GEO DataSets

(Submitter supplied) We have generated single-nucleotide resolution, nascent transcription profiles from HeLa cells by developing Native Elongation Transcript sequencing technology for mammalian chromatin (mNET-seq). Our extensive data sets provide a substantial resource to study mammalian nascent transcript profiles. We reveal unanticipated phosphorylation states for RNA polymerase II C-terminal domain (Pol II CTD) at both gene ends. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL16791 GPL11154

28 Samples

Download data: BW

(Submitter supplied) Non-cleaving Cas9 (dCas9) is widely employed to manipulate specific gene loci often with scant regard for unintended transcriptional effects. We demonstrate here that dCas9 mediates precise transcriptional pausing followed by transcription termination and potential alternative polyadenylation. In contrast, alternative splicing is unaffected, likely requiring more sustained alteration to RNA polymerase II elongation speed. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

20 Samples

Download data: BW

(Submitter supplied) Co-transcriptional splicing of introns is a defining feature of eukaryotic gene expression. We show that the mammalian spliceosome specifically associates with the S5P CTD isoform of RNA polymerase II (Pol II) as it elongates across spliced exons of protein coding genes, both in human Hela and murine lymphoid cell lines. Immuno-precipitation of MNase digested chromatin with phospho CTD specific antibodies reveals that components of the active spliceosome (both snRNA and proteins) form a specific complex with S5P CTD Pol II. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL11154 GPL13112

38 Samples

Download data: BW

(Submitter supplied) Major features of transcription by human RNA polymerase II (Pol II) remain poorly defined due to a lack of quantitative approaches for visualizing Pol II progress at nucleotide resolution. We developed a simple and powerful approach for performing native elongating transcript sequencing (NET-seq) in human cells that globally maps strand-specific Pol II density at nucleotide resolution. NET-seq exposes a mode of antisense transcription that originates downstream and converges on transcription from the canonical promoter. more...

Organism:

Homo sapiens

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL11154

10 Samples

Download data: BEDGRAPH

(Submitter supplied) Numerous long intervening non-coding RNA (lincRNA) are generated from the mammalian genome by RNA polymerase II (Pol II) transcription. Although multiple functions have been ascribed to lincRNA, their synthesis and turnover remain poorly characterised. Here we define systematic differences in transcription and RNA processing between protein-coding and lincRNA genes in human HeLa cells. This is based on a range of nascent transcriptomic approaches applied to different nuclear fractions, including mammalian native elongating transcript sequencing (mNET-seq). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL20301

57 Samples

Download data: BW

(Submitter supplied) Mammalian chromatin is the site of both RNA polymerase II (Pol II) transcription and coupled RNA processing. However, molecular details of such co-transcriptional mechanisms remain obscure, partly due to technical limitations in purifying authentic nascent transcripts. We present a new approach to purify and profile nascent RNA, called Polymerase Intact Nascent Transcript (POINT) technology. This three-pronged methodology maps nascent RNA 5’ends (POINT-5), establishes the kinetics of co-transcriptional splicing patterns (POINT-nano) and profiles whole transcription units (POINT-seq). more...

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL26167 GPL24676

78 Samples

Download data: BB, BW

(Submitter supplied) Active sites of transcription were labelled with biotinylated nucleotide during a run-on reacation, where after an immunoprecipitation with antibodies that target Pol II CTD was conducted. This PRO-IP-seq protocol was conducted in human K562 erythroleukemia cells. The K562 cells were either untreated (NHS) or treated with 30 minutes of heat shock at 42°C (HS).

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL24676 GPL18573

32 Samples

Download data: BIGWIG

(Submitter supplied) RNA polymerase II (Pol II) play an essential role in gene expression. Here, we adapted plant Native Elongation Transcript sequencing and Global Run On sequencing to profile nascent RNA genome wide in Arabidopsis. We found Pol II tends to accumulate downstream of transcription start site and pausing at proximal promoter is an important regulatory step for Pol II transcription although loosely controlled. more...

