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Genome-wide in vivo dynamics of cohesin-mediated loop extrusion and its role in transcription activation

GSE277721 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 176 samples Submitted 2024/10/07 Platform GPL24676Platform GPL34284Platform GPL34281Platform GPL30173Platform GPL34295
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 176 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
Homo sapiens (human)
Samples
176 samples: 176 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.
Paper
Acute NIPBL depletion reveals in vivo dynamics of loop extrusion and its role in transcription activationNature genetics · 2026
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
Acute NIPBL depletion reveals in vivo dynamics of loop extrusion and its role in transcription activation
Popay TM, Pant A, Munting F et al. · Nature genetics 2026 · PMID 41699137 · doi:10.1038/s41588-026-02516-y
This dataset
Open GSE277721 in finder → Find more human 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 GSE277721_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 PRJNA1163536 and SRA study SRP533971. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41699137) ↗
Study design
176 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 176 sample titles: 176 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

+ 136 more — browse all 176 samples with per-sample file links →

Datasets on a similar topic

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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.