GEO series

STAT1 regulates immune-mediated intestinal stem cell proliferation and epithelial regeneration

GSE276126 Mus musculus (mouse) Single-cell RNA-seq 13 samples Submitted 2024/09/09 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 13 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Mus musculus (mouse)
Samples: 13 samples: 10 distinct titles, 3 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: STAT1 regulates immune-mediated intestinal stem cell proliferation and epithelial regenerationNature communications · 2025

Summary (written by the submitters)

The role of the immune system in regulating tissue stem cells remains poorly understood, as does the relationship between immune-mediated tissue damage and regeneration. Graft vs. host disease (GVHD) occurring after allogeneic bone marrow transplantation (allo-BMT) involves immune-mediated damage to the intestinal epithelium and its stem cell compartment.

Read the full summary ↓

To assess impacts of T-cell-driven injury on distinct epithelial constituents, we performed single cell RNA sequencing on intestinal crypts following experimental BMT. Intestinal stem cells (ISCs) from GVHD mice exhibited global transcriptomic changes associated with a substantial Interferon-γ response and upregulation of STAT1. To determine its role in crypt function, STAT1 was deleted within murine intestinal epithelium. Following allo-BMT, STAT1 deficiency resulted in reduced epithelial proliferation and impaired ISC recovery. Similarly, epithelial Interferon-γ receptor deletion also attenuated proliferation and ISC recovery post-transplant. Investigating the mechanistic basis underlying this epithelial response, ISC STAT1 expression in GVHD was found to correlate with upregulation of ISC c-Myc. Furthermore, activated T cells stimulated Interferon-γ- dependent epithelial regeneration in co-cultured organoids, and Interferon-γ directly induced STAT1-dependent c-Myc expression and ISC proliferation. These findings illustrate immunologic regulation of a core tissue stem cell program after damage and support a role for Interferon-γ as a direct contributor to epithelial regeneration.

Published in

STAT1 regulates immune-mediated intestinal stem cell proliferation and epithelial regeneration

Takashima S, Sharma R, Chang W et al. · Nature communications 2025 · PMID 39746933 · doi:10.1038/s41467-024-55227-5

This dataset

Open GSE276126 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 GSE276126_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1154957 and SRA study SRP529833. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39746933) ↗

Study design

10 distinct titles, 3 of them repeated

SI, B6, ×2 SI, BM, ×2 SI, BM + treatment ×2

How we read this: Read from 13 sample titles: 10 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

GSM8491727 SI, day 5, scRNAseq
GSM8491728 SI, day 5 + 6h IFNg, scRNAseq
GSM8491729 SI, day 5 + 24h IFNg, scRNAseq
GSM8491730 SI, day 5 + 48h IFNg, scRNAseq
GSM8491731 SI, B6, replicate 1
GSM8491732 SI, B6, replicate 2
GSM8491733 SI, BM, replicate 1
GSM8491734 SI, BM, replicate 2
GSM8491735 SI, BM + treatment
GSM8491736 SI, BM + treatment2
GSM8491737 SI, B6, naive
GSM8491738 SI, B6, syngeneic BMT
GSM8491739 SI, B6, allogeneic BMT

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