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Unraveling the cohesin-chromatin interface: identifying protein interactions that modulate chromosome structure and function [ChIP-Seq]

GSE288455 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 22 samples Submitted 2025/06/02 Platform GPL24247Platform GPL30172
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 22 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
22 samples: 8 conditions, mostly in duplicateGroups 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.
Paper
Unraveling the cohesin-chromatin interface: identifying protein interactions that modulate chromosome structure and functionEpigenetics & chromatin · 2025
Summary (written by the submitters)
Cohesin is a plieotropic regulator of genom structure and function with several known interactors that aid in regulation of genome organization. A comprehensive cohesin interactome has yet to be established, and we identify several chromatin regulating complexes that interact with the cohesin complex, including the SWI/SNF chromatin remodeling complex.
Read the full summary ↓
SWI/SNF and cohesin co-localize to enhancers, promoters, and CTCF binding sites as deteremined by overlapping ChIP-seq data from mESCs for the cohesin subunit RAD21 and the SWI/SNF subunit BRG1, CTCF, H3K27ac, and H3K4me3. To assessthe functional implications of the cohesin-SWI/SNF interaction we treated mESCs with one of three small molecule drugs targeting the BRG1 subunit of SWI/SNF (ACBI1, PFI-3, BRM014) for either degradation of the complex or perturbation of SWI/SNF function, then performed ChIP-seq for the RAD21 subunit of cohesin. Differential RAD21 peaks in cells treated with a small molecule compared to DMSO control were assessed for overlap with DNA loops (Micro-C).
Published in
Unraveling the cohesin-chromatin interface: identifying protein interactions that modulate chromosome structure and function
Rittenhouse NL, Gohil R, Arricastres JE et al. · Epigenetics & chromatin 2025 · PMID 40452075 · doi:10.1186/s13072-025-00596-4
This dataset
Open GSE288455 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 GSE288455_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 PRJNA1217788 and SRA study SRP560887. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40452075) ↗
Study design
8 conditions, mostly in duplicate
mESCs, RAD21, ×5 mESCs, CTCF, ×5 mESCs, DMSO matched with ACBI1, RAD21, ×2 mESCs, ACBI1, RAD21, ×2 mESCs, DMSO matched with PFI-3, RAD21, ×2 mESCs, PFI-3, RAD21, ×2 mESCs, DMSO matched with BRM014, RAD21, ×2 mESCs, BRM014, RAD21, ×2

Supports a between-group comparison across 22 samples.

How we read this: 8 replicated groups read from 22 sample titles; they account for 22 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
Datasets on a similar topic

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