GEO series

Intestinal secretory differentiation reflects niche-driven phenotypic and epigenetic plasticity of a common signal-responsive terminal cell [ATAC-Seq]

GSE271613 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 10 samples Submitted 2025/04/08 Platform GPL24247

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 10 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: 10 samples: 5 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 secretory differentiation reflects niche-driven phenotypic and epigenetic plasticity of a common signal-responsive terminal cellCell stem cell · 2025

Summary (written by the submitters)

Enterocytes and four classic secretory cell types derive from intestinal epithelial stem cells. Based on morphology, location, and canonical markers, goblet and Paneth cells are considered distinct secretory types. Here, we report high overlap in their transcripts and sites of accessible chromatin, in marked contrast to those of their enteroendocrine or tuft cell siblings.

Read the full summary ↓

Mouse and human goblet and Paneth cells express extraordinary fractions of few antimicrobial genes, which reflect specific responses to local niches. Wnt signaling retains some ATOH1+ secretory cells in crypt bottoms, where absence of BMP signaling potently induces Paneth features. Cells that migrate away from crypt bottoms encounter BMPs and thereby acquire goblet properties. These phenotypes and underlying accessible cis-elements interconvert in post-mitotic cells. Thus, goblet and Paneth properties represent alternative phenotypic manifestations of a common signal-responsive terminal cell type. These findings reveal exquisite niche-dependent cell plasticity and cis-regulatory dynamics in likely response to antimicrobial needs.

Published in

Intestinal secretory differentiation reflects niche-driven phenotypic and epigenetic plasticity of a common signal-responsive terminal cell

Bhattacharya S, Tie G, Singh PNP et al. · Cell stem cell 2025 · PMID 40203837 · doi:10.1016/j.stem.2025.03.005

This dataset

Open GSE271613 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 GSE271613_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 PRJNA1132286 and SRA study SRP518228. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40203837) ↗

Study design

5 conditions, mostly in duplicate

DAPT Only, ATAC ×2 DAPT + WnthiBMPlo, ATAC ×2 DAPT + WntloBMPhi, ATAC ×2 Lgr5+ ISC, ATAC ×2 Enterocytes, ATAC ×2

Supports a between-group comparison across 10 samples.

How we read this: 5 replicated groups read from 10 sample titles; they account for 10 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

GSM8380657 DAPT Only, ATAC rep1 DAPT Only, ATAC
GSM8380658 DAPT Only, ATAC rep2 DAPT Only, ATAC
GSM8380660 DAPT + WnthiBMPlo, ATAC rep1 DAPT + WnthiBMPlo, ATAC
GSM8380662 DAPT + WnthiBMPlo, ATAC rep2 DAPT + WnthiBMPlo, ATAC
GSM8380664 DAPT + WntloBMPhi, ATAC rep1 DAPT + WntloBMPhi, ATAC
GSM8380665 DAPT + WntloBMPhi, ATAC rep2 DAPT + WntloBMPhi, ATAC
GSM8380667 Lgr5+ ISC, ATAC rep1 Lgr5+ ISC, ATAC
GSM8380669 Lgr5+ ISC, ATAC rep2 Lgr5+ ISC, ATAC
GSM8380670 Enterocytes, ATAC rep1 Enterocytes, ATAC
GSM8380671 Enterocytes, ATAC rep2 Enterocytes, ATAC

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