GEO series

Loop extrusion by cohesin plays a role in enhancer-activated gene expression early in differentiation (ChIP-Seq, Rad21 and Stag2)

GSE329202 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 18 samples Submitted 2026/05/02 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
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

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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 GSE329202_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 PRJNA684314 and SRA study SRP297583. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Samples in this study

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+ 18 more — browse all 18 samples with per-sample file links →

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, chip-seq, cohesin, plays, early
GSE163010 Loop extrusion by cohesin plays a role in enhancer-activated gene expression early in differentiation (ATAC-seq) 18 samples shares enhancer-activated, extrusion, cohesin, plays, early
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
GSE295769 Context-dependent regulation of IgH V(D)J recombination by cohesin-STAG1 and cohesin-STAG2 [ChIP-seq] 47 samples shares stag2, chip-seq, cohesin
GSE277289 Cohesin-mediated chromatin remodeling controls the differentiation and function of conventional dendritic cells (RAD21 and CTCF ChIP-seq of Hoxb8-FL differentiation) 9 samples shares rad21, chip-seq, cohesin
GSE278338 ChIP-seq to measure binding of NIPBL/MAU2, RAD21, and CTCF in mouse embryonic stem cells and neural progenitor cells 50 samples shares rad21, chip-seq
GSE312228 Stag2-mediated chromatin dynamics regulates antibody class switch recombination [ChIP-Seq] 17 samples shares stag2, chip-seq
GSE288819 The tumour suppressor STAG2 cooperates with DREAM to maintain quiescence in the urothelium [ChIP-Seq_NU1] 13 samples shares stag2, chip-seq

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