA knockdown against EIF3D in HepG2 cells followed by RNA-seq. (EIF3D_BGHLV16)  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/GSE88nnn/GSE88540/
Series		Accession: GSE88540	ID: 200088540

3470. RAMPAGE from SK-N-DZ (ENCSR786DTS)
(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 RAMPAGE 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 (BED, BIGBED, BIGWIG, GFF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88539/
Series		Accession: GSE88539	ID: 200088539

3471. shRNA RNA-seq from HepG2 (ENCSR784FTX)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against KHDRBS1. (KHDRBS1-BGHLV22)  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/GSE88nnn/GSE88538/
Series		Accession: GSE88538	ID: 200088538

3472. shRNA RNA-seq from K562 (ENCSR783YSQ)
(Submitter supplied) shRNA knockdown against RTF1 in K562 cells followed by RNA-seq. (RTF1 BGKLV13)  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/GSE88nnn/GSE88537/
Series		Accession: GSE88537	ID: 200088537

3473. shRNA RNA-seq from K562 (ENCSR783LUA)
(Submitter supplied) shRNA knockdown against PRPF6 in K562 cells followed by RNA-seq. (PRPF6 BGKLV13)  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/GSE88nnn/GSE88536/
Series		Accession: GSE88536	ID: 200088536

3474. shRNA RNA-seq from HepG2 (ENCSR782MXN)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against SFPQ. (SFPQ_BGHLV26)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88535/
Series		Accession: GSE88535	ID: 200088535

3475. shRNA RNA-seq from HepG2 (ENCSR781YNI)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against SRSF5. (SRSF5-BGHLV23)  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/GSE88nnn/GSE88533/
Series		Accession: GSE88533	ID: 200088533

3476. shRNA RNA-seq from K562 (ENCSR778WPL)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPAB. (HNRNPAB_BGKLV24_B)  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/GSE88nnn/GSE88530/
Series		Accession: GSE88530	ID: 200088530

3477. shRNA RNA-seq from K562 (ENCSR778SIU)
(Submitter supplied) shRNA knockdown against SUPV3L1 in K562 cells followed by RNA-seq. (SUPV3L1_BGKLV19)  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/GSE88nnn/GSE88529/
Series		Accession: GSE88529	ID: 200088529

3478. shRNA RNA-seq from HepG2 (ENCSR778RWJ)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against XPO5. (XPO5-BGHLV22)  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/GSE88nnn/GSE88528/
Series		Accession: GSE88528	ID: 200088528

3479. shRNA RNA-seq from K562 (ENCSR777EDL)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against STAU1. (STAU1_BGKLV29)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88527/
Series		Accession: GSE88527	ID: 200088527

3480. shRNA RNA-seq from HepG2 (ENCSR776SXA)
(Submitter supplied) Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV30B)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88526/
Series		Accession: GSE88526	ID: 200088526

3481. shRNA RNA-seq from K562 (ENCSR775TMW)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against BOP1. (BOP1_BGKLV36)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88525/
Series		Accession: GSE88525	ID: 200088525

3482. shRNA RNA-seq from K562 (ENCSR771ZZL)
(Submitter supplied) RNA-seq on K562 cells treated with a control shRNA against no target. (K-NT-25B)  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/GSE88nnn/GSE88524/
Series		Accession: GSE88524	ID: 200088524

3483. shRNA RNA-seq from HepG2 (ENCSR771QMJ)
(Submitter supplied) shRNA knockdown against GEMIN5 in HepG2 cells followed by RNA-seq. (GEMIN5_BGHLV16)  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/GSE88nnn/GSE88523/
Series		Accession: GSE88523	ID: 200088523

3484. shRNA RNA-seq from K562 (ENCSR770OWW)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against LARP7. (LARP7_BGKLV21)  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/GSE88nnn/GSE88522/
Series		Accession: GSE88522	ID: 200088522

3485. shRNA RNA-seq from K562 (ENCSR770LYW)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against SAFB2. (SAFB2_BGKLV24)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88521/
Series		Accession: GSE88521	ID: 200088521

3486. shRNA RNA-seq from HepG2 (ENCSR769GES)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPA2B1. (HNRNPA2B1-BGHLV23)  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/GSE88nnn/GSE88520/
Series		Accession: GSE88520	ID: 200088520

3487. shRNA RNA-seq from HepG2 (ENCSR767LLP)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against RBFOX2. (RBFOX2_BGHLV26)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88519/
Series		Accession: GSE88519	ID: 200088519

3488. shRNA RNA-seq from K562 (ENCSR762FEO)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against LSM11. (LSM11_BGKLV21)  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/GSE88nnn/GSE88516/
Series		Accession: GSE88516	ID: 200088516

3489. shRNA RNA-seq from HepG2 (ENCSR760EGM)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against RBM39. (RBM39_BGHLV26)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88515/
Series		Accession: GSE88515	ID: 200088515

3490. siRNA RNA-seq from K562 (ENCSR756JGE)
(Submitter supplied) Control siRNA against no target in K562 cells followed by RNA-seq.  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/GSE88nnn/GSE88514/
Series		Accession: GSE88514	ID: 200088514

3491. shRNA RNA-seq from HepG2 (ENCSR755KOM)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against FUBP3. (FUBP3-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/GSE88nnn/GSE88513/
Series		Accession: GSE88513	ID: 200088513

3492. shRNA RNA-seq from K562 (ENCSR754RJA)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against NUFIP2. (NUFIP2_BGKLV34)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88511/
Series		Accession: GSE88511	ID: 200088511

3493. shRNA RNA-seq from K562 (ENCSR746NIM)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPM. (HNRNPM_BGKLV29)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88507/
Series		Accession: GSE88507	ID: 200088507

3494. shRNA RNA-seq from K562 (ENCSR745WVZ)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against PUM1. (PUM1-BGKLV25)  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/GSE88nnn/GSE88506/
Series		Accession: GSE88506	ID: 200088506

3495. shRNA RNA-seq from HepG2 (ENCSR744YVR)
(Submitter supplied) shRNA knockdown against PSIP1 in HepG2 cells followed by RNA-seq. (PSIP1_BGHLV18)  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/GSE88nnn/GSE88505/
Series		Accession: GSE88505	ID: 200088505

3496. shRNA RNA-seq from HepG2 (ENCSR744PAQ)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against LARP4. (LARP4_BGHLV20)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88504/
Series		Accession: GSE88504	ID: 200088504

3497. shRNA RNA-seq from HepG2 (ENCSR741YCA)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against TBRG4. (TBRG4_BGHLV27)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88502/
Series		Accession: GSE88502	ID: 200088502

3498. shRNA RNA-seq from K562 (ENCSR732ICL)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPU. (K-HNRNPU)  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/GSE88nnn/GSE88498/
Series		Accession: GSE88498	ID: 200088498

3499. shRNA RNA-seq from HepG2 (ENCSR728BOL)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against FASTKD1. (FASTKD1-BGHLV22)  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/GSE88nnn/GSE88496/
Series		Accession: GSE88496	ID: 200088496

3500. shRNA RNA-seq from K562 (ENCSR721MXZ)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against ABCF1. (ABCF1_BGKLV29)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88493/
Series		Accession: GSE88493	ID: 200088493

3501. shRNA RNA-seq from HepG2 (ENCSR720BPO)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPA0. (HNRNPA0-BGHLV22)  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/GSE88nnn/GSE88492/
Series		Accession: GSE88492	ID: 200088492

3502. shRNA RNA-seq from K562 (ENCSR717SJA)
(Submitter supplied) shRNA knockdown against XRN2 in K562 cells followed by RNA-seq. (XRN2_BGKLV19)  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/GSE88nnn/GSE88489/
Series		Accession: GSE88489	ID: 200088489

3503. shRNA RNA-seq from K562 (ENCSR715XZS)
(Submitter supplied) shRNA knockdown against XRCC5 in K562 cells followed by RNA-seq. (XRCC5 BGKLV13)  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/GSE88nnn/GSE88488/
Series		Accession: GSE88488	ID: 200088488

3504. shRNA RNA-seq from HepG2 (ENCSR713OLV)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against ATP5C1. (ATP5C1_BGHLV30)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88487/
Series		Accession: GSE88487	ID: 200088487

3505. shRNA RNA-seq from K562 (ENCSR712CSN)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against EIF4G1. (EIF4G1_BGKLV24)  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/GSE88nnn/GSE88486/
Series		Accession: GSE88486	ID: 200088486

3506. shRNA RNA-seq from HepG2 (ENCSR711ZJQ)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against RBM47. (RBM47-BGHLV22)  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/GSE88nnn/GSE88485/
Series		Accession: GSE88485	ID: 200088485

3507. shRNA RNA-seq from HepG2 (ENCSR710NWE)
(Submitter supplied) shRNA knockdown against IGF2BP3 in HepG2 cells followed by RNA-seq. (IGF2BP3-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/GSE88nnn/GSE88484/
Series		Accession: GSE88484	ID: 200088484

3508. shRNA RNA-seq from HepG2 (ENCSR706SXN)
(Submitter supplied) shRNA knockdown against RPL23A in HepG2 cells followed by RNA-seq. (RPL23A_BGHLV18)  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/GSE88nnn/GSE88480/
Series		Accession: GSE88480	ID: 200088480

3509. shRNA RNA-seq from HepG2 (ENCSR701GSV)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against MTPAP. (MTPAP_BGHLV35)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88478/
Series		Accession: GSE88478	ID: 200088478

3510. RAMPAGE from Daoy (ENCSR700NMZ)
(Submitter supplied) The libraries contained in this experiment come from independent growths of cell line Daoy isolated from the cerebellar region of a 4 year old caucasian male with desmoplastic cerebellar medulloblastoma. They are stranded PE101 Illumina Hi-Seq RAMPAGE 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 (BED, BIGBED, BIGWIG, GFF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88476/
Series		Accession: GSE88476	ID: 200088476

3511. shRNA RNA-seq from K562 (ENCSR697GLD)
(Submitter supplied) shRNA knockdown against SRSF4 in K562 cells followed by RNA-seq. (SRSF4 BGKLV13)  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/GSE88nnn/GSE88474/
Series		Accession: GSE88474	ID: 200088474

3512. total RNA-seq from K562 (ENCSR696YIB)
(Submitter supplied) Initial insoluble fractions on K562 Long Total from Lecuyer  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/GSE88nnn/GSE88473/
Series		Accession: GSE88473	ID: 200088473

3513. shRNA RNA-seq from HepG2 (ENCSR696LLZ)
(Submitter supplied) shRNA knockdown against NIP7 in HepG2 cells followed by RNA-seq. (NIP7_BGHLV18)  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/GSE88nnn/GSE88472/
Series		Accession: GSE88472	ID: 200088472

3514. shRNA RNA-seq from HepG2 (ENCSR695XOD)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against CUGBP1. (CUGBP1-BGHLV23)  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/GSE88nnn/GSE88471/
Series		Accession: GSE88471	ID: 200088471

3515. shRNA RNA-seq from HepG2 (ENCSR693MZJ)
(Submitter supplied) shRNA knockdown against HNRNPF in HepG2 cells followed by RNA-seq. (HNRNPF-BGHLV20)  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/GSE88nnn/GSE88470/
Series		Accession: GSE88470	ID: 200088470

3516. shRNA RNA-seq from HepG2 (ENCSR691IVR)
(Submitter supplied) Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV33)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88469/
Series		Accession: GSE88469	ID: 200088469

3517. shRNA RNA-seq from HepG2 (ENCSR689ZJC)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPUL1. (HNRNPUL1_BGHLV26)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88468/
Series		Accession: GSE88468	ID: 200088468

3518. shRNA RNA-seq from HepG2 (ENCSR689PHN)
(Submitter supplied) Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV16)  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/GSE88nnn/GSE88467/
Series		Accession: GSE88467	ID: 200088467

3519. shRNA RNA-seq from HepG2 (ENCSR689MIY)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against UPF1. (UPF1_BGHLV33)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88466/
Series		Accession: GSE88466	ID: 200088466

3520. shRNA RNA-seq from HepG2 (ENCSR685JXU)
(Submitter supplied) shRNA knockdown against RCC2 in HepG2 cells followed by RNA-seq. (RCC2_BGHLV18)  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/GSE88nnn/GSE88463/
Series		Accession: GSE88463	ID: 200088463

3521. shRNA RNA-seq from HepG2 (ENCSR684HTV)
(Submitter supplied) shRNA knockdown against UCHL5 in HepG2 cells followed by RNA-seq. (UCHL5_BGHLV17)  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/GSE88nnn/GSE88462/
Series		Accession: GSE88462	ID: 200088462

3522. shRNA RNA-seq from HepG2 (ENCSR681SMT)
(Submitter supplied) shRNA knockdown against PHF6 in HepG2 cells followed by RNA-seq. (PHF6_BGHLV18)  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/GSE88nnn/GSE88461/
Series		Accession: GSE88461	ID: 200088461

3523. shRNA RNA-seq from K562 (ENCSR678WOA)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against RBM39. (RBM39_BGKLV28)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88459/
Series		Accession: GSE88459	ID: 200088459

3524. shRNA RNA-seq from K562 (ENCSR678MVE)
(Submitter supplied) shRNA knockdown against UCHL5 in K562 cells followed by RNA-seq. (UCHL5_BGKLV19)  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/GSE88nnn/GSE88457/
Series		Accession: GSE88457	ID: 200088457

3525. shRNA RNA-seq from HepG2 (ENCSR676EKU)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against CPSF6. (CPSF6_BGHLV35)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88456/
Series		Accession: GSE88456	ID: 200088456

3526. siRNA RNA-seq from K562 (ENCSR675SDG)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting MAX.  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/GSE88nnn/GSE88455/
Series		Accession: GSE88455	ID: 200088455

3527. shRNA RNA-seq from K562 (ENCSR675KPR)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against RBM3. (K562-RBM3)  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/GSE88nnn/GSE88454/
Series		Accession: GSE88454	ID: 200088454

3528. shRNA RNA-seq from HepG2 (ENCSR674KEK)
(Submitter supplied) Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV18)  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/GSE88nnn/GSE88453/
Series		Accession: GSE88453	ID: 200088453

3529. shRNA RNA-seq from HepG2 (ENCSR674KDQ)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against GRSF1. (GRSF1-BGHLV22)  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/GSE88nnn/GSE88452/
Series		Accession: GSE88452	ID: 200088452

3530. shRNA RNA-seq from HepG2 (ENCSR667RIA)
(Submitter supplied) shRNA knockdown against RPS2 in HepG2 cells followed by RNA-seq. (RPS2_BGHLV18)  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/GSE88nnn/GSE88447/
Series		Accession: GSE88447	ID: 200088447

3531. shRNA RNA-seq from K562 (ENCSR667PLJ)
(Submitter supplied) Control shRNA against no target in K562 cells followed by RNA-seq. (non-target_BGKLV24)  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/GSE88nnn/GSE88446/
Series		Accession: GSE88446	ID: 200088446

3532. shRNA RNA-seq from K562 (ENCSR661HEL)
(Submitter supplied) Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV19-B)  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/GSE88nnn/GSE88443/
Series		Accession: GSE88443	ID: 200088443

3533. shRNA RNA-seq from HepG2 (ENCSR660MZN)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPD. (HNRNPD-BGHLV22)  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/GSE88nnn/GSE88442/
Series		Accession: GSE88442	ID: 200088442

3534. shRNA RNA-seq from K562 (ENCSR660ETT)
(Submitter supplied) shRNA knockdown against EIF3D in K562 cells followed by RNA-seq. (EIF3D_BGKLV19)  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/GSE88nnn/GSE88441/
Series		Accession: GSE88441	ID: 200088441

3535. siRNA RNA-seq from K562 (ENCSR656ZOI)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting LMNB1.  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/GSE88nnn/GSE88440/
Series		Accession: GSE88440	ID: 200088440

3536. shRNA RNA-seq from HepG2 (ENCSR656DQV)
(Submitter supplied) shRNA knockdown against PKM2 in HepG2 cells followed by RNA-seq. (PKM2_BGHLV16)  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/GSE88nnn/GSE88439/
Series		Accession: GSE88439	ID: 200088439

3537. shRNA RNA-seq from HepG2 (ENCSR648BSC)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against PUF60. (PUF60-BGHLV23)  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/GSE88nnn/GSE88434/
Series		Accession: GSE88434	ID: 200088434

3538. shRNA RNA-seq from HepG2 (ENCSR647NYX)
(Submitter supplied) shRNA knockdown against NONO in HepG2 cells followed by RNA-seq. (NONO_BGHLV17)  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/GSE88nnn/GSE88433/
Series		Accession: GSE88433	ID: 200088433

3539. shRNA RNA-seq from HepG2 (ENCSR644AIM)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against SF1. (SF1_BGHLV26)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88430/
Series		Accession: GSE88430	ID: 200088430

3540. shRNA RNA-seq from HepG2 (ENCSR643UFV)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against NOL12. (NOL12-BGHLV23)  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/GSE88nnn/GSE88429/
Series		Accession: GSE88429	ID: 200088429

3541. siRNA RNA-seq from K562 (ENCSR640PVZ)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting MAFK.  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/GSE88nnn/GSE88428/
Series		Accession: GSE88428	ID: 200088428

3542. shRNA RNA-seq from HepG2 (ENCSR639LKS)
(Submitter supplied) shRNA knockdown against FKBP4 in HepG2 cells followed by RNA-seq. (FKBP4_BGHLV17)  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/GSE88nnn/GSE88427/
Series		Accession: GSE88427	ID: 200088427

3543. shRNA RNA-seq from HepG2 (ENCSR635BOO)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against SNRNP70. (SNRNP70_BGHLV35)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88425/
Series		Accession: GSE88425	ID: 200088425

3544. shRNA RNA-seq from HepG2 (ENCSR634KHL)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against HDGF. (HDGF_BGHLV31)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88423/
Series		Accession: GSE88423	ID: 200088423

3545. shRNA RNA-seq from K562 (ENCSR634KBO)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPC. (HNRNPC_BGKLV21)  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/GSE88nnn/GSE88422/
Series		Accession: GSE88422	ID: 200088422

3546. siRNA RNA-seq from K562 (ENCSR631RKH)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting MXI1.  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/GSE88nnn/GSE88420/
Series		Accession: GSE88420	ID: 200088420

3547. shRNA RNA-seq from K562 (ENCSR631RFX)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against MTPAP. (MTPAP_BGKLV34)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88419/
Series		Accession: GSE88419	ID: 200088419

3548. shRNA RNA-seq from HepG2 (ENCSR629RUG)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against NSUN2. (NSUN2_BGHLV35)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88417/
Series		Accession: GSE88417	ID: 200088417

3549. shRNA RNA-seq from K562 (ENCSR628JYB)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against SF1. (K-SF1)  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/GSE88nnn/GSE88416/
Series		Accession: GSE88416	ID: 200088416

3550. shRNA RNA-seq from K562 (ENCSR624XHG)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against RNASEN. (RNASEN50_BGKLV28)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88413/
Series		Accession: GSE88413	ID: 200088413

3551. shRNA RNA-seq from HepG2 (ENCSR624FBY)
(Submitter supplied) shRNA knockdown against LARP7 in HepG2 cells followed by RNA-seq. (LARP7_BGHLV18)  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/GSE88nnn/GSE88412/
Series		Accession: GSE88412	ID: 200088412

3552. shRNA RNA-seq from K562 (ENCSR620PUP)
(Submitter supplied) Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV25)  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/GSE88nnn/GSE88411/
Series		Accession: GSE88411	ID: 200088411

3553. shRNA RNA-seq from HepG2 (ENCSR620OKS)
(Submitter supplied) shRNA knockdown against EFTUD2 in HepG2 cells followed by RNA-seq. (EFTUD2_BGHLV16)  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/GSE88nnn/GSE88410/
Series		Accession: GSE88410	ID: 200088410

3554. shRNA RNA-seq from HepG2 (ENCSR620HAA)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against PPIG. (PPIG_BGHLV27)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88408/
Series		Accession: GSE88408	ID: 200088408

3555. shRNA RNA-seq from K562 (ENCSR618IQH)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against PUS1. (PUS1_BGKLV32)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88407/
Series		Accession: GSE88407	ID: 200088407

3556. shRNA RNA-seq from K562 (ENCSR611LQB)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against PSIP1. (PSIP1_BGKLV21)  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/GSE88nnn/GSE88401/
Series		Accession: GSE88401	ID: 200088401

3557. shRNA RNA-seq from HepG2 (ENCSR610VTA)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against ABCF1. (ABCF1_BGHLV30)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88400/
Series		Accession: GSE88400	ID: 200088400

3558. shRNA RNA-seq from K562 (ENCSR608IAI)
(Submitter supplied) shRNA knockdown against FASTKD2 in K562 cells followed by RNA-seq. (FASTKD2 BGKLV13)  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/GSE88nnn/GSE88397/
Series		Accession: GSE88397	ID: 200088397

3559. siRNA RNA-seq from K562 (ENCSR608CVU)
(Submitter supplied) Control siRNA against no target in K562 cells followed by RNA-seq.  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/GSE88nnn/GSE88396/
Series		Accession: GSE88396	ID: 200088396

