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Epigenetic Memory of Intestinal Epithelial Cells in Inflammatory Bowel Disease [ATAC-seq]

GSE282442 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 26 samples Submitted 2026/02/28 Platform GPL20301
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 26 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
26 samples: 13 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
Intestinal Stem Cells From Patients With Inflammatory Bowel Disease Retain an Epigenetic Memory of InflammationCellular and molecular gastroenterology and hepatology · 2026
Summary (written by the submitters)
The pathogenesis of Inflammatory Bowel Disease (IBD) is a multifactorial process characterized by inflammation and damage to the intestinal barrier, which is made up of intestinal epithelial cells (IECs). Since IBD is a remitting and relapsing disease, we postulated that epigenetic memory exists in IECs following an inflammatory encounter.
Read the full summary ↓
The objective of this study was to uncover the mechanisms of a retained altered IEC epigenetic landscape in the context of IBD. We have generated adult stem cell organoids (containing all epithelial cell lineages) from patients with Ulcerative Colitis (UC); two organoid lines per patient were propagated: 1) from a site of active inflammation and from the same patient, and 2) a never inflamed region. We performed Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) and bulk RNA-seq on each organoid line. Established bioinformatic pipelines were used to determine significantly different chromatin accessibility and differentially expressed genes. Functional significance of the open chromatin regions was assessed by pathway and motif analysis. Treatment with TNF-alpha (10 and 100ng/ml) for 24 hours on the organoids was performed to determine re-activation of pro-inflammatory genes. This study shows for the first time that epithelial cells derived from organoids of IBD patients retain an epigenetic memory of the prior inflammatory state.
Published in
Intestinal Stem Cells From Patients With Inflammatory Bowel Disease Retain an Epigenetic Memory of Inflammation
Hamdan FH, Farhadipour M, Perez I et al. · Cellular and molecular gastroenterology and hepatology 2026 · PMID 41903684 · doi:10.1016/j.jcmgh.2026.101774
This dataset
Open GSE282442 in finder → Find more human 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 GSE282442_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 PRJNA1188590 and SRA study SRP546535. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41903684) ↗
Study design
13 conditions, mostly in duplicate
Subject 83 Inflamed ×2 Subject 115 Noninflamed ×2 Subject 115 Inflamed ×2 Subject 13 Noninflamed ×2 Subject 129 Inflamed ×2 Subject 13 Inflamed ×2 Subject 8 Inflamed ×2 Subject 3 Noninflamed ×2 +5 more

Supports a between-group comparison across 26 samples.

How we read this: 13 replicated groups read from 26 sample titles; they account for 26 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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