GEO series

Elucidating early intestinal stem cell response to bacterial infection

GSE277691 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2026/04/07 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 12 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Mus musculus (mouse)
Samples: 12 samples: 12 samples, each with a distinct title — no replicated groupsGroups 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: An inflammasome-driven differentiation program in intestinal stem cells protects against Salmonella infectionNature immunology · 2026

Summary (written by the submitters)

Intestinal stem cells (ISCs) are the regenerative force of the gut epithelium. Lgr5+-ISC have been shown to respond to changes in their microenvironment by coping with different metabolites, adapting to caloric changes, and recovering from injury and inflammation. However, how pathogenic bacteria affect adult stem cell regeneration and, as a consequence, the overall tissue adaption to infection has yet to be explored in depth.

Read the full summary ↓

Here, we interrogated early Lgr5+ ISC responses to an enteric intracellular pathogen by profiling individual IECs from the mouse small intestine. Utilizing GFP-labeled Salmonella enterica, we isolated intracellular invaded cells to elucidate invasion programs of epithelial cell subsets. In particular, we identified a Salmonella-specific infection signature comprised of antimicrobial peptide (AMP) genes, including the Defensin gene family. Our findings demonstrate that Salmonella enterica targets differentiated Paneth, enterocytes, and stem/progenitor cells at these early stages of infection. In response, a rapid Lg5+ ISC-driven cellular remodeling to enterocyte and Paneth lineages expressing AMP genes is initiated to combat the intruders. Importantly, we uncovered an ISC differentiation program via inflammasome activation to protect the crypt environment, while eliminating infected stem cells from the overall stem cell pool. This novel Lgr5+ stem cell defense mechanism not only protects the gut epithelium from persistent bacterial infection but also promotes tissue regeneration. We propose epithelial remodeling to AMP-secreting cells as a novel innate immune response to handle different gut stresses mediated by Lgr5+ ISCs to maintain organizational principles of gut homeostasis and physiology.

Published in

An inflammasome-driven differentiation program in intestinal stem cells protects against Salmonella infection

Lebon S, Habshush Menachem A, Davidzohn N et al. · Nature immunology 2026 · PMID 42120792 · doi:10.1038/s41590-026-02514-6

This dataset

Open GSE277691 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 GSE277691_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1163364 and SRA study SRP533888. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42120792) ↗

Study design

12 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 12 sample titles: 12 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

GSM8527697 Uninfected control 12h, Batch 1, Replicate 1
GSM8527698 Salmonella 12h post-infection, Batch 1, Replicate 1
GSM8527699 Salmonella 24h post-infection, Batch 1, Replicate 1
GSM8527700 Salmonella 24h post-infection, GFP+, Batch 1, Replicate 1
GSM9617578 Salmonella 24h PI / 24h PI GFP+, Batch 2, Gene Expression
GSM9617579 Listeria 24PI/Control, Batch 4, Gene Expression
GSM9617580 Salmonella Uninfected Control, Batch 5, Gene Expression
GSM9617581 Tomato+, Salmonella+/Ctrl, Batch 5, Gene Expression
GSM9617582 Salmonella 24h PI / 24h PI GFP+, Batch 2, Hash Tag Oligo
GSM9617583 Listeria 24PI/Control, Batch 4, Hash Tag Oligo
GSM9617584 Salmonella Uninfected Control, Batch 5, Hash Tag Oligo
GSM9617585 Tomato+, Salmonella+/Ctrl, Batch 5, Hash Tag Oligo

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