3560. shRNA RNA-seq from K562 (ENCSR606QIX)
(Submitter supplied) shRNA knockdown against BCCIP in K562 cells followed by RNA-seq. (BCCIP_BGKLV19)  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/GSE88nnn/GSE88395/
Series		Accession: GSE88395	ID: 200088395

3561. shRNA RNA-seq from K562 (ENCSR605MFS)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against CUGBP1. (CUGBP1_BGKLV25)  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/GSE88nnn/GSE88394/
Series		Accession: GSE88394	ID: 200088394

3562. shRNA RNA-seq from K562 (ENCSR602AWR)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against TUFM. (TUFM-BGKLV25)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88391/
Series		Accession: GSE88391	ID: 200088391

3563. shRNA RNA-seq from K562 (ENCSR599UDS)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against AARS. (AARS_BGKLV21)  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/GSE88nnn/GSE88389/
Series		Accession: GSE88389	ID: 200088389

3564. shRNA RNA-seq from HepG2 (ENCSR599PXD)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against RBM15. (RBM15_BGHLV31)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88388/
Series		Accession: GSE88388	ID: 200088388

3565. shRNA RNA-seq from K562 (ENCSR598YQX)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against LIN28B. (LIN28B_BGKLV21)  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/GSE88nnn/GSE88387/
Series		Accession: GSE88387	ID: 200088387

3566. shRNA RNA-seq from HepG2 (ENCSR598GKQ)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX59. (DDX59_BGHLV35)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88385/
Series		Accession: GSE88385	ID: 200088385

3567. polyA mRNA RNA-seq from K562 (ENCSR596ACL)
(Submitter supplied) Initial membrane fractions on K562 Long Poly-A+ from Lecuyer  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/GSE88nnn/GSE88384/
Series		Accession: GSE88384	ID: 200088384

3568. polyA mRNA RNA-seq from K562 (ENCSR594NJP)
(Submitter supplied) Initial insoluble fractions on K562 Long Poly-A+ from Lecuyer  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/GSE88nnn/GSE88383/
Series		Accession: GSE88383	ID: 200088383

3569. shRNA RNA-seq from HepG2 (ENCSR594DNW)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against CPSF7. (CPSF7_BGHLV30)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88382/
Series		Accession: GSE88382	ID: 200088382

3570. RAMPAGE from PC-3 (ENCSR585QYX)
(Submitter supplied) The libraries contained in this experiment come from independent growths of cell line PC-3. They are stranded PE101 Illumina Hi-Seq RAMPAGE 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 (BED, BIGBED, BIGWIG, GFF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88377/
Series		Accession: GSE88377	ID: 200088377

3571. shRNA RNA-seq from HepG2 (ENCSR585KOJ)
(Submitter supplied) Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV31B)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88376/
Series		Accession: GSE88376	ID: 200088376

3572. shRNA RNA-seq from K562 (ENCSR584LDM)
(Submitter supplied) shRNA knockdown against DDX27 in K562 cells followed by RNA-seq. (DDX27_BGKLV19)  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/GSE88nnn/GSE88375/
Series		Accession: GSE88375	ID: 200088375

3573. shRNA RNA-seq from HepG2 (ENCSR584JRB)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against NUFIP2. (NUFIP2_BGHLV26)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88374/
Series		Accession: GSE88374	ID: 200088374

3574. shRNA RNA-seq from K562 (ENCSR577OVP)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against DNAJC2. (DNAJC2_BGKLV24)  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/GSE88nnn/GSE88372/
Series		Accession: GSE88372	ID: 200088372

3575. siRNA RNA-seq from K562 (ENCSR576FFB)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting KAT2B.  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/GSE88nnn/GSE88371/
Series		Accession: GSE88371	ID: 200088371

3576. shRNA RNA-seq from HepG2 (ENCSR573UBF)
(Submitter supplied) shRNA knockdown against TFIP11 in HepG2 cells followed by RNA-seq. (TFIP11_BGHLV17)  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/GSE88nnn/GSE88370/
Series		Accession: GSE88370	ID: 200088370

3577. shRNA RNA-seq from K562 (ENCSR572FFX)
(Submitter supplied) Control shRNA against no target in K562 cells followed by RNA-seq. (non-target_BGKLV21)  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/GSE88nnn/GSE88368/
Series		Accession: GSE88368	ID: 200088368

3578. shRNA RNA-seq from HepG2 (ENCSR570CWH)
(Submitter supplied) shRNA knockdown against BCCIP in HepG2 cells followed by RNA-seq. (BCCIP_BGHLV17)  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/GSE88nnn/GSE88366/
Series		Accession: GSE88366	ID: 200088366

3579. shRNA RNA-seq from K562 (ENCSR563YIS)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPL. (HNRNPL_BGKLV25)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88364/
Series		Accession: GSE88364	ID: 200088364

3580. shRNA RNA-seq from K562 (ENCSR562CCA)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against SF1. (SF1_BGKLV28)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88363/
Series		Accession: GSE88363	ID: 200088363

3581. polyA mRNA RNA-seq from HepG2 (ENCSR561FEE)
(Submitter supplied) Initial total fractions on HepG2 Long Poly-A+ from Lecuyer  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/GSE88nnn/GSE88362/
Series		Accession: GSE88362	ID: 200088362

3582. shRNA RNA-seq from K562 (ENCSR560RSZ)
(Submitter supplied) shRNA knockdown against DDX52_06 in K562 cells followed by RNA-seq. (DDX52_BGKLV19)  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/GSE88nnn/GSE88361/
Series		Accession: GSE88361	ID: 200088361

3583. shRNA RNA-seq from K562 (ENCSR558XNA)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against PUF60. (PUF60-BGKLV25)  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/GSE88nnn/GSE88360/
Series		Accession: GSE88360	ID: 200088360

3584. shRNA RNA-seq from K562 (ENCSR556FNN)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against PPIL4. (PPIL4_BGKLV24_B)  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/GSE88nnn/GSE88358/
Series		Accession: GSE88358	ID: 200088358

3585. siRNA RNA-seq from K562 (ENCSR555CYH)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting ZNF180.  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/GSE88nnn/GSE88357/
Series		Accession: GSE88357	ID: 200088357

3586. shRNA RNA-seq from K562 (ENCSR552NBS)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPA0. (HNRNPA0_BGKLV24_B)  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/GSE88nnn/GSE88355/
Series		Accession: GSE88355	ID: 200088355

3587. shRNA RNA-seq from HepG2 (ENCSR547NWD)
(Submitter supplied) shRNA knockdown against AARS in HepG2 cells followed by RNA-seq. (AARS_BGHLV17)  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/GSE88nnn/GSE88352/
Series		Accession: GSE88352	ID: 200088352

3588. polyA mRNA RNA-seq from K562 (ENCSR545DKY)
(Submitter supplied) Initial total fractions on K562 Long Poly-A+ from Lecuyer  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/GSE88nnn/GSE88351/
Series		Accession: GSE88351	ID: 200088351

3589. shRNA RNA-seq from HepG2 (ENCSR542ESY)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against KRR1. (KRR1_BGHLV27)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88348/
Series		Accession: GSE88348	ID: 200088348

3590. polyA mRNA RNA-seq from HepG2 (ENCSR541TIG)
(Submitter supplied) Initial membrane fractions on HepG2 Long Poly-A+ from Lecuyer  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/GSE88nnn/GSE88347/
Series		Accession: GSE88347	ID: 200088347

3591. RAMPAGE from SJCRH30 (ENCSR540YVD)
(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 RAMPAGE 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 (BED, BIGBED, BIGWIG, GFF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88346/
Series		Accession: GSE88346	ID: 200088346

3592. shRNA RNA-seq from HepG2 (ENCSR538QOG)
(Submitter supplied) Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHLV31)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88343/
Series		Accession: GSE88343	ID: 200088343

3593. shRNA RNA-seq from K562 (ENCSR535YPK)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against SFPQ. (SFPQ_BGKLV28)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88342/
Series		Accession: GSE88342	ID: 200088342

3594. shRNA RNA-seq from HepG2 (ENCSR532ZPP)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against EWSR1. (EWSR1_BGHLV31)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88341/
Series		Accession: GSE88341	ID: 200088341

3595. polyA mRNA RNA-seq from K562 (ENCSR530NHO)
(Submitter supplied) Initial nucleus fractions on K562 Long Poly-A+ from Lecuyer  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/GSE88nnn/GSE88339/
Series		Accession: GSE88339	ID: 200088339

3596. shRNA RNA-seq from K562 (ENCSR530BOP)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against SUPT6H. (SUPT6H_BGKLV28)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88338/
Series		Accession: GSE88338	ID: 200088338

3597. shRNA RNA-seq from K562 (ENCSR529MBZ)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against PPIG. (PPIG_BGKLV29)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88337/
Series		Accession: GSE88337	ID: 200088337

3598. shRNA RNA-seq from K562 (ENCSR528ASX)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against GRWD1. (GRWD1_BGKLV21)  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/GSE88nnn/GSE88335/
Series		Accession: GSE88335	ID: 200088335

3599. shRNA RNA-seq from HepG2 (ENCSR527QNC)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against TARDBP. (TARDBP_BGHLV35)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88334/
Series		Accession: GSE88334	ID: 200088334

3600. shRNA RNA-seq from K562 (ENCSR524YXQ)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against SRPK2. (SRPK2_BGKLV34)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88332/
Series		Accession: GSE88332	ID: 200088332

3601. shRNA RNA-seq from HepG2 (ENCSR519KXM)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against SLBP. (SLBP-BGHLV23)  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/GSE88nnn/GSE88331/
Series		Accession: GSE88331	ID: 200088331

3602. shRNA RNA-seq from HepG2 (ENCSR518JXY)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against ZNF622. (ZNF622_BGHLV33)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88330/
Series		Accession: GSE88330	ID: 200088330

3603. shRNA RNA-seq from K562 (ENCSR517JHY)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against MAK16. (MAK16_BGKLV32)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88329/
Series		Accession: GSE88329	ID: 200088329

3604. shRNA RNA-seq from HepG2 (ENCSR517JDK)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against NKRF. (NKRF_BGHLV27)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88328/
Series		Accession: GSE88328	ID: 200088328

3605. shRNA RNA-seq from HepG2 (ENCSR511SYK)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against ACO1. (ACO1_BGHLV31)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88326/
Series		Accession: GSE88326	ID: 200088326

3606. shRNA RNA-seq from K562 (ENCSR511BNY)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against FIP1L1. (FIP1L1_BGKLV29)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88325/
Series		Accession: GSE88325	ID: 200088325

3607. siRNA RNA-seq from K562 (ENCSR509YMP)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting ZMIZ1.  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/GSE88nnn/GSE88322/
Series		Accession: GSE88322	ID: 200088322

3608. shRNA RNA-seq from HepG2 (ENCSR509LIV)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against EIF4G1. (EIF4G1-BGHLV23)  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/GSE88nnn/GSE88321/
Series		Accession: GSE88321	ID: 200088321

3609. RAMPAGE from M059J (ENCSR507GYW)
(Submitter supplied) The libraries contained in this experiment come from independent growths of cell line M059J isolated from a malignant glioblastoma of a 33 year old male. They are stranded PE101 Illumina Hi-Seq RAMPAGE 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 (BED, BIGBED, BIGWIG, GFF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88320/
Series		Accession: GSE88320	ID: 200088320

3610. RAMPAGE from SK-MEL-5 (ENCSR506WDZ)
(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 RAMPAGE 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 (BED, BIGBED, BIGWIG, GFF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88319/
Series		Accession: GSE88319	ID: 200088319

3611. shRNA RNA-seq from HepG2 (ENCSR496ETJ)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against PES1. (PES1_BGHLV31)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88313/
Series		Accession: GSE88313	ID: 200088313

3612. shRNA RNA-seq from K562 (ENCSR495YSS)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against EIF2C2. (K-EIF2C2)  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/GSE88nnn/GSE88312/
Series		Accession: GSE88312	ID: 200088312

3613. shRNA RNA-seq from HepG2 (ENCSR494VSD)
(Submitter supplied) shRNA knockdown against CSDA in HepG2 cells followed by RNA-seq. (CSDA-30-BGHLV20)  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/GSE88nnn/GSE88310/
Series		Accession: GSE88310	ID: 200088310

3614. shRNA RNA-seq from K562 (ENCSR494UDF)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against DKC1. (DKC1_BGKLV32)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88309/
Series		Accession: GSE88309	ID: 200088309

3615. shRNA RNA-seq from K562 (ENCSR492BKM)
(Submitter supplied) shRNA knockdown against FAM120A in K562 cells followed by RNA-seq. (FAM120A_BGKLV19)  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/GSE88nnn/GSE88307/
Series		Accession: GSE88307	ID: 200088307

3616. shRNA RNA-seq from HepG2 (ENCSR490DYI)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPLL. (HNRNPLL_BGHLV35)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88305/
Series		Accession: GSE88305	ID: 200088305

3617. shRNA RNA-seq from HepG2 (ENCSR486AIO)
(Submitter supplied) shRNA knockdown against RPS19 in HepG2 cells followed by RNA-seq. (RPS19_BGHLV16)  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/GSE88nnn/GSE88304/
Series		Accession: GSE88304	ID: 200088304

3618. shRNA RNA-seq from K562 (ENCSR481YXD)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against IGF2BP3. (K-IGF2BP3-25B)  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/GSE88nnn/GSE88302/
Series		Accession: GSE88302	ID: 200088302

3619. shRNA RNA-seq from HepG2 (ENCSR481AYC)
(Submitter supplied) shRNA knockdown against BCLAF1 in HepG2 cells followed by RNA-seq. (BCLAF1_BGHLV17)  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/GSE88nnn/GSE88301/
Series		Accession: GSE88301	ID: 200088301

3620. RAMPAGE from SK-N-DZ (ENCSR479BMI)
(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 RAMPAGE 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 (BED, BIGBED, BIGWIG, GFF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88299/
Series		Accession: GSE88299	ID: 200088299

3621. shRNA RNA-seq from HepG2 (ENCSR477TRX)
(Submitter supplied) shRNA knockdown against EEF2 in HepG2 cells followed by RNA-seq. (EEF2_BGHLV16)  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/GSE88nnn/GSE88298/
Series		Accession: GSE88298	ID: 200088298

3622. siRNA RNA-seq from K562 (ENCSR472UFW)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting CDAN1.  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/GSE88nnn/GSE88295/
Series		Accession: GSE88295	ID: 200088295

3623. shRNA RNA-seq from HepG2 (ENCSR471GIS)
(Submitter supplied) shRNA knockdown against RRP9 in HepG2 cells followed by RNA-seq. (RRP9_BGHLV17)  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/GSE88nnn/GSE88292/
Series		Accession: GSE88292	ID: 200088292

3624. shRNA RNA-seq from K562 (ENCSR470PRV)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPC. (K-HNRNPC-25B)  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/GSE88nnn/GSE88291/
Series		Accession: GSE88291	ID: 200088291

3625. shRNA RNA-seq from HepG2 (ENCSR459EMR)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against TUFM. (TUFM-BGHLV23)  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/GSE88nnn/GSE88287/
Series		Accession: GSE88287	ID: 200088287

3626. shRNA RNA-seq from HepG2 (ENCSR457WBK)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against NUP35. (NUP35_BGHLV27)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88285/
Series		Accession: GSE88285	ID: 200088285

3627. shRNA RNA-seq from K562 (ENCSR455TNF)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against TDP-43. (K562-set1b-shTDP43)  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/GSE88nnn/GSE88283/
Series		Accession: GSE88283	ID: 200088283

3628. shRNA RNA-seq from K562 (ENCSR454KYR)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against SF3A3. (SF3A3_BGKLV34)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88281/
Series		Accession: GSE88281	ID: 200088281

3629. shRNA RNA-seq from K562 (ENCSR453HKS)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against XPO5. (XPO5_BGKLV28)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88280/
Series		Accession: GSE88280	ID: 200088280

3630. shRNA RNA-seq from HepG2 (ENCSR450VQO)
(Submitter supplied) shRNA knockdown against TIAL1 in HepG2 cells followed by RNA-seq. (TIAL1-BHLV20)  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/GSE88nnn/GSE88279/
Series		Accession: GSE88279	ID: 200088279

3631. shRNA RNA-seq from HepG2 (ENCSR447UCG)
(Submitter supplied) shRNA knockdown against SRSF5 in HepG2 cells followed by RNA-seq. (SRSF5 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/GSE88nnn/GSE88276/
Series		Accession: GSE88276	ID: 200088276

3632. siRNA RNA-seq from K562 (ENCSR443QFD)
(Submitter supplied) Control siRNA against no target in K562 cells followed by RNA-seq.  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/GSE88nnn/GSE88275/
Series		Accession: GSE88275	ID: 200088275

3633. shRNA RNA-seq from K562 (ENCSR438MDN)
(Submitter supplied) Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV21-B)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88272/
Series		Accession: GSE88272	ID: 200088272

3634. shRNA RNA-seq from HepG2 (ENCSR426UUG)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against U2AF2. (U2AF2_BGHLV26)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88268/
Series		Accession: GSE88268	ID: 200088268

3635. shRNA RNA-seq from K562 (ENCSR424QCW)
(Submitter supplied) Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV36)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88266/
Series		Accession: GSE88266	ID: 200088266

3636. shRNA RNA-seq from HepG2 (ENCSR424JSU)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against UBE2L3. (UBE2L3-BGHLV23)  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/GSE88nnn/GSE88265/
Series		Accession: GSE88265	ID: 200088265

3637. shRNA RNA-seq from HepG2 (ENCSR422JMS)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against SSRP1. (SSRP1_BGHLV27)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88264/
Series		Accession: GSE88264	ID: 200088264

3638. shRNA RNA-seq from K562 (ENCSR419JMU)
(Submitter supplied) Control shRNA against no target in K562 cells followed by RNA-seq. (non-target_BGKLV24_B)  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/GSE88nnn/GSE88261/
Series		Accession: GSE88261	ID: 200088261

3639. shRNA RNA-seq from K562 (ENCSR416ZJH)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against PABPN1. (PABPN1_BGKLV28)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88259/
Series		Accession: GSE88259	ID: 200088259

3640. shRNA RNA-seq from K562 (ENCSR410ZPU)
(Submitter supplied) shRNA knockdown against BCLAF1 in K562 cells followed by RNA-seq. (BCLAF1_BGKLV19)  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/GSE88nnn/GSE88258/
Series		Accession: GSE88258	ID: 200088258

3641. shRNA RNA-seq from K562 (ENCSR410MIQ)
(Submitter supplied) shRNA knockdown against RPS3 in K562 cells followed by RNA-seq. (RPS3 BGKLV13)  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/GSE88nnn/GSE88256/
Series		Accession: GSE88256	ID: 200088256

3642. shRNA RNA-seq from K562 (ENCSR408SDL)
(Submitter supplied) shRNA knockdown against SMNDC1 in K562 cells followed by RNA-seq. (SMNDC1 BGKLV13)  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/GSE88nnn/GSE88255/
Series		Accession: GSE88255	ID: 200088255

3643. siRNA RNA-seq from K562 (ENCSR401RKW)
(Submitter supplied) Control siRNA against no target in K562 cells followed by RNA-seq.  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/GSE88nnn/GSE88252/
Series		Accession: GSE88252	ID: 200088252

3644. shRNA RNA-seq from K562 (ENCSR398HXV)
(Submitter supplied) shRNA knockdown against NONO in K562 cells followed by RNA-seq. (NONO_BGKLV19)  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/GSE88nnn/GSE88250/
Series		Accession: GSE88250	ID: 200088250

3645. shRNA RNA-seq from K562 (ENCSR398GHW)
(Submitter supplied) shRNA knockdown against GEMIN5 in K562 cells followed by RNA-seq. (GEMIN5_BGKLV19)  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/GSE88nnn/GSE88249/
Series		Accession: GSE88249	ID: 200088249

3646. shRNA RNA-seq from K562 (ENCSR392HSJ)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPF. (HNRNPF_BGKLV21)  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/GSE88nnn/GSE88248/
Series		Accession: GSE88248	ID: 200088248

3647. siRNA RNA-seq from K562 (ENCSR390GWL)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting RCOR1.  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/GSE88nnn/GSE88246/
Series		Accession: GSE88246	ID: 200088246

3648. shRNA RNA-seq from HepG2 (ENCSR389HFU)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against FTO. (FTO_BGHLV35)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88245/
Series		Accession: GSE88245	ID: 200088245

3649. shRNA RNA-seq from HepG2 (ENCSR388CNS)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX47. (DDX47_BGHLV22)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88243/
Series		Accession: GSE88243	ID: 200088243

3650. shRNA RNA-seq from K562 (ENCSR386YEV)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against CCAR1. (CCAR1_BGKLV24)  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/GSE88nnn/GSE88242/
Series		Accession: GSE88242	ID: 200088242

