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Arid1a mediates cell recovery upon gastric injury to prevent tumorigenesis [Multiome]

GSE269928 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 9 samples Submitted 2026/06/30 Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 9 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
9 samples: 8 distinct titles, 1 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.
Summary (written by the submitters)
When tissues and organs are damaged, they undergo a reversible regenerative response. Since it often activates oncogenic signaling pathways, recovery after regeneration must be precisely regulated. However, its underlying mechanisms and relationship with cancer remain unclear. The stomach is constantly exposed to environmental damages such as H.
Read the full summary ↓
pylori infection and ulcer, and undergoes an evolutionally conserved, regenerative response called spasmolytic polypeptide-expressing metaplasia (SPEM). Although this process is highly reversible, occurring in precancerous lesions, the epigenetic regulation underlying SPEM is unknown. Our single-cell chromatin and gene expression analysis defines cell fate and state dynamics in homeostasis, regeneration and recovery. Upon injury, gastric epithelial cells rapidly induce SPEM gene expression under accessible chromatin, while losing the expression and accessibility of differentiation genes. Strikingly, when Arid1a, the second most mutated gastric cancer gene, is deleted in regeneration, it abolishes cell recovery. By analyzing histone modification and chromatin accessibility, as well as mapping the binding sites of ARID1A and BRG1, we demonstrate they promote recovery through the regulation of enhancer activity. Notably, failed recovery by Arid1a loss in combination with Trp53 deletion is sufficient to induce cancer initiation and invasion, providing key insight into the mechanistic relationship between tissue recovery after regeneration and cancer.
This dataset
Open GSE269928 in finder → Find more mouse 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 GSE269928_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 PRJNA1124131 and SRA study SRP514045. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
8 distinct titles, 1 of them repeated
stomach, day7, GEX, ×2

Supports a case/control comparison: 2 samples read as cases, 2 as controls.

How we read this: Read from 9 sample titles: 8 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
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.