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IL-25-induced effector-memory ILC2s mediate small intestinal adaptation [ATAC-seq]

GSE301998 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 36 samples Submitted 2025/07/28 Platform GPL17021
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 36 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
36 samples: 12 conditions, mostly in triplicateGroups 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.
Summary (written by the submitters)
This study used bulk ATAC sequencing of either small intestinal ILC2s or Lgr5+ epithelial stem cells +50 days after an IL-25 regimen or PBS regimen in wild type (ILC2s) or Lgr5DTR-EGFP (epithelial stem cells) mice to study chromatin accessibility.
This dataset
Open GSE301998 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 GSE301998_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 PRJNA1288253 and SRA study SRP599031. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
12 conditions, mostly in triplicate
ILC2s, PBS treated wild type mice, proximal 1… ×3 ILC2s, PBS treated wild type mice, mid 2/3 sm… ×3 ILC2s, PBS treated wild type mice, distal 3/3… ×3 ILC2s, IL25 treated wild type mice, proximal … ×3 ILC2s, IL25 treated wild type mice, mid 2/3 s… ×3 ILC2s, IL25 treated wild type mice, distal 3/… ×3 Lgr5 stem cell, PBS treated wild type mice, p… ×3 Lgr5 stem cell, PBS treated wild type mice, d… ×3 +5 more

Supports a between-group comparison across 35 samples.

How we read this: 12 replicated groups read from 36 sample titles; they account for 35 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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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.