3651. shRNA RNA-seq from K562 (ENCSR385UPQ)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against RBM15. (RBM15_BGKLV32)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88241/
Series		Accession: GSE88241	ID: 200088241

3652. shRNA RNA-seq from HepG2 (ENCSR385TMY)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against RBM17. (RBM17_BGHLV26)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88240/
Series		Accession: GSE88240	ID: 200088240

3653. shRNA RNA-seq from HepG2 (ENCSR385KOY)
(Submitter supplied) shRNA knockdown against DNAJC21 in HepG2 cells followed by RNA-seq. (DNAJC21-46-BGHLV20)  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/GSE88nnn/GSE88239/
Series		Accession: GSE88239	ID: 200088239

3654. polyA mRNA RNA-seq from K562 (ENCSR384ZXD)
(Submitter supplied) Initial cytosolic fractions on K562 Long Poly-A+ from Lecuyer  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/GSE88nnn/GSE88238/
Series		Accession: GSE88238	ID: 200088238

3655. shRNA RNA-seq from K562 (ENCSR384BDV)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against CPSF6. (CPSF6_BGKLV36)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88237/
Series		Accession: GSE88237	ID: 200088237

3656. shRNA RNA-seq from HepG2 (ENCSR382QKD)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against BUD13. (BUD13_BGHLV30)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88235/
Series		Accession: GSE88235	ID: 200088235

3657. shRNA RNA-seq from K562 (ENCSR379VXW)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against FKBP4. (FKBP4_BGKLV21)  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/GSE88nnn/GSE88233/
Series		Accession: GSE88233	ID: 200088233

3658. shRNA RNA-seq from HepG2 (ENCSR376RJN)
(Submitter supplied) Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHLV12-a-b)  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/GSE88nnn/GSE88231/
Series		Accession: GSE88231	ID: 200088231

3659. shRNA RNA-seq from HepG2 (ENCSR376FGR)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against SRSF3. (SRSF3_BGHLV35)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88229/
Series		Accession: GSE88229	ID: 200088229

3660. shRNA RNA-seq from HepG2 (ENCSR374NMJ)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against SF3A3. (SF3A3_BGHLV33)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88228/
Series		Accession: GSE88228	ID: 200088228

3661. shRNA RNA-seq from HepG2 (ENCSR372UWV)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against U2AF1. (U2AF1_BGHLV30)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88226/
Series		Accession: GSE88226	ID: 200088226

3662. shRNA RNA-seq from K562 (ENCSR372DZW)
(Submitter supplied) RNA-seq on K562 cells treated with a control shRNA against no target. (k562-set-11b-shCNTRL)  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/GSE88nnn/GSE88225/
Series		Accession: GSE88225	ID: 200088225

3663. shRNA RNA-seq from K562 (ENCSR368ZRP)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against PAPOLA. (K-PAPOLA-30B)  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/GSE88nnn/GSE88224/
Series		Accession: GSE88224	ID: 200088224

3664. shRNA RNA-seq from HepG2 (ENCSR366FFV)
(Submitter supplied) shRNA knockdown against ILF2 in HepG2 cells followed by RNA-seq. (ILF2-BGHLV20)  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/GSE88nnn/GSE88223/
Series		Accession: GSE88223	ID: 200088223

3665. shRNA RNA-seq from HepG2 (ENCSR364GRM)
(Submitter supplied) Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV23-B)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88221/
Series		Accession: GSE88221	ID: 200088221

3666. shRNA RNA-seq from K562 (ENCSR362XMY)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against UBE2L3. (UBE2L3-BGKLV25)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88220/
Series		Accession: GSE88220	ID: 200088220

3667. shRNA RNA-seq from HepG2 (ENCSR355OQC)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against NAA15. (NAA15_BGHLV30)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88216/
Series		Accession: GSE88216	ID: 200088216

3668. shRNA RNA-seq from HepG2 (ENCSR354XQY)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPAB. (HNRNPAB--BGHLV22)  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/GSE88nnn/GSE88215/
Series		Accession: GSE88215	ID: 200088215

3669. RAMPAGE from HT1080 (ENCSR352ANU)
(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 RAMPAGE 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 (BED, BIGBED, BIGWIG, GFF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88213/
Series		Accession: GSE88213	ID: 200088213

3670. shRNA RNA-seq from K562 (ENCSR351CNN)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against CUGBP1. (K-CUGBP1-26B)  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/GSE88nnn/GSE88211/
Series		Accession: GSE88211	ID: 200088211

3671. RAMPAGE from HT1080 (ENCSR348DYP)
(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 RAMPAGE 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 1 Sample
FTP download: GEO (BED, BIGBED, BIGWIG, GFF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88210/
Series		Accession: GSE88210	ID: 200088210

3672. shRNA RNA-seq from HepG2 (ENCSR347ZHQ)
(Submitter supplied) shRNA knockdown against XRN2 in HepG2 cells followed by RNA-seq. (XRN2_BGHLV17)  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/GSE88nnn/GSE88209/
Series		Accession: GSE88209	ID: 200088209

3673. shRNA RNA-seq from K562 (ENCSR346DZQ)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against NPM1. (NPM1_BGKLV28)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88208/
Series		Accession: GSE88208	ID: 200088208

3674. shRNA RNA-seq from K562 (ENCSR345VVZ)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against DHX30. (DHX30_BGKLV24)  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/GSE88nnn/GSE88207/
Series		Accession: GSE88207	ID: 200088207

3675. shRNA RNA-seq from HepG2 (ENCSR343DHN)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against SBDS. (SBDS-BGHLV22)  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/GSE88nnn/GSE88205/
Series		Accession: GSE88205	ID: 200088205

3676. siRNA RNA-seq from K562 (ENCSR341RCF)
(Submitter supplied) Control siRNA against no target in K562 cells followed by RNA-seq.  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/GSE88nnn/GSE88204/
Series		Accession: GSE88204	ID: 200088204

3677. shRNA RNA-seq from K562 (ENCSR341PZW)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against WDR43. (WDR43_BGKLV34)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88203/
Series		Accession: GSE88203	ID: 200088203

3678. shRNA RNA-seq from K562 (ENCSR336DFS)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against RBFOX2. (RBFOX2_BGKLV24)  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/GSE88nnn/GSE88200/
Series		Accession: GSE88200	ID: 200088200

3679. shRNA RNA-seq from K562 (ENCSR334HNJ)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against DDX47. (K-DDX47)  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/GSE88nnn/GSE88199/
Series		Accession: GSE88199	ID: 200088199

3680. shRNA RNA-seq from K562 (ENCSR334BTA)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against WDR3. (WDR3_BGKLV34)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88198/
Series		Accession: GSE88198	ID: 200088198

3681. shRNA RNA-seq from K562 (ENCSR331DUD)
(Submitter supplied) shRNA knockdown against DDX55 in K562 cells followed by RNA-seq. (DDX55_BGKLV19)  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/GSE88nnn/GSE88196/
Series		Accession: GSE88196	ID: 200088196

3682. shRNA RNA-seq from K562 (ENCSR325OOM)
(Submitter supplied) shRNA knockdown against FUS in K562 cells followed by RNA-seq. (FUS BGKLV13)  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/GSE88nnn/GSE88193/
Series		Accession: GSE88193	ID: 200088193

3683. shRNA RNA-seq from K562 (ENCSR322XVS)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against PHF6. (PHF6_BGKLV21)  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/GSE88nnn/GSE88192/
Series		Accession: GSE88192	ID: 200088192

3684. shRNA RNA-seq from HepG2 (ENCSR318OXM)
(Submitter supplied) shRNA knockdown against UPF2 in HepG2 cells followed by RNA-seq. (UPF2_BGHLV17)  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/GSE88nnn/GSE88189/
Series		Accession: GSE88189	ID: 200088189

3685. shRNA RNA-seq from K562 (ENCSR312SRB)
(Submitter supplied) shRNA knockdown against SRP68 in K562 cells followed by RNA-seq. (SRP68_BGKLV19)  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/GSE88nnn/GSE88185/
Series		Accession: GSE88185	ID: 200088185

3686. shRNA RNA-seq from HepG2 (ENCSR312SFA)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX19B. (DDX19B_BGHLV31)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88184/
Series		Accession: GSE88184	ID: 200088184

3687. shRNA RNA-seq from K562 (ENCSR312HJY)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against CNOT8. (K-CNOT8)  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/GSE88nnn/GSE88182/
Series		Accession: GSE88182	ID: 200088182

3688. siRNA RNA-seq from K562 (ENCSR312FIT)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting UBTF.  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/GSE88nnn/GSE88181/
Series		Accession: GSE88181	ID: 200088181

3689. shRNA RNA-seq from K562 (ENCSR309PPC)
(Submitter supplied) shRNA knockdown against PA2G4 in K562 cells followed by RNA-seq. (PA2G4_BGKLV19)  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/GSE88nnn/GSE88180/
Series		Accession: GSE88180	ID: 200088180

3690. shRNA RNA-seq from HepG2 (ENCSR309HXK)
(Submitter supplied) shRNA knockdown against TRIM56 in HepG2 cells followed by RNA-seq. (TRIM56-BGHLV20)  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/GSE88nnn/GSE88179/
Series		Accession: GSE88179	ID: 200088179

3691. shRNA RNA-seq from HepG2 (ENCSR308IKH)
(Submitter supplied) shRNA knockdown against HNRNPU in HepG2 cells followed by RNA-seq. (HNRNPU-BGHLV20)  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/GSE88nnn/GSE88178/
Series		Accession: GSE88178	ID: 200088178

3692. shRNA RNA-seq from K562 (ENCSR306IOF)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against PARN. (PARN_BGKLV24)  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/GSE88nnn/GSE88176/
Series		Accession: GSE88176	ID: 200088176

3693. shRNA RNA-seq from K562 (ENCSR306EIU)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against CSDA. (CSDA_BGKLV24)  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/GSE88nnn/GSE88175/
Series		Accession: GSE88175	ID: 200088175

3694. shRNA RNA-seq from HepG2 (ENCSR305XWT)
(Submitter supplied) Control shRNA against no target in HepG2 cells followed by RNA-seq. (non-target-BGHLV20)  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/GSE88nnn/GSE88174/
Series		Accession: GSE88174	ID: 200088174

3695. shRNA RNA-seq from K562 (ENCSR300QFQ)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against TRIM56. (TRIM56_BGKLV21)  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/GSE88nnn/GSE88172/
Series		Accession: GSE88172	ID: 200088172

3696. shRNA RNA-seq from HepG2 (ENCSR296ERI)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against PUS1. (PUS1_BGHLV31)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88170/
Series		Accession: GSE88170	ID: 200088170

3697. RAMPAGE from HT-29 (ENCSR295GUQ)
(Submitter supplied) The libraries contained in this experiment come from independent growths of cell line HT-29. They are stranded PE101 Illumina Hi-Seq RAMPAGE 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 (BED, BIGBED, BIGWIG, GFF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88168/
Series		Accession: GSE88168	ID: 200088168

3698. shRNA RNA-seq from K562 (ENCSR286OKW)
(Submitter supplied) shRNA knockdown against CSTF2T in K562 cells followed by RNA-seq. (CSTF2T BGKLV13)  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/GSE88nnn/GSE88163/
Series		Accession: GSE88163	ID: 200088163

3699. shRNA RNA-seq from HepG2 (ENCSR281KCL)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against SUPT6H. (SUPT6H_BGHLV30)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88160/
Series		Accession: GSE88160	ID: 200088160

3700. shRNA RNA-seq from K562 (ENCSR281IUF)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against DDX19B. (DDX19B_BGKLV32)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88159/
Series		Accession: GSE88159	ID: 200088159

3701. shRNA RNA-seq from HepG2 (ENCSR279HMU)
(Submitter supplied) Control shRNA against no target in HepG2 cells followed by RNA-seq. (non-target-BGHLV22)  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/GSE88nnn/GSE88158/
Series		Accession: GSE88158	ID: 200088158

3702. shRNA RNA-seq from HepG2 (ENCSR274KWA)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against CNOT7. (CNOT7-BGHLV22)  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/GSE88nnn/GSE88156/
Series		Accession: GSE88156	ID: 200088156

3703. shRNA RNA-seq from HepG2 (ENCSR269ZAO)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against UTP18. (UTP18_BGHLV33)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88154/
Series		Accession: GSE88154	ID: 200088154

3704. shRNA RNA-seq from HepG2 (ENCSR269SJB)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against CKAP4. (CKAP4_BGHLV31)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88152/
Series		Accession: GSE88152	ID: 200088152

3705. shRNA RNA-seq from K562 (ENCSR269HQA)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against ILF3. (ILF3_BGKLV24)  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/GSE88nnn/GSE88151/
Series		Accession: GSE88151	ID: 200088151

3706. shRNA RNA-seq from K562 (ENCSR268JDD)
(Submitter supplied) shRNA knockdown against EIF2C1 in K562 cells followed by RNA-seq. (EIF2C1 BGKLV13)  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/GSE88nnn/GSE88150/
Series		Accession: GSE88150	ID: 200088150

3707. shRNA RNA-seq from K562 (ENCSR267RHP)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against BUD13. (BUD13_BGKLV29)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88149/
Series		Accession: GSE88149	ID: 200088149

3708. shRNA RNA-seq from HepG2 (ENCSR264TUE)
(Submitter supplied) Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV35)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88148/
Series		Accession: GSE88148	ID: 200088148

3709. shRNA RNA-seq from K562 (ENCSR258VGD)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against EIF3A. (EIF3A_BGKLV24)  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/GSE88nnn/GSE88144/
Series		Accession: GSE88144	ID: 200088144

3710. siRNA RNA-seq from K562 (ENCSR256NQT)
(Submitter supplied) Control siRNA against no target in K562 cells followed by RNA-seq.  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/GSE88nnn/GSE88142/
Series		Accession: GSE88142	ID: 200088142

3711. shRNA RNA-seq from K562 (ENCSR251ABP)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against UPF1. (UPF1_BGKLV34)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88140/
Series		Accession: GSE88140	ID: 200088140

3712. shRNA RNA-seq from HepG2 (ENCSR246RRQ)
(Submitter supplied) Control shRNA against no target in HepG2 cells followed by RNA-seq. (non-target_BGHLV27)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88139/
Series		Accession: GSE88139	ID: 200088139

3713. shRNA RNA-seq from K562 (ENCSR245BNJ)
(Submitter supplied) Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV19-A)  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/GSE88nnn/GSE88138/
Series		Accession: GSE88138	ID: 200088138

3714. shRNA RNA-seq from HepG2 (ENCSR243IGA)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against HSPD1. (HSPD1_BGHLV27)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88137/
Series		Accession: GSE88137	ID: 200088137

3715. RAMPAGE from NCI-H460 (ENCSR239ZQA)
(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 RAMPAGE 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 (BED, BIGBED, BIGWIG, GFF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88135/
Series		Accession: GSE88135	ID: 200088135

3716. shRNA RNA-seq from K562 (ENCSR239BCO)
(Submitter supplied) shRNA knockdown against PTBP1 in K562 cells followed by RNA-seq  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/GSE88nnn/GSE88134/
Series		Accession: GSE88134	ID: 200088134

3717. shRNA RNA-seq from HepG2 (ENCSR237IWZ)
(Submitter supplied) shRNA knockdown against KIAA1967 in HepG2 cells followed by RNA-seq. (KIAA1967_BGHLV18)  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/GSE88nnn/GSE88132/
Series		Accession: GSE88132	ID: 200088132

3718. shRNA RNA-seq from K562 (ENCSR234YMW)
(Submitter supplied) shRNA knockdown against SLTM in K562 cells followed by RNA-seq. (SLTM BGKLV13)  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/GSE88nnn/GSE88129/
Series		Accession: GSE88129	ID: 200088129

3719. shRNA RNA-seq from K562 (ENCSR232XRZ)
(Submitter supplied) shRNA knockdown against SND1 in K562 cells followed by RNA-seq. (SND1 BGKLV13)  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/GSE88nnn/GSE88127/
Series		Accession: GSE88127	ID: 200088127

3720. shRNA RNA-seq from K562 (ENCSR232CPD)
(Submitter supplied) shRNA knockdown against XRCC6 in K562 cells followed by RNA-seq. (XRCC6 BGKLV13)  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/GSE88nnn/GSE88126/
Series		Accession: GSE88126	ID: 200088126

3721. shRNA RNA-seq from K562 (ENCSR231DXJ)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against ATP5C1. (ATP5C1_BGKLV32)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88125/
Series		Accession: GSE88125	ID: 200088125

3722. shRNA RNA-seq from K562 (ENCSR227AVS)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against NOL12. (NOL12-BGKLV25)  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/GSE88nnn/GSE88122/
Series		Accession: GSE88122	ID: 200088122

3723. shRNA RNA-seq from HepG2 (ENCSR222SMI)
(Submitter supplied) shRNA knockdown against RBM27 in HepG2 cells followed by RNA-seq. (RBM27_BGHLV18)  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/GSE88nnn/GSE88119/
Series		Accession: GSE88119	ID: 200088119

3724. shRNA RNA-seq from K562 (ENCSR222LRL)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against CPSF7. (CPSF7_BGKLV24)  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/GSE88nnn/GSE88118/
Series		Accession: GSE88118	ID: 200088118

3725. shRNA RNA-seq from HepG2 (ENCSR222CSF)
(Submitter supplied) shRNA knockdown against DDX28 in HepG2 cells followed by RNA-seq. (DDX28_BGHLV17)  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/GSE88nnn/GSE88117/
Series		Accession: GSE88117	ID: 200088117

3726. shRNA RNA-seq from K562 (ENCSR222COT)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against MBNL1. (MBNL1_BGKLV32)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88116/
Series		Accession: GSE88116	ID: 200088116

3727. shRNA RNA-seq from K562 (ENCSR222ABK)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against HSPD1. (HSPD1_BGKLV29)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88115/
Series		Accession: GSE88115	ID: 200088115

3728. shRNA RNA-seq from HepG2 (ENCSR220TBR)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against DAZAP1. (DAZAP1-BGHLV23)  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/GSE88nnn/GSE88114/
Series		Accession: GSE88114	ID: 200088114

3729. shRNA RNA-seq from K562 (ENCSR219DXZ)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against SBDS. (SBDS_BGKLV24_B)  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/GSE88nnn/GSE88111/
Series		Accession: GSE88111	ID: 200088111

3730. shRNA RNA-seq from HepG2 (ENCSR210RWL)
(Submitter supplied) shRNA knockdown against DDX27 in HepG2 cells followed by RNA-seq. (DDX27_BGHLV17)  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/GSE88nnn/GSE88110/
Series		Accession: GSE88110	ID: 200088110

3731. shRNA RNA-seq from K562 (ENCSR210KJB)
(Submitter supplied) shRNA knockdown against RRP9 in K562 cells followed by RNA-seq. (RRP9_BGKLV19)  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/GSE88nnn/GSE88109/
Series		Accession: GSE88109	ID: 200088109

3732. shRNA RNA-seq from HepG2 (ENCSR210DML)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against PUM2. (PUM2-BGHLV23)  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/GSE88nnn/GSE88108/
Series		Accession: GSE88108	ID: 200088108

3733. shRNA RNA-seq from K562 (ENCSR208GPE)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against DDX1. (DDX1_BGKLV24)  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/GSE88nnn/GSE88107/
Series		Accession: GSE88107	ID: 200088107

3734. RAMPAGE from A172 (ENCSR208AWA)
(Submitter supplied) The libraries contained in this experiment come from independent growths of cell line A172, a glioblastoma cell line derived from a 53 year old male. They are stranded PE101 Illumina Hi-Seq RAMPAGE 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 (BED, BIGBED, BIGWIG, GFF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88106/
Series		Accession: GSE88106	ID: 200088106

3735. shRNA RNA-seq from K562 (ENCSR207QGW)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against EIF2C3. (K-EIF2C3)  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/GSE88nnn/GSE88105/
Series		Accession: GSE88105	ID: 200088105

3736. shRNA RNA-seq from K562 (ENCSR205VSQ)
(Submitter supplied) shRNA knockdown against DDX28 in K562 cells followed by RNA-seq. (DDX28_BGKLV19)  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/GSE88nnn/GSE88104/
Series		Accession: GSE88104	ID: 200088104

3737. shRNA RNA-seq from K562 (ENCSR192GBD)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against PABPC1. (PABPC1_BGKLV24_B)  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/GSE88nnn/GSE88099/
Series		Accession: GSE88099	ID: 200088099

3738. shRNA RNA-seq from K562 (ENCSR192BPV)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against SUGP2. (SUGP2_BGKLV28)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88098/
Series		Accession: GSE88098	ID: 200088098

3739. shRNA RNA-seq from K562 (ENCSR191VWK)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against PNPT1. (PNPT1-BGKLV25)  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/GSE88nnn/GSE88097/
Series		Accession: GSE88097	ID: 200088097

3740. shRNA RNA-seq from K562 (ENCSR188IPO)
(Submitter supplied) shRNA knockdown against GTF2F1 in K562 cells followed by RNA-seq. (GTF2F1 BGKLV13)  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/GSE88nnn/GSE88096/
Series		Accession: GSE88096	ID: 200088096

