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Synergy between regulatory elements can render cohesin dispensable for distal enhancer function

GSE277236 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 118 samples Submitted 2025/11/27 Platform GPL21626Platform GPL21103Platform GPL34328Platform GPL30172Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 118 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
118 samples: 47 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
Synergy between regulatory elements can render cohesin dispensable for distal enhancer functionScience (New York, N.Y.) · 2026
Summary (written by the submitters)
Enhancers are critical genetic elements controlling transcription from promoters, yet how they convey regulatory information across large genomic distances remains unclear. Here, we engineer pluripotent stem cells in which cohesin loop extrusion can be inducibly disrupted without confounding cell cycle defects. Transcriptional dysregulation is cell type-specific, and not all loci with distal enhancers depend equally on cohesin extrusion.
Read the full summary ↓
Using comparative genome editing, we demonstrate that enhancer-promoter communication over just 20 kilobases can require cohesin. However, promoter-proximal elements can support long-range, cohesin-independent enhancer action – even across strong CTCF insulators. Finally, transcriptional dynamics and the emergence of embryonic cell types remain largely robust despite disrupted extrusion. Beyond establishing novel strategies to study cohesin in enhancer biology, our work provides mechanistic insight into cell type- and genomic context-specificity.
Published in
Synergy between regulatory elements can render cohesin dispensable for distal enhancer function
Hansen KL, Adachi AS, Braccioli L et al. · Science (New York, N.Y.) 2026 · PMID 41308125 · doi:10.1126/science.adt4221
This dataset
Open GSE277236 in finder → Find more mouse 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 GSE277236_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 PRJNA1161411 and SRA study SRP533000. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41308125) ↗
Study design
47 conditions, mostly in duplicate
E14_RNAseq_ESC_DMSO_24h ×3 E14_RNAseq_ESC_dTAG13_24h ×3 EA18.1_RNAseq_ESC_DMSO_24h ×3 EA18.1_RNAseq_ESC_dTAG13_24h ×3 EA18.1_RNAseq_ESC_dTAG13_48h ×3 EA18.1_RNAseq_Exit_DMSO_48h ×3 EA18.1_RNAseq_Exit_dTAG13_48h ×3 E14_RNAseq_NPC_DMSO_24h ×3 +44 more

Supports a between-group comparison across 113 samples.

How we read this: 47 replicated groups read from 118 sample titles; they account for 113 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

+ 78 more — browse all 118 samples with per-sample file links →

Datasets on a similar topic

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