Organism:

Arabidopsis thaliana

Type:

Other

Platform:

GPL17639

21 Samples

Download data: TXT

(Submitter supplied) RNA polymerase II (Pol II) play an essential role in gene expression. Here, we adapted mammalian Native Elongation Transcript sequencing and Global Run On sequencing to profile nascent RNA genome wide in Arabidopsis. We found Pol II tends to accumulate downstream of transcription start site and pausing at proximal promoter is an important regulatory step for Pol II transcription although loosely controlled. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL17639 GPL13222 GPL19580

12 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) This study reveals widespread Pol II pausing at single-nucleotide resolution across the human genome with the majority of Pol II pauses occur outside of promoter-proximal gene regions primarily along the gene-body of transcribed genes. We show DNA sequence properties underlying widespread transcriptional pausing including a new pause motif. The study indicates pervasive sequence-induced transcriptional pausing in human cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

4 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) RNA Polymerase II was mapped over 4% of the yeast genome by ChIP, in wild-type and a handful of mutants in transcriptional termination factors. Keywords: ChIP-chip, transcription termination

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL1950

9 Samples

Download data

(Submitter supplied) Activation of immune cells results in extremely rapid functional changes, yet it remains enigmatic how this is accomplished. By combining time-courses of RNA-polymerase-II (RNAPII) Chip-Seq, 4sU-Seq, RNA-Seq and ribosome profiling during Th1 activation we provide a genome-wide view on temporal dynamics for ~10.000 genes. Gene responses vary in time and magnitude and allow the identification of unknown immediate early (IEG) and posttranscriptionally regulated genes. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

10 Samples

Download data: BED, BEDGRAPH, CSV

(Submitter supplied) Activation of immune cells results in rapid functional changes, but how such fast changes are accomplished remains enigmatic. By combining time-courses of 4sU-Seq, RNA-Seq, ribosome profiling and RNA polymerase II (RNAPII) ChIP-Seq during T cell activation, we illustrate genome-wide temporal dynamics for ~10,000 genes. This approach reveals immediate-early as well as posttranscriptionally-regulated genes, but also coupled changes in transcription and translation for >90% of genes. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

24 Samples

Download data: TXT

(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) The advent of quantitative approaches that enable interrogation of transcription at single nucleotide resolution has allowed a novel understanding of transcriptional regulation previously undefined. To better map transcription genome-wide at base pair resolution and with transcription/elongation factor dependency we developed an adapted NET-seq protocol called NET-prism (Native Elongating Transcription by Polymerase-Regulated Immunoprecipitants in the Mammalian genome). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL17021

15 Samples

Download data: BEDGRAPH, BW

(Submitter supplied) To address co-transcriptional pre-mRNA processing events, Saccharomyces nascent RNA was isolated by chromatin fractionation and analyzed on a genome-wide high density tiling microarray. Co-transcriptional splicing efficiencies were derived by determination of intronic relative to exonic sequence concentrations.

Organism:

Saccharomyces cerevisiae; Saccharomyces

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL7250

10 Samples

Download data: CEL, TXT

(Submitter supplied) DNA faces continuous threats from various endogenous and exogenous stresses. When damaged, DNA requires repair to enable proper cell functioning. Cells have evolved multiple repair pathways to maintain genome stability. Transcription mediated by RNA polymerase II (RNA Pol II), which is conventionally linked with gene expression, plays an integral role in DNA repair. Transcription occurring at sites of DNA damage facilitates repair by generating functional transcripts, recruiting DNA repair factors, or modulating chromatin architecture. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20301

24 Samples

Download data: XLSX

(Submitter supplied) MicroRNA (miRNA) play a major role in the post-transcriptional regulation of gene expression. In mammals most miRNA derive from the introns of protein coding genes where they exist as hairpin structures in the primary gene transcript, synthesized by RNA polymerase II (Pol II). These are cleaved co-transcriptionally by the Microprocessor complex, comprising DGCR8 and the RNase III endonuclease Drosha, to release the precursor (pre-)miRNA hairpin, so generating both miRNA and spliced messenger RNA1-4. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

10 Samples

Download data: BW

(Submitter supplied) During maturation, eukaryotic precursor RNAs undergo processing events including intron splicing, 3’-end cleavage, and polyadenylation. Here, we describe nanopore analysis of CO-transcriptional Processing (nano-COP), a method for probing the timing and patterns of RNA processing. An extension of native elongating transcript sequencing (NET-seq), which quantifies transcription genome-wide through short-read sequencing of nascent RNA 3’ ends, nano-COP uses long-read nascent RNA sequencing to observe global patterns of RNA processing. more...

Organism:

Homo sapiens; synthetic construct

Type:

Other

Platforms:

GPL24106 GPL25738

11 Samples

Download data: TSV, TXT