3741. shRNA RNA-seq from HepG2 (ENCSR182GKG)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against KIF1C. (KIF1C_BGHLV31)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88092/
Series		Accession: GSE88092	ID: 200088092

3742. shRNA RNA-seq from HepG2 (ENCSR182DAW)
(Submitter supplied) shRNA knockdown against HNRNPA1 in HepG2 cells followed by RNA-seq. (HNRNPA1-BGHLV20)  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/GSE88nnn/GSE88091/
Series		Accession: GSE88091	ID: 200088091

3743. total RNA-seq from HepG2 (ENCSR181ZGR)
(Submitter supplied) Initial total fractions on HepG2 Long Total from Lecuyer  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/GSE88nnn/GSE88089/
Series		Accession: GSE88089	ID: 200088089

3744. shRNA RNA-seq from K562 (ENCSR181RLB)
(Submitter supplied) shRNA knockdown against EEF2 in K562 cells followed by RNA-seq. (EEF2_BGKLV19)  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/GSE88nnn/GSE88088/
Series		Accession: GSE88088	ID: 200088088

3745. siRNA RNA-seq from K562 (ENCSR181AXM)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting CHD1.  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/GSE88nnn/GSE88087/
Series		Accession: GSE88087	ID: 200088087

3746. shRNA RNA-seq from HepG2 (ENCSR180XTP)
(Submitter supplied) shRNA knockdown against NUSAP1 in HepG2 cells followed by RNA-seq. (NUSAP1_BGHLV18)  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/GSE88nnn/GSE88086/
Series		Accession: GSE88086	ID: 200088086

3747. shRNA RNA-seq from K562 (ENCSR174OYC)
(Submitter supplied) Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV34)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88083/
Series		Accession: GSE88083	ID: 200088083

3748. shRNA RNA-seq from K562 (ENCSR169QQW)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against MSI2. (MSI2_BGKLV25)  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/GSE88nnn/GSE88081/
Series		Accession: GSE88081	ID: 200088081

3749. siRNA RNA-seq from K562 (ENCSR169DSM)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting ARID3A.  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 3 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88080/
Series		Accession: GSE88080	ID: 200088080

3750. shRNA RNA-seq from HepG2 (ENCSR167JPY)
(Submitter supplied) shRNA knockdown against SRP68 in HepG2 cells followed by RNA-seq. (SRP68_BGHLV17)  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/GSE88nnn/GSE88078/
Series		Accession: GSE88078	ID: 200088078

3751. shRNA RNA-seq from K562 (ENCSR165VBD)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against UTP18. (UTP18_BGKLV32)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88076/
Series		Accession: GSE88076	ID: 200088076

3752. shRNA RNA-seq from K562 (ENCSR164TLB)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against ADAR. (ADAR_BGKLV24)  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/GSE88nnn/GSE88075/
Series		Accession: GSE88075	ID: 200088075

3753. shRNA RNA-seq from K562 (ENCSR164MUK)
(Submitter supplied) Control shRNA against no target in K562 cells followed by RNA-seq. (non-target_BGKLV28)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88074/
Series		Accession: GSE88074	ID: 200088074

3754. shRNA RNA-seq from K562 (ENCSR155EZL)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against DDX47. (DDX47_BGKLV25)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88070/
Series		Accession: GSE88070	ID: 200088070

3755. shRNA RNA-seq from HepG2 (ENCSR155BMF)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPL. (HNRNPL-BGHLV23)  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/GSE88nnn/GSE88069/
Series		Accession: GSE88069	ID: 200088069

3756. shRNA RNA-seq from K562 (ENCSR154OBA)
(Submitter supplied) Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV24C)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88068/
Series		Accession: GSE88068	ID: 200088068

3757. shRNA RNA-seq from HepG2 (ENCSR152MON)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against EIF4G2. (EIF4G2-BGHLV23)  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/GSE88nnn/GSE88067/
Series		Accession: GSE88067	ID: 200088067

3758. shRNA RNA-seq from K562 (ENCSR152IWT)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against TRIP6. (TRIP6_BGKLV29)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88066/
Series		Accession: GSE88066	ID: 200088066

3759. shRNA RNA-seq from K562 (ENCSR143UET)
(Submitter supplied) shRNA knockdown against EIF3G in K562 cells followed by RNA-seq. (EIF3G BGKLV13)  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/GSE88nnn/GSE88063/
Series		Accession: GSE88063	ID: 200088063

3760. shRNA RNA-seq from K562 (ENCSR143COQ)
(Submitter supplied) Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV32B)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88062/
Series		Accession: GSE88062	ID: 200088062

3761. shRNA RNA-seq from K562 (ENCSR139BIJ)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against FXR2. (K-FXR2-26B)  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/GSE88nnn/GSE88061/
Series		Accession: GSE88061	ID: 200088061

3762. shRNA RNA-seq from K562 (ENCSR137HKS)
(Submitter supplied) shRNA knockdown against PRPF8 in K562 cells followed by RNA-seq. (PRPF8_BGKLV19)  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/GSE88nnn/GSE88060/
Series		Accession: GSE88060	ID: 200088060

3763. siRNA RNA-seq from K562 (ENCSR136ZPD)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting MAFG.  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/GSE88nnn/GSE88059/
Series		Accession: GSE88059	ID: 200088059

3764. shRNA RNA-seq from HepG2 (ENCSR135LXL)
(Submitter supplied) Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV20B)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88058/
Series		Accession: GSE88058	ID: 200088058

3765. siRNA RNA-seq from K562 (ENCSR129WCZ)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting MAZ.  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 3 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88056/
Series		Accession: GSE88056	ID: 200088056

3766. shRNA RNA-seq from K562 (ENCSR129ROE)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against SMN1. (SMN1_BGKLV24_B)  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/GSE88nnn/GSE88055/
Series		Accession: GSE88055	ID: 200088055

3767. siRNA RNA-seq from K562 (ENCSR126QVF)
(Submitter supplied) Control siRNA against no target in K562 cells followed by RNA-seq.  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/GSE88nnn/GSE88054/
Series		Accession: GSE88054	ID: 200088054

3768. shRNA RNA-seq from K562 (ENCSR126ARZ)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against ILF2. (ILF2_BGKLV24_B)  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/GSE88nnn/GSE88053/
Series		Accession: GSE88053	ID: 200088053

3769. shRNA RNA-seq from HepG2 (ENCSR124KCF)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against STAU1. (STAU1_BGHLV30)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88052/
Series		Accession: GSE88052	ID: 200088052

3770. shRNA RNA-seq from K562 (ENCSR118XYK)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against PUM2. (PUM2-BGKLV25)  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/GSE88nnn/GSE88051/
Series		Accession: GSE88051	ID: 200088051

3771. shRNA RNA-seq from HepG2 (ENCSR118VQR)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against RPS3A. (RPS3A-BGHLV22)  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/GSE88nnn/GSE88050/
Series		Accession: GSE88050	ID: 200088050

3772. shRNA RNA-seq from HepG2 (ENCSR118KUN)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against DKC1. (DKC1_BGHLV31)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88048/
Series		Accession: GSE88048	ID: 200088048

3773. shRNA RNA-seq from K562 (ENCSR118EFE)
(Submitter supplied) Control shRNA against no target in K562 cells followed by RNA-seq. (NTB_BGKLV29)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88047/
Series		Accession: GSE88047	ID: 200088047

3774. shRNA RNA-seq from K562 (ENCSR117WLY)
(Submitter supplied) shRNA knockdown against EFTUD2 in K562 cells followed by RNA-seq. (EFTUD2_BGKLV19)  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/GSE88nnn/GSE88046/
Series		Accession: GSE88046	ID: 200088046

3775. shRNA RNA-seq from HepG2 (ENCSR116YMU)
(Submitter supplied) shRNA knockdown against GNB2L1 in HepG2 cells followed by RNA-seq. (GNB2L1_BGHLV18)  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/GSE88nnn/GSE88045/
Series		Accession: GSE88045	ID: 200088045

3776. shRNA RNA-seq from HepG2 (ENCSR116QBU)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against FIP1L1. (FIP1L1_BGHLV30)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88044/
Series		Accession: GSE88044	ID: 200088044

3777. shRNA RNA-seq from K562 (ENCSR113PYX)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against CNOT7. (CNOT7_BGKLV24_B)  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/GSE88nnn/GSE88043/
Series		Accession: GSE88043	ID: 200088043

3778. shRNA RNA-seq from K562 (ENCSR112YTD)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against SLBP. (SLBP_BGKLV24)  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/GSE88nnn/GSE88041/
Series		Accession: GSE88041	ID: 200088041

3779. shRNA RNA-seq from HepG2 (ENCSR110ZYD)
(Submitter supplied) shRNA knockdown against SAFB2 in HepG2 cells followed by RNA-seq. (SAFB2-57-BGHLV20)  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/GSE88nnn/GSE88040/
Series		Accession: GSE88040	ID: 200088040

3780. shRNA RNA-seq from HepG2 (ENCSR110HAA)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against EIF2S2. (EIF2S2_BGHLV30)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88039/
Series		Accession: GSE88039	ID: 200088039

3781. siRNA RNA-seq from K562 (ENCSR109YDL)
(Submitter supplied) Control siRNA against no target in K562 cells followed by RNA-seq.  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/GSE88nnn/GSE88038/
Series		Accession: GSE88038	ID: 200088038

3782. shRNA RNA-seq from HepG2 (ENCSR105OXX)
(Submitter supplied) shRNA knockdown against MARK2 in HepG2 cells followed by RNA-seq. (MARK2_BGHLV18)  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/GSE88nnn/GSE88034/
Series		Accession: GSE88034	ID: 200088034

3783. RAMPAGE from RPMI-7951 (ENCSR104PJD)
(Submitter supplied) The libraries contained in this experiment come from independent growths of cell line RPMI-7951 isolated from a metastatic site of a malignant melonoma from an 18 year old caucasian female. They are stranded PE101 Illumina Hi-Seq RAMPAGE 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 (BED, BIGBED, BIGWIG, GFF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88033/
Series		Accession: GSE88033	ID: 200088033

3784. shRNA RNA-seq from HepG2 (ENCSR104OLN)
(Submitter supplied) shRNA knockdown against ADAR in HepG2 cells followed by RNA-seq. (ADAR-BGHLV20)  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/GSE88nnn/GSE88032/
Series		Accession: GSE88032	ID: 200088032

3785. shRNA RNA-seq from HepG2 (ENCSR104ABF)
(Submitter supplied) Control shRNA against no target in HepG2 cells followed by RNA-seq. (non-target_BGHLV26)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88031/
Series		Accession: GSE88031	ID: 200088031

3786. shRNA RNA-seq from K562 (ENCSR101OPF)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against SUCLG1. (SUCLG1-BGKLV25)  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/GSE88nnn/GSE88029/
Series		Accession: GSE88029	ID: 200088029

3787. shRNA RNA-seq from K562 (ENCSR098NHI)
(Submitter supplied) shRNA knockdown against RPS19_13 in K562 cells followed by RNA-seq. (RPS19_BGKLV19)  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/GSE88nnn/GSE88026/
Series		Accession: GSE88026	ID: 200088026

3788. RAMPAGE from NCI-H460 (ENCSR093UPQ)
(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 RAMPAGE 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 (BED, BIGBED, BIGWIG, GFF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88022/
Series		Accession: GSE88022	ID: 200088022

3789. shRNA RNA-seq from K562 (ENCSR092WKG)
(Submitter supplied) Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV19-B_repeat)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88021/
Series		Accession: GSE88021	ID: 200088021

3790. siRNA RNA-seq from K562 (ENCSR092LZV)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting both CTCF and RAD21 together.  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/GSE88nnn/GSE88020/
Series		Accession: GSE88020	ID: 200088020

3791. shRNA RNA-seq from HepG2 (ENCSR090UMI)
(Submitter supplied) shRNA knockdown against SMN1 in HepG2 cells followed by RNA-seq. (SMN1-BGHLV20)  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/GSE88nnn/GSE88018/
Series		Accession: GSE88018	ID: 200088018

3792. shRNA RNA-seq from K562 (ENCSR084SCN)
(Submitter supplied) Control shRNA against no target in K562 cells followed by RNA-seq. (non-target BGKLV13)  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/GSE88nnn/GSE88016/
Series		Accession: GSE88016	ID: 200088016

3793. shRNA RNA-seq from HepG2 (ENCSR082YGI)
(Submitter supplied) shRNA knockdown against RPLP0 in HepG2 cells followed by RNA-seq. (RPLP0_BGHLV18)  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/GSE88nnn/GSE88015/
Series		Accession: GSE88015	ID: 200088015

3794. shRNA RNA-seq from K562 (ENCSR082UWF)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against STIP1. (STIP1_BGKLV24_B)  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/GSE88nnn/GSE88014/
Series		Accession: GSE88014	ID: 200088014

3795. shRNA RNA-seq from HepG2 (ENCSR081IAO)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against CCAR1. (CCAR1_BGHLV20)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88013/
Series		Accession: GSE88013	ID: 200088013

3796. shRNA RNA-seq from K562 (ENCSR081EST)
(Submitter supplied) RNA-seq on K562 cells treated with a control shRNA against no target. (K-NT-26B)  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/GSE88nnn/GSE88012/
Series		Accession: GSE88012	ID: 200088012

3797. RAMPAGE from A375 (ENCSR080XAB)
(Submitter supplied) The libraries contained in this experiment come from independent growths of cell line A375. They are stranded PE101 Illumina Hi-Seq RAMPAGE 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 (BED, BIGBED, BIGWIG, GFF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88011/
Series		Accession: GSE88011	ID: 200088011

3798. shRNA RNA-seq from K562 (ENCSR079LMZ)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against DNAJC21. (DNAJC21_BGKLV24)  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/GSE88nnn/GSE88009/
Series		Accession: GSE88009	ID: 200088009

3799. shRNA RNA-seq from K562 (ENCSR077BPR)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against ESF1. (ESF1_BGKLV29)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88008/
Series		Accession: GSE88008	ID: 200088008

3800. shRNA RNA-seq from K562 (ENCSR076PMZ)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against EIF2S2. (EIF2S2_BGKLV29-B)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88007/
Series		Accession: GSE88007	ID: 200088007

3801. siRNA RNA-seq from K562 (ENCSR074DIJ)
(Submitter supplied) Control siRNA against no target in K562 cells followed by RNA-seq.  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/GSE88nnn/GSE88006/
Series		Accession: GSE88006	ID: 200088006

3802. shRNA RNA-seq from HepG2 (ENCSR070LJO)
(Submitter supplied) shRNA knockdown against DDX1 in HepG2 cells followed by RNA-seq. (DDX1-BGHLV20)  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/GSE88nnn/GSE88004/
Series		Accession: GSE88004	ID: 200088004

3803. shRNA RNA-seq from HepG2 (ENCSR067GHD)
(Submitter supplied) Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV30)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88002/
Series		Accession: GSE88002	ID: 200088002

3804. siRNA RNA-seq from K562 (ENCSR067CAG)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting CTCF.  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/GSE88nnn/GSE88001/
Series		Accession: GSE88001	ID: 200088001

3805. shRNA RNA-seq from HepG2 (ENCSR067AUG)
(Submitter supplied) shRNA knockdown against DDX59 in HepG2 cells followed by RNA-seq. (DDX59_BGHLV18)  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/GSE88nnn/GSE88000/
Series		Accession: GSE88000	ID: 200088000

3806. total RNA-seq from HepG2 (ENCSR061SFU)
(Submitter supplied) Initial nucleus fractions on HepG2 Long Total from Lecuyer  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/GSE87nnn/GSE87999/
Series		Accession: GSE87999	ID: 200087999

3807. shRNA RNA-seq from K562 (ENCSR060KRD)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against TROVE2. (TROVE2_BGKLV19-B_rpt)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87998/
Series		Accession: GSE87998	ID: 200087998

3808. shRNA RNA-seq from HepG2 (ENCSR060IWW)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against ESF1. (ESF1_BGHLV30)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87997/
Series		Accession: GSE87997	ID: 200087997

3809. polyA mRNA RNA-seq from HepG2 (ENCSR058OSL)
(Submitter supplied) Initial nucleus fractions on HepG2 Long Poly-A+ from Lecuyer  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/GSE87nnn/GSE87996/
Series		Accession: GSE87996	ID: 200087996

3810. RAMPAGE from SK-MEL-5 (ENCSR054RIR)
(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 RAMPAGE 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 (BED, BIGBED, BIGWIG, GFF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87995/
Series		Accession: GSE87995	ID: 200087995

3811. shRNA RNA-seq from HepG2 (ENCSR052IYH)
(Submitter supplied) shRNA knockdown against HNRNPC in HepG2 cells followed by RNA-seq. (HNRNPC-BGHLV20)  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/GSE87nnn/GSE87993/
Series		Accession: GSE87993	ID: 200087993

3812. siRNA RNA-seq from K562 (ENCSR051NHG)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting RAD21.  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 3 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87992/
Series		Accession: GSE87992	ID: 200087992

3813. shRNA RNA-seq from K562 (ENCSR048BWH)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPA1. (HNRNPA1_BGKLV21-B)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87990/
Series		Accession: GSE87990	ID: 200087990

3814. shRNA RNA-seq from HepG2 (ENCSR047VPW)
(Submitter supplied) shRNA knockdown against FAM120A in HepG2 cells followed by RNA-seq. (FAM120A_BGHLV16)  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/GSE87nnn/GSE87989/
Series		Accession: GSE87989	ID: 200087989

3815. shRNA RNA-seq from K562 (ENCSR047IUS)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPU. (HNRNPU_BGKLV21-B)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87988/
Series		Accession: GSE87988	ID: 200087988

3816. shRNA RNA-seq from K562 (ENCSR047AJA)
(Submitter supplied) shRNA knockdown against SUB1 in K562 cells followed by RNA-seq. (SUB1 BGKLV13)  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/GSE87nnn/GSE87987/
Series		Accession: GSE87987	ID: 200087987

3817. siRNA RNA-seq from K562 (ENCSR045TQN)
(Submitter supplied) RNA-seq on K562 cells treated with siRNA targeting ATF3.  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/GSE87nnn/GSE87986/
Series		Accession: GSE87986	ID: 200087986

3818. shRNA RNA-seq from HepG2 (ENCSR042QTH)
(Submitter supplied) Control shRNA against no target in HepG2 cells followed by RNA-seq. (non-target-BGHLV23)  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/GSE87nnn/GSE87985/
Series		Accession: GSE87985	ID: 200087985

3819. siRNA RNA-seq from K562 (ENCSR041KOX)
(Submitter supplied) Control siRNA (1x Buffer, 3x siRNA) against no target in K562 cells followed by RNA-seq.  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/GSE87nnn/GSE87983/
Series		Accession: GSE87983	ID: 200087983

3820. total RNA-seq from K562 (ENCSR040YBR)
(Submitter supplied) Initial nucleus fractions on K562 Long Total from Lecuyer  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/GSE87nnn/GSE87982/
Series		Accession: GSE87982	ID: 200087982

3821. shRNA RNA-seq from HepG2 (ENCSR040WAK)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against CALR. (CALR_BGHLV23)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87981/
Series		Accession: GSE87981	ID: 200087981

3822. shRNA RNA-seq from K562 (ENCSR040FSN)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against EIF4G2. (EIF4G2_BGKLV25)  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/GSE87nnn/GSE87980/
Series		Accession: GSE87980	ID: 200087980

3823. total RNA-seq from K562 (ENCSR038WEK)
(Submitter supplied) Initial membrane fractions on K562 Long Total from Lecuyer  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/GSE87nnn/GSE87979/
Series		Accession: GSE87979	ID: 200087979

3824. shRNA RNA-seq from K562 (ENCSR034VBA)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPUL1. (HNRNPUL1_BGKLV28)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87977/
Series		Accession: GSE87977	ID: 200087977

3825. shRNA RNA-seq from K562 (ENCSR032YMP)
(Submitter supplied) Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV29)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87975/
Series		Accession: GSE87975	ID: 200087975

3826. shRNA RNA-seq from K562 (ENCSR031RZS)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against TAF1168. (K-TAF1168-30B)  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/GSE87nnn/GSE87974/
Series		Accession: GSE87974	ID: 200087974

3827. shRNA RNA-seq from K562 (ENCSR031RRO)
(Submitter supplied) Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV25B)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87973/
Series		Accession: GSE87973	ID: 200087973

3828. shRNA RNA-seq from K562 (ENCSR029LGJ)
(Submitter supplied) shRNA knockdown against DDX51 in K562 cells followed by RNA-seq. (DDX51_BGKLV19)  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/GSE87nnn/GSE87971/
Series		Accession: GSE87971	ID: 200087971

3829. shRNA RNA-seq from HepG2 (ENCSR028YAQ)
(Submitter supplied) shRNA knockdown against PA2G4 in HepG2 cells followed by RNA-seq. (PA2G4_BGHLV16)  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/GSE87nnn/GSE87969/
Series		Accession: GSE87969	ID: 200087969

