← BioTransfer GEO Dataset Finder
GEO series

ChIP-seq to measure binding of NIPBL/MAU2, RAD21, and CTCF in mouse embryonic stem cells and neural progenitor cells

GSE278338 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 50 samples Submitted 2025/09/27 Platform GPL21103Platform GPL30172
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 50 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
50 samples: 17 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)
Mammalian chromosomes are folded by the cohesin complex, which creates chromatin loops that are extruded as cohesin translocates along the chromatin fiber. This dynamic process regulates gene expression by controlling the frequency of contacts between enhancers and promoters. We analyzed where in the genome loop extrusion occurs to discover where extrusion initiates and whether particular regions are extruded more than others.
Read the full summary ↓
We measured NIPBL/MAU2 binding in mouse embryonic stem cells and neural progenitor cells, and found that NIPBL/MAU2 is enriched at enhancers compared to promoters. We used the amount of cohesin binding at CTCF sites as a readout of cohesin traffic, and found that the NIPBL/MAU2 binding sites only modestly boost nearby cohesin levels.
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 GSE278338 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 GSE278338_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 PRJNA1166675 and SRA study SRP535480. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41308125) ↗
Study design
17 conditions, mostly in duplicate
Untagged ESCs, RAD21 ChIP, ×4 Untagged ESCs, CTCF ChIP, ×4 Untagged ESCs, input for RAD21,CTCF ChIP ×4 E14_ESC_HA ×3 E14_ESC_input ×3 EA18.1_ESC_HA ×2 EA19.1_ESC_HA ×2 EA18.1_ESC_input ×2 +17 more

Supports a between-group comparison across 42 samples.

How we read this: 17 replicated groups read from 50 sample titles; they account for 42 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

+ 10 more — browse all 50 samples with per-sample file links →

Datasets on a similar topic

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

Share this dataset

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.