GEO DataSets

Analysis of Ls174T colon cancer cells following doxycyclin-induction of a dominant-negative Tcf4 transgene, or a shRNA against β-catenin, to block the Wnt signal transduction pathway. Results provide insight into molecular mechanisms downstream of a defined signal transduction pathway.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 cell line, 4 protocol sets

Platform:

GPL570

Series:

GSE18560

12 Samples

Download data: CEL

(Submitter supplied) Routine methods for assaying steady-state mRNA levels such as RNA-seq and micro-arrays are commonly used as readouts to study the role of transcription factors (TFs) in gene expression regulation. However, cellular RNA levels do not solely depend on activity of TFs and subsequent transcription by RNA polymerase II (Pol II), but are also affected by RNA turnover rate. Here, we demonstrate that integrated analysis of genome-wide TF occupancy, Pol II binding and steady-state RNA levels provide important insights in gene regulatory mechanisms. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9520

12 Samples

Download data: BED

(Submitter supplied) Microarray-based gene expression data were generated from RNA from Ls174T colorectal carcinoma cell lines in which Wnt-dependent transcriptional activity can be abrogated by inducible overexpression of a dominant-negative form of Tcf4 or siRNA against β-catenin.

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4386

Platform:

GPL570

12 Samples

Download data: CEL

(Submitter supplied) The goal of this study was to understand changes that occur in RNA polymerase II occupancy upon heat shock using ChIP-seq in mouse cells.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13112 GPL11002

4 Samples

Download data: BEDGRAPH

(Submitter supplied) The goal of this study was to determine how RNA poymerase II (Pol II) occupancy changed in response to herpes simplex virus-1 (HSV-1) infection using ChIP-seq of Pol II. ChIP assays were performed 4 hours after cells were infected (or mock infected) with HSV-1. Because host cell Pol II transcribes the HSV-1 genome, the ChIP-seq data also reveal polymerase occupancy on the viral genome.

Organism:

Human alphaherpesvirus 1 strain KOS; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19845 GPL13112

3 Samples

Download data: BEDGRAPH

(Submitter supplied) We used precision nuclear run on (PRO-seq) to determine the location of Pol II at 3 hours post infection with HSV-1 in human epithelial cells. We found HSV-1 decreased Pol II on approxomately 2/3 of cellular genes, but increased Pol II on others. For more than 85% of genes for which transcriptional terminatin could be statistically assed, Pol II was displaced to positions downstream of the normal termination zone suggesting extensive termination defects. more...

Organism:

Drosophila melanogaster; Homo sapiens

Type:

Other

Platforms:

GPL22339 GPL18573

12 Samples

Download data: BW

(Submitter supplied) Recent genome-wide chromatin immunoprecipitation coupled high throughput sequencing (ChIP-seq) analyses performed in various eukaryotic organisms, analysed RNA Polymerase II (Pol II) pausing around the transcription start sites of genes. In this study we have further investigated genome-wide binding of Pol II downstream of the 3' end of the annotated genes (EAGs) by ChIP-seq in human cells. At almost all expressed genes we observed Pol II occupancy downstream of the EAGs suggesting that Pol II pausing 3' from the transcription units is a rather common phenomenon. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9052

2 Samples

Download data: BED

(Submitter supplied) To explore the global mechanisms of estrogen-regulated transcription, we used chromatin immunoprecipitation coupled with DNA microarrays to determine the localization of RNA polymerase II (Pol II), estrogen receptor alpha (ERalpha), steroid receptor coactivator proteins (SRC), and acetylated histones H3/H4 (AcH) at estrogen-regulated promoters in MCF-7 cells with or without estradiol (E2) treatment. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL571 GPL570 GPL6229

24 Samples

Download data: CEL, GPR

(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:

GPL16791

26 Samples

Download data

(Submitter supplied) Control of gene expression is one of the most complex yet continuous physiological processes impacting cellular homeostasis. RNA polymerase II (Pol II) transcription is tightly regulated at promoter-proximal regions by intricate dynamic processes including Pol II pausing, release into elongation, and premature termination. Here, we identify PTEN interacting with the Pol II transcription machinery and dephosphorylating Pol II C-terminal domain in vitro. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

8 Samples

Download data: TXT

(Submitter supplied) Control of gene expression is one of the most complex yet continuous physiological processes impacting cellular homeostasis. RNA polymerase II (Pol II) transcription is tightly regulated at promoter-proximal regions by intricate dynamic processes including Pol II pausing, release into elongation, and premature termination. Here, we identify PTEN interacting with the Pol II transcription machinery and dephosphorylating Pol II C-terminal domain in vitro. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