3830. shRNA RNA-seq from K562 (ENCSR023HWI)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against KHDRBS1. (KHDRBS1_BGKLV24)  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/GSE87nnn/GSE87962/
Series		Accession: GSE87962	ID: 200087962

3831. RAMPAGE from HT1080 (ENCSR022PAU)
(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 RAMPAGE 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 (BED, BIGBED, BIGWIG, GFF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87960/
Series		Accession: GSE87960	ID: 200087960

3832. polyA mRNA RNA-seq from HepG2 (ENCSR019MXZ)
(Submitter supplied) Initial insoluble fractions on HepG2 Long Poly-A+ from Lecuyer  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/GSE87nnn/GSE87958/
Series		Accession: GSE87958	ID: 200087958

3833. shRNA RNA-seq from HepG2 (ENCSR016XPB)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against NPM1. (NPM1_BGHLV26)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87957/
Series		Accession: GSE87957	ID: 200087957

3834. shRNA RNA-seq from K562 (ENCSR014VQS)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against RECQ1. (K-RECQ1-30B)  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/GSE87nnn/GSE87956/
Series		Accession: GSE87956	ID: 200087956

3835. shRNA RNA-seq from HepG2 (ENCSR012DAF)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against APOBEC3C. (APOBE-BGHLV22)  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/GSE87nnn/GSE87955/
Series		Accession: GSE87955	ID: 200087955

3836. shRNA RNA-seq from HepG2 (ENCSR011BBS)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against SART3. (SART3-BGHLV22)  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/GSE87nnn/GSE87954/
Series		Accession: GSE87954	ID: 200087954

3837. shRNA RNA-seq from K562 (ENCSR007XKL)
(Submitter supplied) shRNA knockdown against NFX1 in K562 cells followed by RNA-seq. (NFX1 BGKLV13)  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/GSE87nnn/GSE87953/
Series		Accession: GSE87953	ID: 200087953

3838. RAMPAGE from SK-MEL-5 (ENCSR007RIV)
(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 RAMPAGE 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 (BED, BIGBED, BIGWIG, GFF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87952/
Series		Accession: GSE87952	ID: 200087952

3839. shRNA RNA-seq from K562 (ENCSR004RGI)
(Submitter supplied) shRNA knockdown against RPS10 in K562 cells followed by RNA-seq. (RPS10 BGKLV13)  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/GSE87nnn/GSE87951/
Series		Accession: GSE87951	ID: 200087951

3840. shRNA RNA-seq from HepG2 (ENCSR004OSI)
(Submitter supplied) shRNA knockdown against DNAJC2 in HepG2 cells followed by RNA-seq. (DNAJC2-57-BGHLV20)  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/GSE87nnn/GSE87950/
Series		Accession: GSE87950	ID: 200087950

3841. shRNA RNA-seq from HepG2 (ENCSR003LSA)
(Submitter supplied) RNA-seq on HepG2 cells treated with an shRNA knockdown against SNRNP200. (SNRNP200_BGHLV26)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87948/
Series		Accession: GSE87948	ID: 200087948

3842. shRNA RNA-seq from K562 (ENCSR000YYN)
(Submitter supplied) RNA-seq on K562 cells treated with an shRNA knockdown against AKAP8. (AKAP8_BGKLV32)  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: GPL16791 2 Samples
FTP download: GEO (BIGWIG, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87946/
Series		Accession: GSE87946	ID: 200087946

3843. RAMPAGE from K562 (ENCSR000AER)
(Submitter supplied) The libraries contained in this experiment come from independent growths of cell line K562.  They are stranded PE101 Illumina Hi-Seq RAMPAGE 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 (BED, BIGBED, BIGWIG, GFF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87922/
Series		Accession: GSE87922	ID: 200087922

3844. Tristetraprolin disables prostate cancer maintenance by impairing proliferation and metabolic function
(Submitter supplied) Tristetraprolin (TTP) is an RNA-binding protein that post-transcriptionally suppresses gene expression by delivering mRNA cargo to processing bodies (P-bodies) where the mRNA is degraded. TTP functions as a tumor suppressor in a mouse model of B cell lymphoma, and in some human malignancies low TTP expression correlates with reduced survival. Here we report important prognostic and functional roles for TTP in human prostate cancer. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87532/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA345046
Series		Accession: GSE87532	ID: 200087532

3845. Tumor-Specific Retrogene NANOGP8 Reprograms Prostate Cancer Cells to Castration Resistance by Engaging the FOXA1/AR Signaling Axis and MYC
(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 31 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74800/
Series		Accession: GSE74800	ID: 200074800

3846. Tumor-Specific Retrogene NANOGP8 Reprograms Prostate Cancer Cells to Castration Resistance by Engaging the FOXA1/AR Signaling Axis and MYC [RNA-seq]
(Submitter supplied) Targeted disruption of the embryonic stem cell (ESC) self-renewal and pluripotency factor NANOG diminishes cancer cell clonogenic growth in vitro and tumor development in vivo. NANOG has also been shown to augment CSC properties and propel the emergence of castration-resistance prostate cancer (CRPC) phenotypes. Here, we investigate the molecular mechanisms underlying NANOG-mediated oncogenesis and prostate cancer progression to androgen independence. 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/GSE74nnn/GSE74798/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA301565
Series		Accession: GSE74798	ID: 200074798

3847. Single cell RNA-seq analysis of oligodendroglioma
(Submitter supplied) To understand the diversity of expression states within oligodendroglioma tumors, we obtained six freshly resected samples, profiled ~1000 cells from each tumor and examined their diversity.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 4825 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70630/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA289244
Series		Accession: GSE70630	ID: 200070630

3848. Cross-species transcriptome profiling identifies new alveolar epithelial type I cell-specific genes
(Submitter supplied) Diseases involving the distal lung alveolar epithelium include chronic obstructive pulmonary disease (COPD), idiopathic pulmonary fibrosis (IPF) and lung adenocarcinoma. Accurate labeling of specific cell types is critical for determining the contribution of each to pathogenesis of these diseases. The distal lung alveolar epithelium is comprised of two cell types, alveolar epithelial type 1 (AT1) and type 2 (AT2) cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66627/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA277526
Series		Accession: GSE66627	ID: 200066627

3849. Genome-wide Gene Expression Profiling in DLBCL Cell Lines Treated with CUDC-907
(Submitter supplied) CUDC-907 is a small-molecule dual-acting inhibitor of HDACs and PI3Ks, which effectively suppresses the growth and survival of MYC-altered DLBCL. To evaluate the effect of CUDC-907 on MYC-associated genes, two DLBCL cell lines were treated with CUDC-907, a total of 948 differentially regulated genes were identified. 24 genes from the CUDC-907–regulated 948-gene set present either in the "HALLMARK_MYC_TARGETS_V1” 200-gene set or in the “HALLMARK_MYC_TARGETS_V2” 58-gene set in the Molecular Signatures Database (MSigDB). 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/GSE89nnn/GSE89339/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA352043
Series		Accession: GSE89339	ID: 200089339

3850. FOXA1 overexpression mediates endocrine resistance by increasing IL-8 in oestrogen receptor-positive 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: GPL9052 17 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75372/
Series		Accession: GSE75372	ID: 200075372

3851. Gene expression profiling of tamoxifen-resistant breast cancer MCF7L cells
(Submitter supplied) Endocrine resistance is a major obstacle in treating estrogen receptor α (ER)-positive (+) breast cancer.  In order to better understand the mechanism of endocrine resistance, we established a stable tamoxifen-resistant (TamR) MCF7L cell model by culturing the parental (P) MCF7L cells in the presence of 100 nM of 4-hydroxytamoxifen (4HT) for over 6 months.  To characterize the transcriptomic profiles in these cells, we performed an RNA-seq analysis.
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/GSE75nnn/GSE75369/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA304011
Series		Accession: GSE75369	ID: 200075369

3852. Widespread chromatin accessibility at repetitive elements links embryonic stem cells with human cancer
(Submitter supplied) Examination of chromatin accessibility in three human embryonic stem cell lines unexpectedly identified a stem cell signature consisting of widespread enrichment of repetitive elements (RE).  Integrating genomic and biochemical approaches we found that RE in accessible chromatin are flanked by well positioned nucleosomes and distinct histone modifications, similar to that of other regulatory elements. 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 (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75172/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA302676
Series		Accession: GSE75172	ID: 200075172

3853. RNA sequencing of Formalin-Fixed, Paraffin-Embedded Specimens for Gene Expression Quantification and Data Mining
(Submitter supplied) We compared the RNAseq data consistency between Ribo-Zero and RNase H kits
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/GSE74nnn/GSE74270/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA299608
Series		Accession: GSE74270	ID: 200074270

3854. DNA methylome analysis of pediatric acute lymphoblastic leukemia cells reveals stochastic de novo DNA methylation in CpG islands.
(Submitter supplied) We used whole genome bisulfite sequencing (WGBS) to determine the DNA methylation levels at single base-pair resolution of four patients with different subtypes of pediatric ALL together with RNA-sequencing to increase our understanding of the leukemic transformation in ALL.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform: GPL10999 49 Samples
FTP download: GEO (BED, BEDGRAPH, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76270/
Series		Accession: GSE76270	ID: 200076270

3855. CXCR4 regulates extra-medullary myeloma through epithelial-mesenchymal transition-like transcriptional activation
(Submitter supplied) We have developed EMD- and BM-prone and defined the presence of an EMT-like mRNA signature in both EMD- and BM-prone clones.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (RPKM) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68538/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA283034
Series		Accession: GSE68538	ID: 200068538

3856. Global loss of epigenetic and transcriptional fidility defines a subclass of cancer with immunotherapy resistance
(Submitter supplied) We report that some cancers have extensive loss of epigenetic and transcriptional fidelity, characterized widespread spurious transcription and mRNA processing defects (Loss of transcriptional fidelity: LTF+). LTF impairs transcriptional elongation and imposes a highly specific molecular phenotype where pathways regulated by long genes, such as those involved in inflammatory response are consistently impaired in LTF+ tumors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85870/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA339588
Series		Accession: GSE85870	ID: 200085870

3857. RNA-seq analysis of mRNAs immunoprecipitated by wild-type (WT), phospho-mimetic (S200D), or phospho-null (S200A) FLAG-LIN28A
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL18573 36 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83906/
Series		Accession: GSE83906	ID: 200083906

3858. RNA-seq analysis of mRNAs immunoprecipitated by wild-type (WT) or phospho-mimetic (S200D) FLAG-LIN28A in PA1 cells
(Submitter supplied) To explore the effect of LIN28 (S200) phosphorylation on LIN28's association with mRNAs on a transcriptome-wide scale, we performed mRNA-seq on RNAs immunoprecipitated (RIP-seq) by wild-type (WT) or phospho-mimetic (S200D) LIN28 in PA1 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 18 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83905/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA327371
Series		Accession: GSE83905	ID: 200083905

3859. RNA-seq analysis of mRNAs immunoprecipitated by wild-type (WT) or phospho-null (S200A) FLAG-LIN28A in HeLa cells
(Submitter supplied) To explore the effect of LIN28 (S200) phosphorylation on LIN28's association with mRNAs on a transcriptome-wide scale, we performed mRNA-seq on RNAs immunoprecipitated (RIP-seq) by wild-type (WT) or phospho-null (S200A) LIN28 in HeLa cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 18 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83904/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA327372
Series		Accession: GSE83904	ID: 200083904

3860. An interaction with Ewing's sarcoma breakpoint protein EWS defines the specific oncogenic mechanism of ETS factors rearranged in prostate cancer
(Submitter supplied) ERG activates prostate cancer specific gene expression program by recuriting RNA binding protein EWS
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81493/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA321758
Series		Accession: GSE81493	ID: 200081493

3861. Merkel cell polyomavirus small T antigen promotes pro-glycolytic metabolic perturbations required for transformation
(Submitter supplied) Merkel cell polyomavirus (MCPyV) is an etiological agent of Merkel cell carcinoma (MCC), a highly aggressive skin cancer. The MCPyV small tumor antigen (ST) is required for maintenance of MCC and can transform normal cells. To gain insight into cellular perturbations induced by MCPyV ST, we performed transcriptome analysis of normal human fibroblasts with inducible expression of ST. MCPyV ST dynamically alters the cellular transcriptome with increased levels of glycolytic genes, including the monocarboxylate lactate transporter SLC16A1 (MCT1). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 78 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79968/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA317534
Series		Accession: GSE79968	ID: 200079968

3862. Tracing Enhancer Networks using Epigenetic Traits (TENET)
(Submitter supplied) Although technological advances now allow increased tumor profiling, a detailed understanding of the mechanisms leading to the development of different cancers remains elusive. Our approach towards understanding the molecular events that lead to cancer is to characterize changes in transcriptional regulatory networks between normal and tumor tissue. Because enhancer activity is thought to be critical in regulating cell fate decisions, we have focused our studies on distal regulatory elements and transcription factors that bind to these elements. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL11154 GPL18573 29 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78913/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA314348
Series		Accession: GSE78913	ID: 200078913

3863. Overexpression of PHF8 promotes an EMT-related gene signature in MCF10A cells
(Submitter supplied) PHF8 exerts distinct functions in different types of cancer. However, the mechanisms underlying its specific functions in each case remain obscure. To establish whether overexpression of PHF8 regulates the TGF-β induced the epithelial-mesenchymal transition (EMT), we treated MCF10A-Mock (control) and MCF10A-PHF8wt (overexpressing wild-type PHF8) cells with TGF-β1 for 0, 24, 48 and 72 hours and performed RNA-seq in biological duplicates. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 16 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74377/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA299891
Series		Accession: GSE74377	ID: 200074377

3864. Gene expression of collecting duct carcinoma of the kidney
(Submitter supplied) The genetic landscape and molecular features of collecting duct carcinoma (CDC) of the kidney remain largely unknown. Herein, we performed whole exome sequencing (WES) and transcriptome sequencing (RNASeq) on 7 CDC samples (CDC1 -7). Among the 7 samples, 4 samples with matched non-tumor tissue were used for copy number analysis by SNP array data. No recurrent somatic SNVs were observed except for MLL, which was found to be mutated (p.V297I and p.F407C) in 2 samples. more...
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/GSE89nnn/GSE89122/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA350320
Series		Accession: GSE89122	ID: 200089122

3865. CD133+ vs. CD133- cells in GBML8, a primary glioblastoma tumorsphere culture
(Submitter supplied) CD133+ and CD133- cells were FACS islated from GBML8 cells to find gene signatures upregulated in cancer stem cells
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/GSE85nnn/GSE85297/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA338124
Series		Accession: GSE85297	ID: 200085297

3866. Modeling the ESR1 tyrosine 537 mutation with CRISPR-Cas9 for mechanistic studies and evaluation of therapeutic approaches for metastatic 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 GPL16791 17 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78286/
Series		Accession: GSE78286	ID: 200078286

3867. Modeling the ESR1 tyrosine 537 mutation with CRISPR-Cas9 for mechanistic studies and evaluation of therapeutic approaches for metastatic breast cancer [RNA-Seq]
(Submitter supplied) Estrogen receptor-α (ERα) is an important driver of breast cancer and is the target for hormonal therapies, anti-estrogens and drugs that limit estrogen biosynthesis (aromatase inhibitors). Mutations in the ESR1 gene identified in metastatic breast cancer provide a potential mechanism for acquired resistance to hormone therapies. We have used CRISPR-Cas9 mediated genome editing in the MCF-7 breast cancer cell line, generating MCF-7-Y537S. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 11 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78285/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA313091
Series		Accession: GSE78285	ID: 200078285

3868. Pan-cancer transcriptomic analysis associates long non-coding RNAs with key mutational driver events
(Submitter supplied) To identify genes regulated by NFE2L2 (Nrf2), we selected a lung cancer cell line (A549) in which NFE2L2 is normally active. Three transfections using siRNAs targeting NFE2L2 and four control transfections using two different negative control siRNAs were done. As a result, we found several genes up or down regulated in response to NFE2L2 inactivation in these cells.
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/GSE75nnn/GSE75452/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA299393
Series		Accession: GSE75452	ID: 200075452

3869. Direct regulation of alternative splicing by SMAD3 through interaction with PCBP1 is essential for the tumor-promoting role of TGF-beta
(Submitter supplied) To assess the global impact of TGF-beta on alternative splicing, we conducted RNA-seq of total RNAs isolated from various lines of HeLa cells that were generated for this study and treated without or with TGF-beta and EGF. Using rMAT tool from the RNA-Seq data and annotation of transcripts in GTF format, we identified differential alternative splicing events between untreated and treated cell lines. 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/GSE72nnn/GSE72419/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA290799
Series		Accession: GSE72419	ID: 200072419

3870. AZ1366: An inhibitor of tankyrase and the canonical Wnt pathway that limits the persistence of non-small cell lung cancer cells following EGFR inhibition
(Submitter supplied) EGFR-mut NSCLC lines show differential suceptibility to inhibition of tankyrase in the presence of EGFR inhibitors
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/GSE80802/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA320000
Series		Accession: GSE80802	ID: 200080802

3871. Large-scale epigenetic reprogramming is punctuated late during the evolution of pancreatic cancer progression [RNA-Seq]
(Submitter supplied) During pancreatic cancer progression, heterogeneous subclonal populations evolve in the primary tumor that possess differing capacities to metastasize and cause patient death. However, the genetics of metastasis reflects that of the primary tumor, and PDAC driver mutations arise early. This raises the possibility than an epigenetic process could be operative late. Using an exceptional resource of paired patient samples, we found that different metastatic subclones from the same patient possessed remarkably divergent malignant properties and global epigenetic programs. 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/GSE63nnn/GSE63124/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA266736
Series		Accession: GSE63124	ID: 200063124

3872. Large-scale epigenetic reprogramming is punctuated late during the evolution of pancreatic cancer progression
(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; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL11154 GPL9138 60 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63126/
Series		Accession: GSE63126	ID: 200063126

3873. Nuclear TIGAR mediates an epigenetic-metabolic loop via Nrf2 for cancer therapeutics resistance
(Submitter supplied) Epigenetic and metabolic reprogrammings are implicated in cancer progression with unclear mechanisms. We report here that the histone methyltransferase NSD2 drives cancer cell and tumor resistance to therapeutics such as tamoxifen, doxorubicin, and radiation by reprogramming of glucose metabolism. NSD2 coordinately up-regulates expression of TIGAR, HK2 and G6PD and stimulates pentose phosphate pathway (PPP) production of NADPH for ROS reduction. 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/GSE62613/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA264542
Series		Accession: GSE62613	ID: 200062613

3874. MOF acetyl transferase regulates transcription and respiration in mitochondria
(Submitter supplied) Histone acetylation is sensitive to metabolic cues, however interplay between histone acetyl transferases and cellular metabolism remains poorly understood. Here we report the localization of a classical nuclear HAT- MOF and members of Non-Specific Lethal complex in mitochondria. MOF regulates expression of oxidative phosphorylation (OXPHOS) genes, residing in both nuclear and mitochondrial genomes, selectively in aerobically respiring cells. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL17021 GPL16791 19 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77784/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA311550
Series		Accession: GSE77784	ID: 200077784

3875. Gene expression profiling associated with knockdown of RNF20 in human normal and malignant lung epithelial cell lines
(Submitter supplied) The experiment was designed to display differential gene expression profiling in one lung epithelial cell BEAS2-B, and three lung cancer cell lines A549, H1299, H460 cells upon knockdown of RNF20, by using RNAseq technology.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88943/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA349163
Series		Accession: GSE88943	ID: 200088943

3876. Impact of RNA degradation on fusion detection by RNA-seq
(Submitter supplied) Purpose: Popular methods for library preparation in RNA-seq such as Illumina TruSeq® RNA v2 kit use a poly-A pulldown strategy. Such methods can cause loss of coverage at the 5’ end of genes, impacting the ability to detect fusions when used on degraded samples. The goal of this study was to quantify the effects RNA degradation has on fusion detection when using poly-A selected mRNA and to identify the variables involved in this process Methods: Total RNA was extracted from solid tumor tissue and whole blood using the Qiagen® miRNeasy Micro and Mini kits, respectively. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 29 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80126/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA318407
Series		Accession: GSE80126	ID: 200080126

3877. Hypoxia Mediated Downregulation of miRNA Biogenesis Leads to Increased Tumor 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; Non-coding RNA profiling by array
Platforms: GPL16288 GPL13264 28 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE52nnn/GSE52744/
Series		Accession: GSE52744	ID: 200052744

3878. RNA-seq analysis of Hypoxia and Normoxia cultured cancer cells
(Submitter supplied) Purpose: To study differential mRNA and precursor miRNA expression under hypoxia exposure in cancer cells. We treated ovarian cancer cell line A2780 under hypoxia condition at different time points. Normoxi acultured cells at corresponding time point were used as controls.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL16288 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE52nnn/GSE52695/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA229843
Series		Accession: GSE52695	ID: 200052695

