GEO series

Loop extrusion by cohesin plays a role in enhancer-activated gene expression early in differentiation (ATAC-seq)

GSE163010 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 18 samples Submitted 2026/04/14 Platform GPL19057

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 18 samples

What it is: ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism: Mus musculus (mouse)
Samples: 18 samples: 18 samples, each with a distinct title — no replicated groupsGroups 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)

Enhancers and their target promoters often come into close physical proximity when activated. This may be explained by a variety of mechanisms, including cohesin-mediated chromatin loop extrusion. However, acute depletion of cohesin does not cause widespread changes in gene expression. We have tested the role of cohesin-mediated loop extrusion in gene expression at the mouse alpha-globin locus during erythropoiesis.

Read the full summary ↓

Acute depletion of cohesin disrupts alpha-globin expression at early but not late stages of differentiation. Furthermore, when single or multiple CTCF sites, known to block cohesin, are placed between the alpha-globin enhancers and promoters, alpha-gene expression is disrupted. Importantly, the CTCF site’s orientation is critical, suggesting that within this activated domain, in definitive erythroid cells cohesin predominantly but not exclusively, translocates from the enhancers to the promoters. We find that loop extrusion does play an important role in establishing enhancer-promoter proximity and consequent expression of inducible genes during differentiation.

This dataset

Open GSE163010 in finder → Find more mouse ChIP / ATAC / CUT&Tag 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 GSE163010_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA684315 and SRA study SRP297581. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

18 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 18 sample titles: 18 distinct titles with little repetition. 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

GSM4970149 D2H3_Fwd_EB_ATAC
GSM4970150 D3F3_EB_Fwd_ATAC
GSM4970151 F2D3_Fwd_EB_ATAC
GSM4970152 D2D6_Rev_EB_ATAC
GSM4970153 D3H2_EB_Rev_ATAC
GSM4970154 F2G6_Rev_ATAC_EB
GSM4970155 EB_ATAC_wt_A
GSM4970156 EB_ATAC_wt_B
GSM4970157 EB_ATAC_wt_C
GSM4970158 5-1_Fwd_FL_ATAC
GSM4970159 5-4_Fwd_FL_ATAC
GSM4970160 i-2_Fwd_FL_ATAC
GSM4970161 f-3_Rev_FL_ATAC
GSM4970162 g-1_Rev_FL_ATAC
GSM4970163 g-4_Rev_FL_ATAC
GSM4970164 5-2_wt_FL_ATAC
GSM4970165 g7_WT_FL_ATAC
GSM4970166 f-4_WT_ATAC_FL

Datasets on a similar topic

GSE163008 Loop extrusion by cohesin plays a role in enhancer-activated gene expression early in differentiation (ChIP-seq) 26 samples shares enhancer-activated, extrusion, cohesin, plays, early, loop
GSE163012 Loop extrusion by cohesin plays a role in enhancer-activated gene expression early in differentiation 109 samples shares enhancer-activated, extrusion, cohesin, plays, early, loop
GSE306301 Cohesin-mediated loop extrusion and enhancer-associated factors additively contribute to Sox2 looping with its distal enhancer. 81 samples shares extrusion, cohesin, loop
GSE264614 Emerging cooperativity between Oct4 and Sox2 governs the pluripotency network in mouse early embryos [ATAC-seq] 44 samples shares atac-seq, early
GSE245683 ATAC-seq of mouse cortex undergoing early degradation after traumatic brain injury (TBI) 12 samples shares atac-seq, early
GSE245399 ATAC-seq analysis of early T cell progenitors from various gene deficient mice 12 samples shares atac-seq, early
GSE288605 Context-Dependent and Gene-Specific Role of Chromatin Architecture Mediated by Histone Modifiers and Loop-extrusion Machinery 96 samples shares extrusion, loop
GSE256073 De novo formation of cis-regulatory contacts in the absence of NIPBL-driven chromatin loop extrusion 30 samples shares extrusion, loop

Search all mouse ChIP / ATAC / CUT&Tag datasets in GEO →

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.