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Links from GEO DataSets

Items: 20

1.
Full record GDS4386

Ls174T colon cancer cell line response to Wnt signaling inhibition

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
2.

Integrated genome-wide analysis of transcription factor occupancy, RNA polymerase II binding and steady-state RNA levels identify differentially regulated functional gene classes

(Submitter supplied) Routine methods for assaying steady-state mRNA levels such as RNA-seq and micro-arrays are commonly used as readouts to study the role of transcription factors (TFs) in gene expression regulation. However, cellular RNA levels do not solely depend on activity of TFs and subsequent transcription by RNA polymerase II (Pol II), but are also affected by RNA turnover rate. Here, we demonstrate that integrated analysis of genome-wide TF occupancy, Pol II binding and steady-state RNA levels provide important insights in gene regulatory mechanisms. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL9520
12 Samples
Download data: BED
Series
Accession:
GSE36349
ID:
200036349
3.

Deciphering the Wnt-dependent gene signature in colorectal cancer cells

(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
Series
Accession:
GSE18560
ID:
200018560
4.

Genome-wide occupancy of RNA polymerase II before and after heat shock in mouse cells

(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:
GPL11002 GPL13112
4 Samples
Download data: BEDGRAPH
Series
Accession:
GSE66513
ID:
200066513
5.

RNA polymerase II ChIP-seq in HSV-1 and mock infected cells

(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:
Mus musculus; Human alphaherpesvirus 1 strain KOS
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL19845 GPL13112
3 Samples
Download data: BEDGRAPH
Series
Accession:
GSE66487
ID:
200066487
6.

Herpes Simplex Virus 1 dramatically alters loading and positioning of RNA Polymerase II on host genes early in infection

(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:
Homo sapiens; Drosophila melanogaster
Type:
Other
Platforms:
GPL22339 GPL18573
12 Samples
Download data: BW
Series
Accession:
GSE106126
ID:
200106126
7.

RNA polymerase II pausing downstream of core histone genes is different from genes producing polyadenylated transcripts

(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
Series
Accession:
GSE34001
ID:
200034001
8.

Genomic analyses of TF binding, histone acetylation and gene expression reveal classes of E2-regulated promoters

(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:
GPL570 GPL6229 GPL571
24 Samples
Download data: CEL, GPR
Series
Accession:
GSE9253
ID:
200009253
9.

PTEN modulates gene transcription by redistributing genome-wide RNA polymerase II occupancy

(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
Series
Accession:
GSE124659
ID:
200124659
10.

PTEN modulates gene transcription by redistributing genome-wide RNA polymerase II occupancy [RNA-seq]

(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
11.

PTEN modulates gene transcription by redistributing genome-wide RNA polymerase II occupancy [ChIP-seq]

(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
Series
Accession:
GSE124657
ID:
200124657
12.

Temporal ChIP-on-Chip of RNA-Polymerase-II to detect novel gene activation events during photoreceptor maturation

(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
Series
Accession:
GSE19999
ID:
200019999
13.

Stably-paused genes revealed through inhibition of transcription initiation by the TFIIH inhibitor Triptolide

(Submitter supplied) Transcription by RNA Polymerase II (Pol II) in metazoan is regulated in several steps, including preinitiation complex (PIC) formation, initiation, Pol II escape, productive elongation, cotranscriptional RNA-processing and termination. Genome-wide studies have demonstrated that the phenomenon of promoter-bound Pol II pausing is widespread, especially for genes involved in developmental and stimulus-responsive pathways. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL11154
23 Samples
Download data: BW
14.

RNA Polymerase II Dynamics along the Intestinal Crypt-Villus Axis

(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
Series
Accession:
GSE244918
ID:
200244918
15.

The Hox transcription factor Ultrabithorax binds RNA and regulates co-transcriptional splicing through an interplay with RNA polymerase II

(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
Series
Accession:
GSE171547
ID:
200171547
16.

The Hox Transcription Factor Ubx stabilizes Lineage Commitment by Suppressing Cellular Plasticity [ChIP-seq]

(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
Series
Accession:
GSE121752
ID:
200121752
17.

The Hox Transcription Factor Ubx stabilizes Lineage Commitment by Suppressing Cellular Plasticity [RNA-seq]

(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
Series
Accession:
GSE121670
ID:
200121670
18.

Genome-wide maps of Tamoxifen resistance MCF7 cell line

(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
Series
Accession:
GSE26083
ID:
200026083
19.

NelfA (Whsc2) promoter occupancy is required for active gene transcription during cardiac hypertrophy

(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
Series
Accession:
GSE135829
ID:
200135829
20.

Analysis of genome wide changes in RNA polymerase II occupancy in murine cells during heat shock and recovery

(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
Series
Accession:
GSE108185
ID:
200108185
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