3879. Novel metastatic models of human esophageal adenocarcinoma highlight the importance of E-cadherin in cancer metastasis
(Submitter supplied) We report the identification of FLO-1, and derivation of its isogenic companion FLO-1LM, as two spontaneously metastatic cell line models of human esophageal adenocarcinoma (EAC). We performed genome-wide RNAseq comparing FLO-1LM and FLO-1 parental cells to gain molecular insights into the phenotypic differences between these two cell lines. Using an adjusted p-value<0.05, a total of 375 (307 downregulated, 68 upregulated) genes were differentially regulated in FLO-1LM compared with parental cells. 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/GSE88nnn/GSE88802/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA348681
Series		Accession: GSE88802	ID: 200088802

3880. OmoMYC blunts promoter invasion by oncogenic MYC to inhibit gene expression characteristic of MYC-dependent tumors
(Submitter supplied) MYC genes have both essential roles during normal development and exert oncogenic functions during tumorigenesis. Expression of a dominant-negative allele of MYC, termed OmoMYC, can induce rapid tumor regression in mouse models with little toxicity for normal tissues. How OmoMYC discriminates between physiological and oncogenic functions of MYC is unclear. We have solved the crystal structure of OmoMYC and show that it forms a stable homodimer and as such recognizes DNA in the same manner as the MYC/MAX heterodimer. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms: GPL18573 GPL19057 GPL11002 44 Samples
FTP download: GEO (TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77328/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA310063
Series		Accession: GSE77328	ID: 200077328

3881. Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant mRNA signatures
(Submitter supplied) Tumor-infiltrating macrophages, NK cells, CD8+ and CD4+ T cells sorted from clear cell renal cell carcinoma patient specimens.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84697/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA330854
Series		Accession: GSE84697	ID: 200084697

3882. Human liver RNA-seq data corresponding to uninfected non-malignant, HCV infected non-malignant, and HCV+ HCC tissue
(Submitter supplied) We aimed to identify epigenetic regulators of transcription that may be involved in the development and the progression of HCV-associated HCC.  We used directional RNAseq for transcriptome profiling that we correlate with genome wide DNA methylation data.
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/GSE82nnn/GSE82177/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA324260
Series		Accession: GSE82177	ID: 200082177

3883. Epigenetic targeting of immunocheckpoint PD-L1 by BET bromodomain inhibition
(Submitter supplied) Epigenetic regulators have emerged as exciting targets for cancer therapy.  Additionally, restoration of antitumor immunity by blocking the PD-L1 signaling using antibodies has proven to be beneficial in cancer therapy. Here we show that BET bromodomain inhibition suppresses PD-L1 expression and restores antitumor immunity in ovarian cancer. CD274 (encoding PD-L1) is a direct target of BRD4-mediated gene transcription. 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/GSE81nnn/GSE81698/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA322328
Series		Accession: GSE81698	ID: 200081698

3884. polyA mRNA RNA-seq from HeLa-S3 (ENCSR000CPR)
(Submitter supplied) The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line HeLa-S3. They are stranded PE76 Illumina GAIIx 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: GPL10999 2 Samples
FTP download: GEO (BED, BIGBED, BIGWIG, GTF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86661/
Series		Accession: GSE86661	ID: 200086661

3885. polyA mRNA RNA-seq from K562 (ENCSR000CPH)
(Submitter supplied) The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line K562. They are stranded PE76 Illumina GAIIx 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: GPL10999 2 Samples
FTP download: GEO (BED, BIGBED, BIGWIG, GTF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86660/
Series		Accession: GSE86660	ID: 200086660

3886. polyA mRNA RNA-seq from HepG2 (ENCSR000CPE)
(Submitter supplied) The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line HepG2. They are stranded PE76 Illumina GAIIx 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: GPL10999 2 Samples
FTP download: GEO (BED, BIGBED, BIGWIG, GTF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86659/
Series		Accession: GSE86659	ID: 200086659

3887. polyA mRNA RNA-seq from A549 (ENCSR000CON)
(Submitter supplied) The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line A549. They are stranded PE76 Illumina GAIIx 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: GPL10999 2 Samples
FTP download: GEO (BED, BIGBED, BIGWIG, GTF, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86657/
Series		Accession: GSE86657	ID: 200086657

3888. Muscleblind-like 1 suppresses breast cancer metastatic colonization and stabilizes metastasis suppressor transcripts
(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: GPL11154 GPL10558 16 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76488/
Series		Accession: GSE76488	ID: 200076488

3889. MBNL1-dependent modulation of gene expression in MDA-MB-231 breast cancer cells
(Submitter supplied) To identify MBNL1-dependent changes in gene expression, MDA-MB-231 cells expressing either control or MBNL1-targeting shRNAs were transcriptomically profiled.
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/GSE76487/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA307562
Series		Accession: GSE76487	ID: 200076487

3890. Therapeutic targeting of GCB- and ABC-DLBCLs by rationally designed BCL6 inhibitors
(Submitter supplied) BCL6 inhibitor induces derepression of BCL6 target genes and shows a similar transcriptional program to BCL6 siRNA
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 18 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79888/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA317329
Series		Accession: GSE79888	ID: 200079888

3891. Loss of CREBBP results in H3K27Ac loss at enhancers and gene expression repression in lymphoma cells
(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: GPL13112 GPL11154 57 Samples
FTP download: GEO (BIGBED, BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79686/
Series		Accession: GSE79686	ID: 200079686

3892. Loss of CREBBP results in gene expression repression in lymphoma cells
(Submitter supplied) KD of CREBBP at lymphoma cell line, MD901, results in reduced expression
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/GSE79nnn/GSE79684/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA316707
Series		Accession: GSE79684	ID: 200079684

3893. Transcriptomic analyses for the CSC-like properties under monolayer and sphere culture conditions in 293T and MCF-7 cells
(Submitter supplied) In order to verify the CSC-like properties in 3D spheres of 293T cells as compared to monolayer, MCF-7 breast cancer cells under monolayer and sphere culture conditions were used as a control. Corresponding author: Chul Geun Kim, Department of Life Science, Hanyang University, Seoul 133-791, Korea (e-mail, cgkim@hanyang.ac.kr).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 4 Samples
FTP download: GEO (TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86896/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA342854
Series		Accession: GSE86896	ID: 200086896

3894. Therapeutic targeting of GCB- and ABC-DLBCL by rationally designed BCL6 inhibitor
(Submitter supplied) Rationale: The BCL6 oncogene is constitutively activated by chromosomal translocations and amplification in ABC-DLBCLs, a class of DLBCLs that respond poorly to current therapies. Yet the role of BCL6 in maintaining these lymphomas has not been investigated. BCL6 mediates its effects by recruiting corepressors to an extended groove motif. Development of effective BCL6 inhibitors requires compounds exceeding the binding affinity of these corepressors. 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/GSE80nnn/GSE80351/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA318650
Series		Accession: GSE80351	ID: 200080351

3895. Molecular analysis of renal cell carcinoma with unclassfied histology
(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
Platforms: GPL18602 GPL16791 22 Samples
FTP download: GEO (CEL, OSCHP) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85971/
Series		Accession: GSE85971	ID: 200085971

3896. Molecular analysis of renal cell carcinoma with unclassfied histology [gene expression]
(Submitter supplied) Renal cell carcinomas with unclassified histology (uRCC) constitute a significant portion of aggressive non-clear cell RCC (nccRCC) that have no standard therapy. The oncogenic drivers in these tumors are unknown. We performed a molecular analysis of 62 high-grade primary uRCC, incorporating targeted cancer gene sequencing, RNA sequencing, Single Nucleotide Polymorphism array, fluorescence in-situ hybridization, immunohistochemistry, and cell-based assays. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 7 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85897/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA339705
Series		Accession: GSE85897	ID: 200085897

3897. Multi-parametric profiling of non-small cell lung cancers reveals distinct immunophenotypes
(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: GPL19965 GPL11154 221 Samples
FTP download: GEO (RCC) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84799/
Series		Accession: GSE84799	ID: 200084799

3898. Single-cell profiling of non small cell lung cancer associated B-cells.
(Submitter supplied) Background: Immune checkpoint blockade improves survival in a subset of patients with non-small cell lung cancer (NSCLC), but robust biomarkers that predict response to PD-1 pathway inhibitors are lacking.  Furthermore, our understanding of the diversity of the NSCLC tumor immune microenvironment remains limited.    Methods: We performed comprehensive flow-cytometric immunoprofiling on both tumor and immune cells from 51 NSCLCs and integrated this analysis with clinical and histopathologic characteristics, next generation sequencing, mRNA expression, and PD-L1 immunohistochemistry (IHC). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 192 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84789/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA331162
Series		Accession: GSE84789	ID: 200084789

3899. Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Escherichia coli; Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL16791 GPL18133 GPL16686 24 Samples
FTP download: GEO (CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87712/
Series		Accession: GSE87712	ID: 200087712

3900. Mechanistic evaluation and transcriptional signature of a Glutathione S-transferase Omega 1 inhibitor
(Submitter supplied) Glutathione S-transferase omega 1 (GSTO1) is an atypical GST isoform that is overexpressed in several cancers and has been implicated in drug resistance. Currently, no small-molecule drug targeting GSTO1 is under clinical development. In this study we show that silencing of GSTO1 with siRNA significantly impairs cancer cell viability, validating GSTO1 as a potential new target in oncology. We report on the development and characterization of a series of chloroacetamide-containing potent GSTO1 inhibitors. 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/GSE85nnn/GSE85899/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA339733
Series		Accession: GSE85899	ID: 200085899

3901. Histone H2A T120 phophorylation promotes oncogenic transformation via upregulation of cyclin D1y
(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; Expression profiling by array
Platforms: GPL9052 GPL16417 GPL6883 20 Samples
FTP download: GEO (IDAT, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84968/
Series		Accession: GSE84968	ID: 200084968

3902. p53 activity results in DNA replication fork processivity
(Submitter supplied) p53 induces cell death upon DNA damage, but this may not confer all of its tumor suppressor activity. We report that p53 activation enhances the processivity of DNA replication, as monitored by multi-label fiber assays, whereas removal of p53 reduces fork progression. This was observed in tumor-derived U2OS cells, but also in murine embryonic fibroblasts with heterozygous or homozygous p53 deletion, and in freshly isolated thymocytes from mice with differential p53 status. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 15 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87668/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA345510
Series		Accession: GSE87668	ID: 200087668

3903. Analysis  of active enhancers and direct androgen receptor target genes in VCaP prostate cancer cells
(Submitter supplied) Androgen receptor (AR) is typically overexpressed in castration-resistant prostate cancer (CRPC). CRPC-derived VCaP cells display an excessive number of chromatin AR-binding sites (ARBs). This study analyzed direct transcription programs of the AR, the prevalence of AR enhancers and the transcriptional regulators involved in the regulation of at the enhancer regions. The analysis utilized global nuclear run-on sequencing (GRO-seq). 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, BEDGRAPH, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84432/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA329137
Series		Accession: GSE84432	ID: 200084432

3904. The histone H3.3K36M mutation reprograms the epigenome of chondroblastomas
(Submitter supplied) Over 90% of chondroblastomas contain a heterozygous mutation replacing lysine 36 with methionine (K36M) in the histone H3 variant H3.3. The role of the H3.3K36M mutation in tumorigenesis of this typically benign bone tumor with high recurrence rates is unknown. Here, we show that H3K36 di- and tri-methylation (me2 and me3) levels are reduced globally in chondroblastomas, as well as in chondrocytes stably expressing the H3.3K36M mutation because the H3.3M36 mutation protein inhibits the activity of lysine methyl transferases, MMSET and SetD2. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 49 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75234/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA302855
Series		Accession: GSE75234	ID: 200075234

3905. Bromodomain-containing Protein 4 (BRD4) is Required for the Maintenance of a Mammary Epithelial Phenotype
(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 11 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72933/
Series		Accession: GSE72933	ID: 200072933

3906. Bromodomain-containing Protein 4 (BRD4) is Required for the Maintenance of a Mammary Epithelial Phenotype [RNA-Seq]
(Submitter supplied) Bromodomain-containing protein 4 (BRD4) is an important epigenetic reader which promotes gene transcription to modulate cell-specific functions and is under intensive investigation for its potential as an anti-tumor therapeutic target. However, the role of BRD4 in non-transformed cells remains unclear. Here we demonstrate that BRD4 is required for the expression of epithelial-specific genes and suppression of stem cell-like properties by binding to the distal regions of epithelial-related 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/GSE72nnn/GSE72932/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA295369
Series		Accession: GSE72932	ID: 200072932

3907. Crosstalk between androgen and proinflammatory signaling activates a distinct transcription program in prostate cancer cells
(Submitter supplied) Crosstalk of androgen signaling induced with dihydrotestosterone (DHT) and proinflammatory signaling induced with tumor necrosis-factor alpha (TNFa) was analyzed in prostate cancer cells (LNCaP) by following chromatin binding of androgen receptor (AR), p65 (activating subunit of nuclear-factor kappa-B [NFkB]), FOXA1 and PIAS1+2 chromatin binding using ChIP-seq and transcriptional changes using GRO-seq.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing
Platform: GPL11154 46 Samples
FTP download: GEO (BED, TDF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83860/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA327218
Series		Accession: GSE83860	ID: 200083860

3908. EPRS is a Critical Regulator of Cell Proliferation and Estrogen Signaling in ER+ Breast Cancer
(Submitter supplied) Aminoacyl tRNA synthetases (ARSs) are a class of enzymes with well-conserved housekeeping functions in cellular translation.  Recent evidence suggests that ARS genes may participate in a wide array of cellular processes, and may contribute to the pathology of autoimmune disease, cancer, and other diseases.  Several studies have suggested a role for the glutamyl prolyl tRNA synthetase (EPRS) in breast cancers, although none has demonstrated any underlying mechanism about how EPRS contributes to carcinogenesis. 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/GSE81162/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA318910
Series		Accession: GSE81162	ID: 200081162

3909. Whole genome analysis of the methylome and hydroxymethylome in normal and malignant lung and liver
(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; Other
Platform: GPL11154 40 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70091/
Series		Accession: GSE70091	ID: 200070091

3910. Whole genome analysis of the methylome and hydroxymethylome in normal and malignant lung and liver [RNA-Seq]
(Submitter supplied) DNA methylation at the 5-postion of cytosine (5mC) is a well-established epigenetic modification which regulates gene expression and cellular plasticity in development and disease. The ten-eleven translocation (TET) gene family is able to oxidize 5mC to 5-hydroxmethylcytosine (5hmC), providing an active mechanism for DNA demethylation, and may also provide its own regulatory function. Here we applied oxidative bisulfite sequencing to generate whole-genome DNA methylation and hydroxymethylation maps at single-base resolution in paired human liver and lung normal and cancer. 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/GSE70nnn/GSE70089/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA287623
Series		Accession: GSE70089	ID: 200070089

3911. BRD4 localization to lineage-specific enhancers is associated with a distinct transcription factor repertoire
(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 80 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE82nnn/GSE82297/
Series		Accession: GSE82297	ID: 200082297

3912. mRNA expression profile of Lymphocytes
(Submitter supplied) Vα24 invariant natural killer T (iNKT) cells are a subset of T lymphocytes implicated in the regulation of broad immune responses. They recognize lipid antigens presented by CD1d on antigen-presenting cells and induce both innate and adaptive immune responses, which enhance effective immunity against cancer, represent promising therapeutic target. However, reduced iNKT-cell numbers and function have been observed in many patients with cancer. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 17 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76371/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA307108
Series		Accession: GSE76371	ID: 200076371

3913. CPEB4 RNA immunoprecipitation and sequencing (RIP-seq) in SK-Mel-103 melanoma cells
(Submitter supplied) Identification of the mRNAs bound by CPEB4 in melanoma cells
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 4 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75773/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA305305
Series		Accession: GSE75773	ID: 200075773

3914. ChIP-seq and RNA-seq in BGC823 cells after downregulation of GAS1 expression
(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 15 Samples
FTP download: GEO (TDF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63765/
Series		Accession: GSE63765	ID: 200063765

3915. A novel lncRNA GAS1 promotes gastric carcinogenesis and acts as a modular scaffold of WDR5 and KAT2A complexes to specify the histone modification pattern [RNA-seq]
(Submitter supplied) To elucidate whether GAS1 plays a role in gastric cancer tumorigenesis, a RNA-seq analysis was performed to compare the gene expression profiles of GAS1 shRNA and control shRNA transfectants.
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/GSE63764/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA269027
Series		Accession: GSE63764	ID: 200063764

3916. Transcriptome changes due to nuclear penetration of cancer extracellular vesicles
(Submitter supplied) Extracellular membrane vesicles (EVs) function as vehicles of intercellular communication in autocrine or paracrine manner. We report that cancer-derived EV biomaterials reach nuclei of human melanoma and breast carcinoma cells and multipotent mesenchymal stromal cells  (MSCs) through Rab7+ late endosome subdomains that penetrate into nuclear envelope invaginations. MSCs were exposed to cancer Evs in the presence or absence of drugs that block nucler import or export through the nuclear pores. 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/GSE83nnn/GSE83559/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA326339
Series		Accession: GSE83559	ID: 200083559

3917. LncRNAs specific signature in acute myeloid leukemia with intermediate risk
(Submitter supplied) The aim of this study was to investigate the role of lncRNAs in acute myeloid leukemia with normal cytogenetics (NC-AML). To this end, we used RNA-sequencing approach on forty NC-AML to evaluate the lncRNAs expression profile.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 40 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62852/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA265845
Series		Accession: GSE62852	ID: 200062852

3918. Effect daunorubicin treatment on the transcriptome of HCT116 cells [RNA-seq]
(Submitter supplied) We used RNA-seq to measure the transcriptome of HCT116 in response to the DNA damaging agent daunorubicin
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86190/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA340780
Series		Accession: GSE86190	ID: 200086190

3919. Whole transcriptome splicing analysis in isogenic lung epithelial and adenocarcinoma cell lines with or without a recurrent splicing factor mutation, U2AF1 (S34F)
(Submitter supplied) The splicing factor gene, U2AF1, is recurrently mutated in a variety of human cancers, including lung adenocarcinomas.  The most frequent U2AF1 mutant, U2AF1 p.Ser34Phe (S34F), induces specific changes in pre-mRNA splicing, but it is unclear how these splicing changes are regulated. We have used genomic editing methods to modify the U2AF1 gene locus in an immortalized human bronchial epithelial cell line (HBEC3kt) and in human lung adenocarcinoma cells with pre-existing U2AF1 alleles, creating a U2AF1 S34F allele in the endogenous locus of HBEC3kts and inactivating U2AF1 S34F alleles in two lung adenocarcinoma cell lines (H441 and HCC78). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL11154 16 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80136/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA318018
Series		Accession: GSE80136	ID: 200080136

3920. The methylome of Alu repeats in colon cancer (RNA-Seq)
(Submitter supplied) Poly-A messenger RNA data for the NSUMA-based assessment of Alu repeats methylation status in colorectal cancer
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/GSE87nnn/GSE87400/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA344664
Series		Accession: GSE87400	ID: 200087400

3921. Epigenomic Profiling of Primary Gastric Adenocarcinoma Reveals Super-enhancer Heterogeneity
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Methylation profiling by genome tiling array; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Genome variation profiling by SNP array
Platforms: GPL13534 GPL11154 GPL6801 259 Samples
FTP download: GEO (BED, BEDGRAPH, CEL, IDAT, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85467/
Series		Accession: GSE85467	ID: 200085467

3922. Epigenomic Profiling of Primary Gastric Adenocarcinoma Reveals Super-enhancer Heterogeneity [RNA-seq]
(Submitter supplied) Regulatory elements in cancer remain poorly characterized in primary solid tumors. Here we applied microscale histone modification profiling to delineate the landscape of somatic promoters and super-enhancers in primary gastric adenocarcinoma, analyzing 94 epigenomic  profiles of primary tumors, normal tissues, and cell lines
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 27 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85465/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA338610
Series		Accession: GSE85465	ID: 200085465

3923. Quantitative profiling of the UGT transcriptome in human drug metabolizing tissues
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 30 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE82nnn/GSE82292/
Series		Accession: GSE82292	ID: 200082292

3924. Divergent expression and metabolic functions of human glucuronosyltransferases through alternative splicing
(Submitter supplied) Purpose: Maintenance of cellular homeostasis and xenobiotics detoxification relies on the glucuronidation pathway mediated by 19 human UDP-glucuronosyltransferase enzymes (UGTs) encoded by 10 highly homologous genes. Recent evidence suggests that alternative splicing largely expands the human UGT transcriptome. Results: we establish the quantitative portrait of the UGT transcriptome in major metabolic organs and characterize cellular functions of selected alternative UGT isoforms with novel in-frame sequences. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 15 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80463/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA318998
Series		Accession: GSE80463	ID: 200080463

3925. Spatial proximity to fibroblasts impacts molecular features and therapeutic sensitivity of breast cancer cells influencing clinical outcomes
(Submitter supplied) Using a 3D co-culture model, we identified significant sub-type-specific changes in the gene expression, metabolic, and therapeutic sensitivity profiles of breast cancer cells in contact with cancer-associated fibroblasts (CAFs). CAF-induced gene expression signatures predicted clinical outcome and immune-related differences in the microenvironment. We found that CAFs strongly protect carcinoma cells from lapatinib, attributable to its reduced accumulation in carcinoma cells and an elevated apoptotic threshold. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL16791 GPL18573 23 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80333/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA318622
Series		Accession: GSE80333	ID: 200080333

