GEO series

Cohesin acts as a transcriptional gatekeeper by restraining pause–release to promote processive elongation [RNA-seq]

GSE300577 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2026/07/07 Platform GPL11154

At a glance

RNA-seq (gene expression) · human · 18 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Homo sapiens (human)
Samples: 18 samples: 6 conditions, mostly in triplicateGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.

Summary (written by the submitters)

Cohesin organizes 3D chromatin architecture, including promoter–enhancer loops, yet its loss has surprisingly modest effects on steady-state gene expression. We address this paradox by demonstrating that cohesin acts at different stages of transcription in human cells. First, it promotes Pol II promoter recruitment by facilitating enhancer–promoter communication that maintains active promoter chromatin states.

Read the full summary ↓

Second, it delays pause release by transiently associating with the transcriptional machinery during the pause–release transition. Kinetic modelling suggests that reduced Pol II recruitment and enhanced pause release have compensatory effects, contributing to minimal changes in steady-state gene expression across genes upon cohesin loss. In contrast, cohesin depletion impairs robust transcriptional induction in response to external stimuli. Moreover, cohesin ensures sufficient pausing duration as a quality-control-like step to promote elongation complex assembly and transcription processivity. Here, we show that cohesin regulates multiple transcriptional steps, offering mechanistic insight into cohesin-related diseases, including cancers and cohesinopathies.

This dataset

Open GSE300577 in finder → Find more human RNA-seq datasets →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE300577_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1281417 and SRA study SRP594173. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 conditions, mostly in triplicate

RNAseq, ctrl, ×3 RNAseq, aux, ×3 RNAseq, XRN2, KD, ×3 RNAseq, aux, XRN2, KD, ×3 RNAseq, SMC1, ctrl, ×3 RNAseq, SMC1, aux, ×3

Supports a between-group comparison across 18 samples.

How we read this: 6 replicated groups read from 18 sample titles; they account for 18 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM9064761 RNAseq, ctrl, rep1 RNAseq, ctrl,
GSM9064762 RNAseq, aux, rep1 RNAseq, aux,
GSM9064763 RNAseq, ctrl, rep2 RNAseq, ctrl,
GSM9064764 RNAseq, aux, rep2 RNAseq, aux,
GSM9064765 RNAseq, ctrl, rep3 RNAseq, ctrl,
GSM9064766 RNAseq, aux, rep3 RNAseq, aux,
GSM9064767 RNAseq, XRN2, KD, rep1 RNAseq, XRN2, KD,
GSM9064768 RNAseq, aux, XRN2, KD, rep1 RNAseq, aux, XRN2, KD,
GSM9064769 RNAseq, XRN2, KD, rep2 RNAseq, XRN2, KD,
GSM9064770 RNAseq, aux, XRN2, KD, rep2 RNAseq, aux, XRN2, KD,
GSM9064771 RNAseq, XRN2, KD, rep3 RNAseq, XRN2, KD,
GSM9064772 RNAseq, aux, XRN2, KD, rep3 RNAseq, aux, XRN2, KD,
GSM9064773 RNAseq, SMC1, ctrl, rep1 RNAseq, SMC1, ctrl,
GSM9064774 RNAseq, SMC1, aux, rep1 RNAseq, SMC1, aux,
GSM9064775 RNAseq, SMC1, ctrl, rep2 RNAseq, SMC1, ctrl,
GSM9064776 RNAseq, SMC1, aux, rep2 RNAseq, SMC1, aux,
GSM9064777 RNAseq, SMC1, ctrl, rep3 RNAseq, SMC1, ctrl,
GSM9064778 RNAseq, SMC1, aux, rep3 RNAseq, SMC1, aux,

Datasets on a similar topic

GSE300574 Cohesin acts as a transcriptional gatekeeper by restraining pause–release to promote processive elongation [TT-seq] 4 samples shares restraining, gatekeeper, processive, elongation, cohesin, release, promote
GSE260852 Cohesin acts as a transcriptional gatekeeper by restraining pause–release to promote processive elongation [ChIP-seq] 68 samples shares restraining, gatekeeper, processive, elongation, cohesin, release, promote
GSE300575 Cohesin acts as a transcriptional gatekeeper by restraining pause–release to promote processive elongation [ChIP-seq] 22 samples shares restraining, gatekeeper, processive, elongation, cohesin, release, promote
GSE336388 Cohesin acts as a transcriptional gatekeeper by restraining pause–release to promote processive elongation 15 samples shares restraining, gatekeeper, processive, elongation, cohesin, release, promote
GSE280102 A CDK11-dependent RNA polymerase II pause-release checkpoint precedes CDK9-mediated transition to transcriptional elongation [RNA-seq] 29 samples shares elongation, release, rna-seq
GSE294526 The USP11/TCEAL1 complex promotes transcription elongation to sustain oncogenic gene expression in neuroblastoma [RNA-seq II] 21 samples shares elongation, promote, rna-seq
GSE297204 Senataxin Promotes RNA Polymerase II Elongation [Hap1_DRBrelease_TTseq] 18 samples shares elongation, release, promote
GSE265884 Tripartite phosphorylation of SPT5 by CDK9 times pause release and tunes elongation rate of RNA polymerase II (RNA-Seq) 10 samples shares elongation, release, rna-seq

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