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Influence of NIPBL Knockdown-Induced Alterations in Cohesin Loop Extrusion on CTCF Loops, Enhancer-Promoter Connectivity, and PRC Domain Contacts During hESC Differentiation into Pancreatic Lineages

GSE288172 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 263 samples Submitted 2026/03/31 Platform GPL24676
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 263 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
263 samples: 258 distinct titles, 5 of them repeatedGroups 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
Impaired cohesin loading disrupts pancreatic differentiation by Polycomb-driven chromatin rewiring and loop collapseCommunications biology · 2026
Summary (written by the submitters)
Cell differentiation is orchestrated by precise enhancer-promoter interactions that rely on three-dimensional (3D) chromatin organization, influenced by cohesin dynamics and architectural proteins such as CTCF and NIPBL. In this study, we investigated the effects of knocking down NIPBL, a critical cohesin loading factor, in human embryonic stem cells (hESCs) and their differentiated pancreatic lineages.
Read the full summary ↓
Our results demonstrate that NIPBL depletion leads to a global loss of cohesin occupancy and altered chromatin architecture, particularly affecting enhancer-promoter loops and CTCF loops. Notably, while CTCF anchors maintain cohesin, enhancer-promoter interactions diminish significantly, highlighting the role of cohesive loading in transcriptional regulation. Additionally, we observed disrupted interactions within Polycomb Repressive Complex (PRC) domains and super enhancers, suggesting that NIPBL is crucial for maintaining the structural integrity of these regulatory elements. The study reveals that cohesin loading and loop extrusion processes are vital for establishing and preserving 3D chromatin interactions essential for gene expression during pancreatic differentiation. These findings underscore the intricate relationships between chromatin organization and gene regulation, with implications for understanding developmental processes and diseases associated with chromatin dysregulation.
Published in
Impaired cohesin loading disrupts pancreatic differentiation by Polycomb-driven chromatin rewiring and loop collapse
Yu L, Liu Y, Zhang J et al. · Communications biology 2026 · PMID 41826481 · doi:10.1038/s42003-026-09838-x
This dataset
Open GSE288172 in finder → Find more human 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 GSE288172_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 PRJNA1216384 and SRA study SRP560279. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41826481) ↗
Study design
258 distinct titles, 5 of them repeated
H9-siNIPBL-N1_RNA-Seq ×2 H9-siNIPBL-UNC3866-D4+N1_RNA-Seq ×2 H9-siNIPBL-UNC3866-D4_RNA-Seq ×2 H9-siNIPBL-WT_RNA-Seq ×2 H9-siNIPBL-S4PP2XN1XUNC3866_RNA-Seq_B ×2

How we read this: Read from 263 sample titles: 258 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

+ 223 more — browse all 263 samples with per-sample file links →

Datasets on a similar topic

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