3926. TUT-DIS3L2 is a mammalian surveillance pathway for aberrant structured non-coding RNAs.
(Submitter supplied) Uridylation of various cellular RNA species at the 3' end has been generally linked to RNA degradation. In mammals, uridylated pre-let-7 miRNAs and mRNAs are targeted by the 3' to 5' exoribonuclease DIS3L2. Mutations in DIS3L2 have been associated with Perlman syndrome and with Wilms tumor susceptibility. Using in vivo cross-linking and immunoprecipitation (CLIP) method, we discovered the DIS3L2-dependent cytoplasmic uridylome of human cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL11154 9 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81537/
Series		Accession: GSE81537	ID: 200081537

3927. Uridylation-mediated RNA quality control pathway in mammalian cytoplasm [RNA-Seq]
(Submitter supplied) Uridylation of various cellular RNA species at the 3’ end has been generally linked to RNA degradation. Uridylated pre-miRNAs in mammals and uridylated mRNAs in fission yeast are targeted by the 3′ to 5′ exoribonuclease DIS3L2. In humans, DIS3L2 mutations have been associated with Perlman syndrome development and Wilms tumor susceptibility. In this work, we employ crosslinking in vivo and immunoprecipitation (CLIP) method to assess the RNA binding capacity of human DIS3L2 on a genome-wide scale. 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/GSE81nnn/GSE81534/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA321872
Series		Accession: GSE81534	ID: 200081534

3928. MCF10A H-Ras RNA-Seq
(Submitter supplied) Paired-end sequencing of Vector and H-Ras expressing cell lines: p53-del and WT-p53 We found that activated forms of H-Ras and PIK3CA oncogene lead to repression of p63, a p53 family member. They also lead to induction of EMT, a cancer-related process. Our results suggest that, through Ras regulation of p63, this oncogene can drive mammary epithelial cells towards greater invasive ability.
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/GSE81nnn/GSE81593/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA322079
Series		Accession: GSE81593	ID: 200081593

3929. Unique long non-coding RNA expression signature in ETV6/RUNX1-driven B-cell precursor acute lymphoblastic leukemia
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Non-coding RNA profiling by array; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL18573 GPL19197 103 Samples
FTP download: GEO (TAB, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79873/
Series		Accession: GSE79873	ID: 200079873

3930. RNA-sequencing of B-ALL cell lines, REH treated with LNA GapmeRs against four lncRNAs
(Submitter supplied) Overwhelming evidence indicates that long non-coding RNAs have essential roles in tumorigenesis. Nevertheless, their expression and role in pediatric B-cell precursor acute lymphoblastic leukemia has not been extensively explored. Here, we conducted a comprehensive analysis of the long non-coding RNA transcriptome in ETV6/RUNX1 positive BCP-ALL, one of the most frequent subtypes of pediatric leukemia. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 27 Samples
FTP download: GEO (TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79872/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA317295
Series		Accession: GSE79872	ID: 200079872

3931. RNA-sequencing of two the B-ALL cell lines, REH and 697
(Submitter supplied) Overwhelming evidence indicates that long non-coding RNAs have essential roles in tumorigenesis. Nevertheless, their expression and role in pediatric B-cell precursor acute lymphoblastic leukemia has not been extensively explored. Here, we conducted a comprehensive analysis of the long non-coding RNA transcriptome in ETV6/RUNX1 positive BCP-ALL, one of the most frequent subtypes of pediatric leukemia. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79871/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA317296
Series		Accession: GSE79871	ID: 200079871

3932. Developing a Novel Two-Dimensional Culture System to Enrich Human Prostate Luminal Progenitors That Can Function as a Cell of Origin for Prostate Cancer
(Submitter supplied) Elucidating the cell of origin of cancer has great significance in stratifying patients into appropriate treatment groups and for developing novel targeted therapies. Early studies demonstrate that only stem-like basal cells in the normal human prostate (NHP) can function as the cell of origin for prostate cancer (PCa). Here, we show that the organoids derived from bulkNHPluminal cells can also be tumorigenically transformed. 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/GSE74nnn/GSE74698/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA301175
Series		Accession: GSE74698	ID: 200074698

3933. Gene and microRNA expression changes induced by overexpression of SphK1 in papillary thyroid cancer cells
(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 8 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87312/
Series		Accession: GSE87312	ID: 200087312

3934. Gene and microRNA expression changes induced by overexpression of SphK1 in papillary thyroid cancer cells [RNA-seq]
(Submitter supplied) The oncogenic roles of Sphingosine kinase 1 (SphK1) in various cancers, including thyroid cancer, have been well demonstrated. However, miRNAs associated with the oncogenic roles of SphK1 remains largely unknown. The goal of this study is to detect the global gene and microRNA (miRNA) expression in response to Sphk1 over-expression and identify potential therapeutic targets. To achieve this, SphK1 was stably overexpressed in papillary thyroid cancer cell line TPC1. more...
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/GSE87nnn/GSE87307/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA344306
Series		Accession: GSE87307	ID: 200087307

3935. S-adenosyl-methionine treatment selectively block liver cancer cell lines transformation and invasiveness by alterations of cancer- and invasion specific transcriptome and methylome
(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 12 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87242/
Series		Accession: GSE87242	ID: 200087242

3936. S-adenosyl-methionine treatment selectively block liver cancer cell lines transformation and invasiveness by alterations of cancer- and invasion specific transcriptome and methylome (RNA-Seq)
(Submitter supplied) S-adenosyl methionine (SAM) is a ubiquitous methyl donor that was reported to have chemo- protective activity against liver cancer, however the molecular footprint of SAM has been unknown. We show here that SAM selectively inhibits growth, transformation and invasiveness of hepatocellular carcinoma cell lines but not normal primary liver cells. Analysis of the transcriptome of SAM treated and untreated cancer cell lines HepG2 and SKHep1 and primary liver cells reveals pathways involved in cancer and metastasis that are upregulated in cancer cells and silenced by SAM. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87240/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA343945
Series		Accession: GSE87240	ID: 200087240

3937. Candidate genes and pathways downstream of PAX8 involved in ovarian high-grade serous carcinoma
(Submitter supplied) Our goal was to identify candidate genes and pathways regulated by PAX8 that could be additional targets for the therapy of ovarian carcinoma. To reach this aim, we have determined the molecular profiles of ovarian cancer cells and in parallel of Fallopian tube epithelial cells by mean of a silencing approach followed by an RNA-seq analysis
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 12 Samples
FTP download: GEO (TXT, XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79572/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA316212
Series		Accession: GSE79572	ID: 200079572

3938. Genome-wide expression profile in FH-deficient vs FH-competent cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL17021 GPL16791 47 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77542/
Series		Accession: GSE77542	ID: 200077542

3939. Genome-wide expression profile in FH-deficient (UOK262) vs FH-competent (UOK262pFH) human cells derived from metastatsis to the mediastinum of a HLRCC patient
(Submitter supplied) Comparison of the transcriptome of human kideny cancer cells either wild-type for FH or FH-deficient. The UOK262 cells were isolated from mediastinum metastasis of a HLRCC patient (Yang et al. Cancer Genetics and Cytogenetics, Volume 196, Issue 1, 1 January 2010, Pages 45–55). FH function was restored in the UOK262 by re-expressing the FH transcript from an exogenous plasmid.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 27 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77538/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA310751
Series		Accession: GSE77538	ID: 200077538

3940. Profiles of prostate cancer cell lines
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Other; Expression profiling by high throughput sequencing
Platform: GPL11154 32 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87153/
Series		Accession: GSE87153	ID: 200087153

3941. Adaptation of a RAS pathway activation signature from FF to FFPE tissues in colorectal 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: GPL15048 GPL11154 GPL22404 326 Samples
FTP download: GEO (CEL, RCC) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86566/
Series		Accession: GSE86566	ID: 200086566

3942. Adaptation of a RAS pathway activation signature from FF to FFPE tissues in colorectal cancer (FFPE RNA-Seq III)
(Submitter supplied) Background: The KRAS gene is mutated in about 40% of colorectal cancer (CRC) cases, which has been clinically validated as a predictive mutational marker of intrinsic resistatnce to anti-EGFR inhibitor (EGFRi) therapy. Since nearly 60% of patients with a wild type KRAS fail to respond to EGFRi treatment, there is a need to develop more reliable molecular signatures to better predict response. Here we address the challenge of adapting a gene expression signature predictive of RAS pathway activation, created using fresh frozen (FF) tissues, for use with more widely available formalin fixed paraffin-embedded (FFPE) tissues. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 54 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86564/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA342194
Series		Accession: GSE86564	ID: 200086564

3943. Adaptation of a RAS pathway activation signature from FF to FFPE tissues in colorectal cancer (FFPE RNA-Seq II)
(Submitter supplied) Background: The KRAS gene is mutated in about 40% of colorectal cancer (CRC) cases, which has been clinically validated as a predictive mutational marker of intrinsic resistatnce to anti-EGFR inhibitor (EGFRi) therapy. Since nearly 60% of patients with a wild type KRAS fail to respond to EGFRi treatment, there is a need to develop more reliable molecular signatures to better predict response. Here we address the challenge of adapting a gene expression signature predictive of RAS pathway activation, created using fresh frozen (FF) tissues, for use with more widely available formalin fixed paraffin-embedded (FFPE) tissues. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 56 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86563/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA342184
Series		Accession: GSE86563	ID: 200086563

3944. Adaptation of a RAS pathway activation signature from FF to FFPE tissues in colorectal cancer (FFPE RNA-Seq I)
(Submitter supplied) Background: The KRAS gene is mutated in about 40% of colorectal cancer (CRC) cases, which has been clinically validated as a predictive mutational marker of intrinsic resistatnce to anti-EGFR inhibitor (EGFRi) therapy. Since nearly 60% of patients with a wild type KRAS fail to respond to EGFRi treatment, there is a need to develop more reliable molecular signatures to better predict response. Here we address the challenge of adapting a gene expression signature predictive of RAS pathway activation, created using fresh frozen (FF) tissues, for use with more widely available formalin fixed paraffin-embedded (FFPE) tissues. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 54 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86562/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA342185
Series		Accession: GSE86562	ID: 200086562

3945. Genome-wide epigenetic analyses and Transcriptional analysis  in NB4 cells expressing PML-RARalpha
(Submitter supplied) Illumina High-Throughput ChIP Sequencing profiling was performed using the H3K9K14ac antibody in NB4 cells treated with the compounds ATRA, MS-275,MC2392 (a hybrid molecule of ATRA with a 2-aminoanilide tail of the HDAC inhibitor MS-275) or solvent, DMSO. We find that MC2392 induces changes in H3 acetylation at a small subset of PML-RARα binding sites but also in regions not regulated by ATRA. Moreover, MC2392 alters expression of a number of stress-responsive and apoptotic genes.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL9052 GPL10999 12 Samples
FTP download: GEO (BED, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE50nnn/GSE50958/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA219427
Series		Accession: GSE50958	ID: 200050958

3946. Single-nucleotide-resolution mapping of HBV promoters using CAGE
(Submitter supplied) We provide a comprehensive map of transcription start sites (TSSs) for HBV at single nucleotide resolution using CAGE.
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL13112 11 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84186/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA328244
Series		Accession: GSE84186	ID: 200084186

3947. Loss of HDAC-mediated repression and gain of NF-kB activation underlies cytokine induction in ARID1A and PIK3CA mutation-driven ovarian cancer
(Submitter supplied) ARID1A is frequently mutated in ovarian clear-cell carcinoma (OCCC) and often co-exists with activating mutations of PIK3CA. Although induction of pro-inflammatory cytokines has been observed in this cancer, the mechanism by which the two mutations synergistically activate cytokine genes remains elusive. Here we established an in vitro model of OCCC by introducing ARID1A knock-down and mutant PIK3CA in a normal human ovarian epithelial cell line, which resulted in cell transformation and cytokine gene induction. more...
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 (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86004/
Series		Accession: GSE86004	ID: 200086004

3948. Germline NLRP1 mutations cause skin inflammatory and cancer susceptibility syndromes via inflammasome activation
(Submitter supplied) We profiled the transcriptional changes in N/TERT-1 immortalized keratinocytes after doxycylin induction of gain-of-function mutants of the inflammasome sensor protein  NLRP1.
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/GSE85nnn/GSE85791/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA339398
Series		Accession: GSE85791	ID: 200085791

3949. Bi-allelic Alteration and Dysregulation of the Hippo Pathway in Mucinous Tubular and Spindle Cell Carcinoma of the Kidney
(Submitter supplied) Mucinous tubular and spindle cell carcinoma (MTSCC) is a relatively rare subtype of renal cell carcinoma with distinctive morphologic and cytogenetic features. Here we carry out whole exome and transcriptome sequencing of a multi-institutional cohort of MTSCC (n=22). We demonstrate the presence of either biallelic loss of Hippo pathway tumor suppressor genes (TSGs) and/or evidence of alteration of Hippo pathway genes in 85% of samples. 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/GSE85nnn/GSE85969/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA339849
Series		Accession: GSE85969	ID: 200085969

3950. Inhibition of DNA methylation promotes breast tumor sensitivity to netrin-1 interference
(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 10 Samples
FTP download: GEO (BIGWIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80177/
Series		Accession: GSE80177	ID: 200080177

3951. Inhibition of DNA methylation promotes breast tumor sensitivity to netrin-1 interference [RNA-Seq]
(Submitter supplied) Results provide the animal proof of concept that inhibition of DNA methylation can sensitize solid tumors to antibodies mediating tumor cell apoptosis.
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/GSE80176/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA318239
Series		Accession: GSE80176	ID: 200080176

3952. Identification Of Candidate Anti-Cancer Molecular Mechanisms Of Compound Kushen Injection Using Functional Genomics
(Submitter supplied) Compound Kushen Injection (CKI) has been clinically used in China for over 15 years to treat various types of solid tumours.  However, because such Traditional Chinese Medicine (TCM) preparations are complex mixtures of plant secondary metabolites, it is essential to explore their underlying molecular mechanisms in a systematic fashion.  We have used the MCF-7 breast cancer cell line as an initial in vitro model to identify CKI induced changes in gene expression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL16791 27 Samples
FTP download: GEO (GTF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78512/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA313184
Series		Accession: GSE78512	ID: 200078512

3953. Global Regulation of Alternative RNA Splicing by the SR-Rich Protein RBM39
(Submitter supplied) RBM39 is extensively involved in alternative splicing of RNA and helps regulate transcript levels. RBM39 may modulate alternative splicing similarly to U2AF65 by either directly binding to RNA or recruiting other splicing factors, such as U2AF65.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 3 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86846/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA342707
Series		Accession: GSE86846	ID: 200086846

3954. RNA-Seq analysis of human medulloblastoma cell lines with SOX9 overexpression
(Submitter supplied) SOX9 is a master transcription factor that regulates development and stem cell programs. However, its potential oncogenic activity and regulatory mechanisms that control SOX9 protein stability are poorly understood. Here we show that SOX9 is a substrate of FBW7, a tumor suppressor and a SCF (Skp1-Cul1-F-box)-type ubiquitin ligase. FBW7 recognizes a conserved degron surrounding threonine 236 (T236) in SOX9 that is phosphorylated by GSK3 kinase. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17301 3 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84320/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA328820
Series		Accession: GSE84320	ID: 200084320

3955. N-Myc induces an EZH2-mediated transcriptional program driving Neuroendocrine Prostate Cancer
(Submitter supplied) The transition from castration resistant prostate adenocarcinoma (CRPC) to neuroendocrine prostate cancer (NEPC) is emerging as an important mechanism of treatment resistance. NEPC are associated with over-expression and gene amplification of MYCN (encoding N-Myc). N-Myc is a bona fide driver oncogene in several rare tumor types, but its role in prostate cancer progression is not well established.  Integrating a novel genetically engineered mouse model and human prostate cancer transcriptome data, we show that N-Myc over-expression leads to the development of poorly differentiated, invasive prostate cancer that is molecularly similar to human NEPC tumors which includes an abrogation of AR signaling and induction of Polycomb Repressive Complex 2 signaling and that N-Myc interacts with AR and this interaction depends on Enhancer of Zeste Homolog 2. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL9185 GPL9052 38 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86532/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA342161
Series		Accession: GSE86532	ID: 200086532

3956. Global transcriptome analysis in the MYCN-amplified neuroblastoma cell line IMR5-75 upon inducible MYCN-knockdown
(Submitter supplied) Inducible MYCN-knockdown, followed by RNA-seq analysis in the MYCN-amplified neuroblastoma cell line IMR5-75, reveals profound time-dependent transcriptome changes.
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/GSE80nnn/GSE80397/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA318814
Series		Accession: GSE80397	ID: 200080397

3957. RNA expression analysis of neuroblastoma cell lines treated with epigenetic drugs
(Submitter supplied) The impact of drugs inhibiting DNA methylation (5-aza-2'-deoxycytodine, DAC) and EZH2 (EPZ-6438) on the neuroblastoma transcriptome was analyzed in two neuroblastoma cell lines. Parallel analyses investigated associated changes in histone modification and DNA methylation.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 16 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79859/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA317239
Series		Accession: GSE79859	ID: 200079859

3958. Strand-oriented RNAseq of LNCaP prostate cancer cells in culture for 48 h in the absence of androgen
(Submitter supplied) The goal of this study was to use NGS RNAseq deep-sequencing in order to characterize the complement of polyadenylated mRNAs and lncRNAs expressed in LNCaP, a prostate cancer cell line. RNA-seq data were processed as aggregates of the two biological replicates to increase resulting transcriptome coverage. Trimmed reads were mapped with TopHat v.2.0.12 and Bowtie v.2.2.3, and a custom GTF file to guide transcriptome assembly. 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/GSE79nnn/GSE79301/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA315431
Series		Accession: GSE79301	ID: 200079301

3959. Gene expression analysis of human adenomas.
(Submitter supplied) Gene expression profiling was carried out in 7 matched colon adenoma samples and normal mucosa to characterize the molecular mechanisms relevant to the etiology ofadenoma and human colorectal carcinoma development.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 14 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72820/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA295149
Series		Accession: GSE72820	ID: 200072820

3960. The bromodomain protein BRD4 regulates splicing during heat shock
(Submitter supplied) During heat stress cyto-protective genes including heat shock proteins are transcriptionally up-regulated and post-transcriptional splicing is inhibited. In contrast, co-transcriptional mRNA-splicing is maintained. These factors closely resemble the proteotoxic stress response during tumor development. The bromodomain protein BRD4 has been identified as an integral member of the oxidative stress as well as of the inflammatory response. 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/GSE73nnn/GSE73471/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA297109
Series		Accession: GSE73471	ID: 200073471

3961. Adenosine-to-inosine RNA editing controls cathepsin S expression in atherosclerosis by enabling HuR-mediated post-transcriptional regulation
(Submitter supplied) Adenosine-to-inosine (A-to-I) RNA editing, which is catalyzed by a family of adenosine deaminase acting on RNA (ADAR) enzymes, is important in the epitranscriptomic regulation of RNA metabolism. However, the role of A-to-I RNA editing in vascular disease is unknown. Here we show that cathepsin S mRNA (CTSS), which encodes a cysteine protease associated with angiogenesis and atherosclerosis, is highly edited in human endothelial cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 38 Samples
FTP download: GEO (CSV, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE60nnn/GSE60217/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA257780
Series		Accession: GSE60217	ID: 200060217

3962. Transcriptome profiling of 5 human adenocarcinoma cell lines
(Submitter supplied) Purpose: The aim of this study is to compare the transcriptome profiles of a limited number of lung cancer cell lines with the intention of selecting the two most similar cell lines for a mixture experiment (GSE64098). Methods - Cell Culture: Five lung adenocarcinoma cell lines (H2228, NCI-H1975, HCC827, H838 and A549) from a range of passages (2-4) were grown on 2 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: GPL11154 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86337/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA341465
Series		Accession: GSE86337	ID: 200086337

3963. RNA-Seq analysis RPE1 cells following exposure to Nutlin-3 to identify target genes of p53 [tpo12]
(Submitter supplied) Tetraploidization, or genome doubling, is a prominent event in tumorigenesis, primarily because cell division in polyploid cells is error-prone and produces aneuploid cells.  This study investigates changes in gene expression evoked in acute and adapted tetraploid cells and their impact on cell-cycle progression.  Acute polyploidy was generated by knockdown of essential regulator of cytokinesis Anillin, which resulted in cytokinesis failure and formation of binucleate cells, or by chemical inhibition of Aurora kinases, causing abnormal mitotic exit with formation of single cells with aberrant nuclear morphology. 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/GSE86nnn/GSE86104/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA340264
Series		Accession: GSE86104	ID: 200086104

