GEO DataSets

(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) 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

(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) Hydra have a remarkable ability to regenerate after bisection or dissociation. Thus, Hydra is a unique model for studying the mechanisms underlying stemness and self renewal biology. The regeneration of Hyrda offers unique way to investigate molecular mechanisms leading to the establishment of organizer activity during animal development. Here we have investigated the genome-wide occurrence of RNA Polymearse II and Histone H3 in Hydra vulgaris.

Organism:

Hydra vulgaris

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19432

6 Samples

Download data: BED

(Submitter supplied) We report the PRO-seq data generated from our analysis of RNA Polymerase II location along the HSV-1 genome at 3 and 6 hpi. This data set includes analysis of the 3hr time point in cells infected in the presence of cycloheximide and the 6hr time point in cells infected in the presence of phosphonoacetic acid, flavopiridol and acyclovir. We have compared the data set to a cytoplasmic mRNA seq data set which is also included. more...

Organism:

Homo sapiens; Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL22339 GPL18573

26 Samples

Download data: BW

(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

(Submitter supplied) We prepared and sequenced Start-seq libraries from rat (Rattus norgevicus) primary neural progenitor cells. Over 48 million uniquely mappable reads from two independent biological replicates allowed us to define the TSSs of 7,365 known genes in the rn6 genome, reannotating 2,503 TSSs by more than 5 base pairs, characterize promoter-associated antisense transcription, and profile Pol II pausing. By combining TSS data with polyA-selected RNA sequencing, we also identified thousands of potential new genes producing stable RNA as well as non-genic transcripts representing possible regulatory elements. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18694

6 Samples

Download data: BW, TSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL19057

9 Samples

Download data: BW

(Submitter supplied) The pluripotency of embryonic stem cells (ESCs) relies on appropriate responsiveness to developmental cues. Promoter-proximal pausing of RNA polymerase II (Pol II) has been suggested to play a role in keeping genes poised for future activation. To identify the role of Pol II pausing in regulating ESC pluripotency, we have generated mouse ESCs carrying a mutation in the pause-inducing factor SPT5. Consistent with previous in vitro studies showing the pausing deficiency of this mutant SPT5, our genomic analysis reveals genome-wide reduction of paused Pol II in mutant mESCs. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

7 Samples

Download data: BW

(Submitter supplied) The pluripotency of embryonic stem cells (ESCs) relies on appropriate responsiveness to developmental cues. Promoter-proximal pausing of RNA polymerase II (Pol II) has been suggested to play a role in keeping genes poised for future activation. To identify the role of Pol II pausing in regulating ESC pluripotency, we have generated mouse ESCs carrying a mutation in the pause-inducing factor SPT5. Consistent with previous in vitro studies showing the pausing deficiency of this mutant SPT5, our genomic analysis reveals genome-wide reduction of paused Pol II in mutant mESCs. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

2 Samples

Download data: BW

(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

(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:

GPL13112 GPL19845

3 Samples

Download data: BEDGRAPH

(Submitter supplied) Yeast mRNAs are polyadenylated at multiple sites in their 3’ untranslated regions (3’UTRs), and poly(A) site usage is regulated by the rate of transcriptional elongation by RNA polymerase II (Pol II). Slow Pol II derivatives favor upstream poly(A) sites and fast Pol II derivatives favor downstream poly(A) sites. Transcriptional elongation and polyadenylation are linked at the nucleotide level, presumably reflecting Pol II dwell time at each residue that influences the level of polyadenylation. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL19756 GPL27812

12 Samples

Download data: BW, TXT

(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) We exploited the phosphorylation state of the RNAPII CTD to assess the transcriptional status of most P. falciparum genes across the IDC. We raised highly specific monoclonal antibodies against three forms of the parasite CTD, namely unphosphorylated, Ser5-P and Ser2/5-P, and used these in ChIP-on-chip type experiments to map the genome-wide recruitment and activity of RNAPII.

Organism:

Plasmodium falciparum

Type:

Expression profiling by array; Genome binding/occupancy profiling by array

Platform:

GPL11250

71 Samples

Download data: GPR, TXT

(Submitter supplied) Production of mRNA depends critically on the rate of RNA polymerase II (Pol II) elongation. To dissect Pol II dynamics in mouse ES cells, we inhibited Pol II transcription at either initiation or promoter-proximal pause escape with Triptolide or Flavopiridol, and tracked Pol II kinetically using GRO-seq. Both inhibitors block transcription of more than 95% of genes, showing that pause escape, like initiation, is a ubiquitous and crucial step within the transcription cycle. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15103

19 Samples

Download data: BEDGRAPH

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9185

22 Samples

Download data: TXT, WIG

(Submitter supplied) It is unclear how epigenetic changes regulate the induction of erythroid-specific genes during terminal erythropoiesis. Here we use global mRNA sequencing (mRNA-seq) and chromatin immunoprecipitation coupled to high-throughput sequencing (CHIP-seq) to investigate the changes that occur in mRNA levels, RNA Polymerase II (Pol II) occupancy and multiple post-translational histone modifications when erythroid progenitors differentiate into late erythroblasts. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9185

4 Samples

Download data: TXT

(Submitter supplied) Here we globally analyzed mRNA and epigenetic changes in both early erythroid progenitors and late erythroblasts. Concomitant with gene induction there was an increase in RNA Pol II binding and activation marks near the transcriptional start site (TSS) and the elongation mark H3K79me2 (but not H3K36me3),both near the TSS and along the full gene length. In contrast, most repressed genes became depleted of elongation marks. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9185

18 Samples

Download data: TXT, WIG

(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

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