18 Samples

Download data: BIGWIG

(Submitter supplied) RNA Polymerase-II active regions were mapped comparing mouse neural retina tissue at age P25 and P2 to find novel gene activation predictions during maturation of photoreceptors. Over 800 predictions of increased activation were novel compared to previous mRNA expression array studies.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL5811

3 Samples

Download data: BED, CEL

(Submitter supplied) Transcription by RNA Polymerase II (Pol II) in metazoan is regulated in several steps, including preinitiation complex (PIC) formation, initiation, Pol II escape, productive elongation, cotranscriptional RNA-processing and termination. Genome-wide studies have demonstrated that the phenomenon of promoter-bound Pol II pausing is widespread, especially for genes involved in developmental and stimulus-responsive pathways. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

23 Samples

Download data: BW

(Submitter supplied) The mechanisms underlying intestinal epithelial differentiation are essential for maintaining intestinal health. Gene expression analysis reveals vast changes in the transcriptome as cells transition from crypts to villi, impacting nearly 4000 genes. The regulatory mechanisms driving transcriptome shifts during intestinal differentiation remain incompletely understood. Using ChIP-seq and multi-omic analyses, we have identified differential recruitment of Pol II to gene promoters as the primary driver of transcriptomic shifts during differentiation. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

12 Samples

Download data: BW, CSV, TXT

(Submitter supplied) Transcription Factors (TFs) play a pivotal role in cell fate decision by coordinating gene expression programs. Although most TFs act at the DNA layer, few TFs bind RNA and modulate splicing. Yet, the mechanistic cues underlying TFs activity in splicing remain elusive. Focusing on the Drosophila Hox TF Ultrabithorax (Ubx), our work shed light on a novel layer of Ubx function at the RNA level. Transcriptome and genome-wide binding profiles in embryonic mesoderm and Drosophila cells indicate that Ubx regulates mRNA expression and splicing to promote distinct outcomes in defined cellular contexts. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19132

9 Samples

Download data: TXT

(Submitter supplied) During development cells become gradually restricted in their differentiation potential by the repression of alternative cell fates. While we know that the Polycomb complex plays a crucial role in this process, it still remains unclear how alternative fate genes are specifically targeted for silencing in different cell lineages. We address this question by studying Ultrabithorax (Ubx), a multi-lineage transcription factor (TF) of the Hox class, in the mesodermal and neuronal lineages using sorted nuclei of Drosophila embryos and by interfering with Ubx in mesodermal cells that have already initiated differentiation. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13304

60 Samples

Download data: BED

(Submitter supplied) During development cells become gradually restricted in their differentiation potential by the repression of alternative cell fates. While we know that the Polycomb complex plays a crucial role in this process, it still remains unclear how alternative fate genes are specifically targeted for silencing in different cell lineages. We address this question by studying Ultrabithorax (Ubx), a multi-lineage transcription factor (TF) of the Hox class, in the mesodermal and neuronal lineages using sorted nuclei of Drosophila embryos and by interfering with Ubx in mesodermal cells that have already initiated differentiation. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

14 Samples

Download data: TXT

(Submitter supplied) We report the ER alpha regulatory network of Tamoxifen resistance MCF7 cell line using the Chromatin immunoprecipitated high-throughput sequencing technology (ChIP-seq). By Integrating the gene expression data (previously reported) with the ChIP-seq data, we generated ER alpha regulatory network and pathways. For ER alpha regulatory network, hub TFs with enriched motifs were identified from ER alpha peak together with PolII peaks. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9052

4 Samples

Download data: BED

(Submitter supplied) We examineD the genomic oppucpany and role of negative elongation factor A (NelfA) aka, Wolf-Hirschhorn syndrome candidate 2 (Whsc2), a critical component of the negative elongation complex in hearts undergoing pressure-overload induced cardiac hypertrophy. Alignment of high resolution genome wide occupancy data of NelfA, RNA Pol II, TFIIB and H3k9ac (datasets for pol II, TFIIB and H3kac submitted before) from control and hypertrophied hearts reveal that NelfA associates with all active gene promoters. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

3 Samples

Download data: BW, PDF, XLSX

(Submitter supplied) The goal of this study was to reveal changes in genome-bound RNA polymerase II in response to heat shock, and monitor the recovery of bound RNA polymerase II as cells return to homeostasis.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

6 Samples

Download data: BEDGRAPH