3964. RNA-Seq analysis of proliferating 4N and 2N RPE1 cells derived from single cell clones following inhibition of Aurora B to induce polyploidization [tpo10]
(Submitter supplied) Tetraploidization, or genome doubling, is a prominent event in tumorigenesis, primarily because cell division in polyploid cells is error-prone and produces aneuploid cells.  This study investigates changes in gene expression evoked in acute and adapted tetraploid cells and their impact on cell-cycle progression.  Acute polyploidy was generated by knockdown of essential regulator of cytokinesis Anillin, which resulted in cytokinesis failure and formation of binucleate cells, or by chemical inhibition of Aurora kinases, causing abnormal mitotic exit with formation of single cells with aberrant nuclear morphology. more...
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/GSE86nnn/GSE86103/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA340265
Series		Accession: GSE86103	ID: 200086103

3965. RNA-Seq analysis of 4N and 2N RPE1 cells following polyploid induction via cytokinesis failure by siRNA knockdown of Anillin [tpo8]
(Submitter supplied) Tetraploidization, or genome doubling, is a prominent event in tumorigenesis, primarily because cell division in polyploid cells is error-prone and produces aneuploid cells.  This study investigates changes in gene expression evoked in acute and adapted tetraploid cells and their impact on cell-cycle progression.  Acute polyploidy was generated by knockdown of essential regulator of cytokinesis Anillin, which resulted in cytokinesis failure and formation of binucleate cells, or by chemical inhibition of Aurora kinases, causing abnormal mitotic exit with formation of single cells with aberrant nuclear morphology. 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/GSE86nnn/GSE86102/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA340266
Series		Accession: GSE86102	ID: 200086102

3966. RNA-Seq analysis of 4N and 2N RPE1 cells following polyploid induction via cytokinesis failure or Aurora kinase inhibition [tpo3]
(Submitter supplied) Tetraploidization, or genome doubling, is a prominent event in tumorigenesis, primarily because cell division in polyploid cells is error-prone and produces aneuploid cells.  This study investigates changes in gene expression evoked in acute and adapted tetraploid cells and their impact on cell-cycle progression.  Acute polyploidy was generated by knockdown of essential regulator of cytokinesis Anillin, which resulted in cytokinesis failure and formation of binucleate cells, or by chemical inhibition of Aurora kinases, causing abnormal mitotic exit with formation of single cells with aberrant nuclear morphology. 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/GSE86nnn/GSE86101/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA340267
Series		Accession: GSE86101	ID: 200086101

3967. Differentially expressed genes in certinib-resistant NB-1 xenografts
(Submitter supplied) The goal of this study is to elucidate the molecular mechanism that allowed NB-1 xenograft tumors to grow out in the presence of continued ALK inhibition.  Poly(A)-selected RNA was extracted from tissues of NB-1 tumors that progressed on ceritinib treatment and those treated with a vehicle to identify differentially expressed genes between these two groups.
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/GSE82nnn/GSE82143/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA324126
Series		Accession: GSE82143	ID: 200082143

3968. Changes in RNA expression in human oral cavity carcinoma cells as a result of LDB1 reduction
(Submitter supplied) The study was designed to identify differential expressed genes between human oral cavity carcinoma cell lines with and without LDBI knockout
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/GSE79nnn/GSE79183/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA315120
Series		Accession: GSE79183	ID: 200079183

3969. Gene expression analysis of TIL rich HPV driven head and neck tumours reveals a distinct B-cell signature when compared to HPV independent tumours.
(Submitter supplied) Purpose: Human papilloma virus (HPV) associated head and neck squamous cell carcinoma (HNSCC) has a better prognosis than HPV(-) negative cancer. This may be due, in part, to the higher number of tumour infiltrating lymphocytes (TIL) in HPV(+) tumours. We used RNAseq to evaluate whether these differences in clinical behaviour could be explained simply by a numerical difference in TILs or whether there was a fundamental difference between TILs in these two settings. more...
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/GSE72nnn/GSE72536/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA294293
Series		Accession: GSE72536	ID: 200072536

3970. Tumor hypoxia causes DNA hypermethylation by reducing TET activity
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Methylation profiling by array; Methylation profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL16304 GPL17021 99 Samples
FTP download: GEO (IDAT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71403/
Series		Accession: GSE71403	ID: 200071403

3971. Tumor hypoxia causes DNA hypermethylation by reducing TET activity (RNA-Seq)
(Submitter supplied) Hypermethylation of tumor suppressor gene (TSG) promoters confers growth advantages to cancer cells, but how these changes arise is poorly understood. Here, we report that tumor hypoxia reduces the activity of oxygen-dependent TET enzymes, which catalyze DNA de-methylation through 5-methylcytosine oxidation. This occurs independently of hypoxia-associated alterations in TET gene expression, basal metabolism, HIF activity or nuclear reactive oxygen species, but directly depends on oxygen shortage. 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/GSE71nnn/GSE71401/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA291093
Series		Accession: GSE71401	ID: 200071401

3972. Long Non-coding RNA PICSAR Promotes Growth of Cutaneous Squamous Cell Carcinoma by Regulating ERK1/2 Activity
(Submitter supplied) Keratinocyte-derived cutaneous squamous cell carcinoma (cSCC) is the most common metastatic skin cancer, and its incidence is increasing globally. Long non-coding RNAs (lncRNAs) are involved in various biological processes, and their role in cancer progression is emerging. Whole transcriptome analysis of cSCC cells (n=8) and normal human epidermal keratinocytes (NHEKs, n=4) revealed overexpression of long intergenic ncRNA (LINC00162) in cSCC cells (GSE66412). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77950/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA312186
Series		Accession: GSE77950	ID: 200077950

3973. Analyzing the interactions of mRNAs, miRNAs, lncRNAs and circRNAs to predict competing endogenous RNA networks in glioblastoma
(Submitter supplied) Cross-talk between competitive endogenous RNAs (ceRNAs) may play a critical role in revealing potential mechanisms of tumor development and physiology. Glioblastoma is the most common type of malignant primary brain tumor, and the mechanisms of tumor genesis and development in glioblastoma are unclear. Here, to investigate the role of non-coding RNAs and the ceRNA network in glioblastoma, we performed paired-end RNA sequencing and microarray analyses to obtain the expression profiles of mRNAs, lncRNAs circRNAs and miRNAs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Other
Platform: GPL16791 6 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86202/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA340880
Series		Accession: GSE86202	ID: 200086202

3974. LINC00520 is Induced by Src, STAT3, and PI3K and Plays a Functional Role in Breast Cancer
(Submitter supplied) Long non-coding RNAs (lncRNAs) have been implicated in normal cellular homeostasis as well as pathophysiological conditions, including cancer. Here we performed global gene expression profiling of mammary epithelial cells transformed by oncogenic v-Src, and identified a large subset of uncharacterized lncRNAs potentially involved in breast cancer development. Specifically, our analysis revealed a novel lncRNA, LINC00520 that is upregulated upon ectopic expression of oncogenic v-Src, in a manner that is dependent on the transcription factor STAT3. 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/GSE86nnn/GSE86159/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA340383
Series		Accession: GSE86159	ID: 200086159

3975. L-MYC Expression Maintains Self Renewal and Prolongs Multipotency of Primary Human Neural Stem Cells
(Submitter supplied) These data support the therapeutic development of immortalized LM-NSC008 cells for allogeneic use in brain tumors, TBI and other CNS diseases
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/GSE84nnn/GSE84166/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA328167
Series		Accession: GSE84166	ID: 200084166

3976. Total RNA sequencing of HCT116 cells with vitamin C, 5-Aza-CdR and combination treatment compared to untreated cells II
(Submitter supplied) Total RNA sequenceing method was used to compare the differential expression of genes in HCT116 cells with vitamin C, 5-Aza-CdR and combination treatment compared to untreated cells
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77034/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA309301
Series		Accession: GSE77034	ID: 200077034

3977. Total RNA sequencing of HCT116 cells with vitamin C, 5-Aza-CdR and combination treatment compared to untreated cells I
(Submitter supplied) Total RNA sequenceing method was used to compare the differential expression of genes in HCT116 cells with vitamin C, 5-Aza-CdR and combination treatment compared to untreated cells
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/GSE77nnn/GSE77032/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA309303
Series		Accession: GSE77032	ID: 200077032

3978. A germline mutation of CDKN2A and a novel RPLP1-C19MC fusion detected in a rare melanotic neuroectodermal tumor of infancy: a case report
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome variation profiling by genome tiling array; Expression profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing
Platforms: GPL22155 GPL15520 GPL16791 5 Samples
FTP download: GEO (TXT, VCF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84431/
Series		Accession: GSE84431	ID: 200084431

3979. A germline mutation of CDKN2A and a novel RPLP1-C19MC fusion detected in a rare melanotic neuroectodermal tumor of infancy: a case report [Seq]
(Submitter supplied) Purpose: Melanotic neuroectodermal tumor of infancy (MNTI) is exceptionally rare and occurs predominantly in the head and neck (92.8% cases). A 2-month-old female patient presented with a mass arising in the fibula which was excised at our surgical center. This is only the eighth case of MNTI affecting an extremity, and the first reported in the fibula. To understand better the etiology of this MNTI, we used high-throughput sequencing technology to carry out an exhaustive genomic, transcriptomic and epigenetic characterization on the excised primary tumor and a derived cell line. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing
Platforms: GPL15520 GPL16791 3 Samples
FTP download: GEO (TXT, VCF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84430/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA329138
Series		Accession: GSE84430	ID: 200084430

3980. Normal stroma suppresses cancer cell proliferation via mechanosensitive regulation of JMJD1a-mediated transcription
(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: GPL16791 GPL10558 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83370/
Series		Accession: GSE83370	ID: 200083370

3981. Normal stroma suppresses cancer cell proliferation via mechanosensitive regulation of JMJD1a-mediated transcription [RNA-Seq]
(Submitter supplied) gene expression data from 3 pairs of cancer associated fibroblasts and normal fibroblasts from the same individual
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/GSE83nnn/GSE83314/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA325541
Series		Accession: GSE83314	ID: 200083314

3982. Identifying RBBP4-regulated transcriptome in T98G glioblastoma (GBM) cells using RNA sequencing, and epigenome screening for genes regulated by RBBP4 in GBM 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 6 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72477/
Series		Accession: GSE72477	ID: 200072477

3983. Identifying RBBP4-regulated transcriptome in T98G glioblastoma cells using RNA sequencing (RNA-seq)
(Submitter supplied) Retinoblastoma-binding protein 4 (RBBP4) is a chromatin modifying protein regulating multiple cellular functions. We have identified RBBP4 as a critical modulator of therapy response in glioblastoma (GBM). The purpose of this study was to identify genes through which RBBP4 regulates this important role with expectation of identifying candidates for therapy sensitizing strategy in GBM, and perhaps in other human malignancies.
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/GSE72nnn/GSE72475/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA294118
Series		Accession: GSE72475	ID: 200072475

3984. Human Osteosarcoma Transcriptome
(Submitter supplied) Osteosarcoma (OS) is one of the most aggressive bone malignancy. Sub-optimal therapy has irretrievably compromised chances of survival of OS patients for years. Also lack of extensive research on this rare disease has hindered its therapeutic development. Cisplatin (CDDP) is an integral part of current treatment regime for OS. However, despite the proven benefits of CDDP, acquisition of resistance impedes therapy. 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/GSE86nnn/GSE86053/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA340140
Series		Accession: GSE86053	ID: 200086053

3985. ZNF750 is a lineage-specific tumor suppressor in squamous cell carcinoma
(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 6 Samples
FTP download: GEO (CEL, FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86015/
Series		Accession: GSE86015	ID: 200086015

3986. ZNF750 is a lineage-specific tumor suppressor in squamous cell carcinoma [UMSCC1]
(Submitter supplied) ZNF750 controls epithelial homeostasis by regulating epidermal-differentiation genes, a role underscored by its pathogenic mutations in esophageal squamous cell cancers (SCCs). However, the precise role of ZNF750 in SCC cell biology remains unclear. In this study, we report that ZNF750 is exclusively deleted, mutated and underexpressed in human SCCs, and low ZNF750 expression is associated with poor survival. 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/GSE86nnn/GSE86014/
Series		Accession: GSE86014	ID: 200086014

3987. HER2 expression identifies dynamic functional states within circulating breast cancer cells
(Submitter supplied) Circulating tumour cells in women with advanced oestrogen-receptor (ER)-positive/human epidermal growth factor receptor 2 (HER2)-negative breast cancer acquire a HER2-positive subpopulation after multiple courses of therapy. In contrast to HER2-amplified primary breast cancer, which is highly sensitive to HER2-targeted therapy, the clinical significance of acquired HER2 heterogeneity during the evolution of metastatic breast cancer is unknown. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 74 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75367/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA304018
Series		Accession: GSE75367	ID: 200075367

3988. IL-15 activates mTOR and primes stress-activated gene-expression leading to prolonged anti-tumor capacity of NK cells
(Submitter supplied) Treatment of hematological malignancies by adoptive transfer of activated natural killer (NK) cells is limited by poor post-infusion persistence. We compared the ability of interleukin-2 (IL-2) and IL-15 to sustain human NK cell functions following cytokine withdrawal to model post-infusion performance. In contrasts to IL-2, IL-15 mediated stronger signaling through the IL-2/15 receptor complex and provided functional advantages. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 40 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77808/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA311600
Series		Accession: GSE77808	ID: 200077808

3989. RUNX1 contributes to higher-order chromatin organization and gene regulation in breast cancer cells.
(Submitter supplied) RUNX1 is a transcription factor functioning both as an oncogene and a tumor suppressor in breast cancer. RUNX1 alters chromatin structure in cooperation with chromatin modifier and remodeling enzymes. In this study, we examined the relationship between RUNX1-mediated transcription and genome organization. We characterized genome-wide RUNX1 localization and performed RNA-seq and Hi-C in RUNX1-depleted and control MCF-7 breast cancer cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platform: GPL11154 14 Samples
FTP download: GEO (BED, MATRIX, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75070/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA302327
Series		Accession: GSE75070	ID: 200075070

3990. Noncoding somatic and inherited single-nucleotide variants converge to promote ESR1 expression in breast cancer
(Submitter supplied) Sustained expression of the estrogen receptor-α (ESR1) drives two-thirds of breast cancer and defines the ESR1-positive subtype. ESR1 engages enhancers upon estrogen stimulation to establish an oncogenic expression program1. Somatic copy number alterations involving the ESR1 gene occur in approximately 1 % of ESR1-positive breast cancers2–5, suggesting that other mechanisms underlie the persistent expression of ESR1. 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/GSE74nnn/GSE74718/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA301239
Series		Accession: GSE74718	ID: 200074718

3991. Targeting Chromatin Regulators Inhibits Leukemogenic Gene Expression in NPM1 Mutant Leukemia
(Submitter supplied) Homeobox (HOX) proteins and the receptor tyrosine kinase FLT3 are frequently highly expressed and mutated in acute myeloid leukemia (AML). Aberrant HOX expression is found in nearly all AMLs that harbor a mutation in the Nucleophosmin (NPM1) gene, and FLT3 is concomitantly mutated in approximately 60% of these cases. Little is known how mutant NPM1 (NPM1mut) cells maintain aberrant gene expression. Here, we demonstrate that the histone modifiers MLL1 and DOT1L control HOX and FLT3 expression and differentiation in NPM1mut AML. Using a CRISPR-Cas9 genome editing domain screen, we show NPM1mut AML to be exceptionally dependent on the menin binding site in MLL1. Pharmacological small-molecule inhibition of the menin-MLL protein interaction had profound anti-leukemic activity in human and murine models of NPM1mut AML in vitro and in vivo. Combined pharmacological inhibition of menin-MLL and DOT1L resulted in dramatic suppression of HOX and FLT3 expression, induction of differentiation, and superior activity against NPM1mut leukemia. Together, MLL1 and DOT1L are chromatin regulators that control HOX, MEIS1 and FLT3 expression and are therapeutic targets in NPM1mut AML. Combinatorial small-molecule inhibition has synergistic on target activity and constitutes a novel therapeutic concept for this common AML subtype.
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/GSE85nnn/GSE85107/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA336184
Series		Accession: GSE85107	ID: 200085107

3992. Recurrent somatic mutations in POLR2A define a distinct subset of meningiomas
(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: GPL10558 GPL11154 GPL16791 184 Samples
FTP download: GEO (BED, FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85135/
Series		Accession: GSE85135	ID: 200085135

3993. Recurrent somatic mutations in POLR2A define a distinct subset of meningiomas [RNA-seq]
(Submitter supplied) RNA polymerase II mediates the transcription of all protein-coding genes in eukaryotic cells, a process that is fundamental to life. Genomic mutations in this enzyme have not been previously linked to any pathology in humans, a testament to its indispensable role in cell biology. Based on a combination of next-generation genomic analyses of 775 meningiomas, we report that recurrent somatic p.Gln403Lys or p.Leu438_His439del mutations in POLR2A, which encodes the catalytic subunit of RNA polymerase II, are sufficient to hijack this essential enzyme and drive neoplasia. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 19 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85133/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA336283
Series		Accession: GSE85133	ID: 200085133

3994. Transcriptional changes induced by Brd4 inhibitor, AZD5153, in cancer cell lines
(Submitter supplied) We sequenced mRNA from 12 human cancer cell lines treated with DMSO or AZD5153 for 24h to determine compound mechanism of action
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/GSE85nnn/GSE85840/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA339566
Series		Accession: GSE85840	ID: 200085840

3995. An integrative transcriptomics approach identifies miR-503 as a candidate master regulator of the estrogen response [RNA-seq]
(Submitter supplied) Estrogen receptor α (ERα) is an important biomarker of breast cancer severity and a common therapeutic target. Recent studies have demonstrated that in addition to its role in promoting proliferation, ERα also protects tumors against metastatic transformation. Current therapeutics antagonize ERα and interfere with both beneficial and detrimental signaling pathways stimulated by ERα. The goal of this study is to uncover the dynamics of coding and non-coding RNA (microRNA) expression in response to estrogen stimulation and identify potential therapeutic targets that more specifically inhibit ERα-stimulated growth and survival pathways without interfering with its protective features. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 30 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78167/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA312817
Series		Accession: GSE78167	ID: 200078167

3996. 53BP1 integrates DNA repair and p53-dependent cell fate decisions via distinct mechanisms
(Submitter supplied) The tumor suppressor protein 53BP1, a pivotal regulator of DNA double-strand break (DSB) repair,  was  first  identified  as  a  p53-interacting  protein  over  two  decades  ago,  however  its direct  contributions  to  p53-dependent  cellular  activities  remain  undefined.  Here,  we  reveal 53BP1 stimulates  genome-wide  p53-dependent  gene  transactivation  and repression  events  in response  to  ionizing  radiation  (IR)  and  synthetic  p53  activation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 36 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84986/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA335834
Series		Accession: GSE84986	ID: 200084986

3997. The pentose phosphate pathway regulates the circadian clock
(Submitter supplied) The circadian clock is a ubiquitous timekeeping system that organizes the behavior and physiology of organisms over the day and night. The clockwork orchestrates a multitude of metabolic processes as illustrated by previous global transcriptomics and proteomics studies, and the existence of daily rhythms of reduction and oxidation (redox) in a range of diverse species. However, the reciprocal question of whether metabolism can alter the clockwork remains largely unaddressed. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL11154 GPL16791 34 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74439/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA300419
Series		Accession: GSE74439	ID: 200074439

3998. Enriched retinal ganglion cells derived from human embryonic stem cells (RNA-seq)
(Submitter supplied) We performed the whole transcriptome analysis in human H9 ES cells and in retinal ganglion cells (RGC) derived from H9 ES cells.
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/GSE84nnn/GSE84639/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA330714
Series		Accession: GSE84639	ID: 200084639

3999. A systematic view on Influenza induced host shut-off
(Submitter supplied) Influenza A viruses (IAV) induces drastic host shut-off during infection. We use RNA-seq and ribosome profiling to systematically look at host genes RNA and translation levels along IAV infection. We show that host shutoff is mainly achieved by reduction in cellular mRNAs levels and that the high translation levels of IAV transcripts are driven by their strong accumulation compared to host transcripts. more...
Organism:	Influenza A virus; Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL11154 GPL21979 17 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE82nnn/GSE82232/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA324409
Series		Accession: GSE82232	ID: 200082232

4000. Differential Gene Expression Time Course of Normal Human Immortalized (iPrECs) vs Tumorigenic (EMP-iPrECs) Prostate Epithelial Cells during In Vitro Prostate Epithelial Cell Differentiation
(Submitter supplied) The first goal of this project was to identify differentially expressed genes associated with human prostate epithelial cells (PrEC) differentiation over a 2+ week time course that are associated with and potentially required for normal PrEC differentiation (J Cell Sci 123:266-76, 2010).  The second goal was to determine how these differentially expressed genes are changed when the same cells are transformed into tumorigenic cells (EMP-iPrECs) through overexpression of Erg, Myc, and shRNA to Pten (Cancer Res 74:3357-68, 2014). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 36 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77460/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA310418
Series		Accession: GSE77460	ID: 200077460

