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Caspases 3 and 7 restrict intestinal inflammation by regulating stem cell function and gsdmd-mediated pyroptosis

GSE297859 Mus musculus (mouse) RNA-seq (gene expression) 42 samples Submitted 2026/02/13 Platform GPL34290
At a glance

RNA-seq (gene expression) · mouse · 42 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
42 samples: 8 conditions, mostly with about 6 replicates eachGroups 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
Caspase-3/7 deficiency results in enhanced intestinal inflammation and reduced tumorigenesisScience advances · 2026
Summary (written by the submitters)
Aberrant intestinal epithelial cell (IEC) death is a hallmark of inflammatory bowel disease (IBD), observed in patient samples and animal models of colitis. While multiple cell death pathways contribute to disease pathogenesis, the dominant modalities and their regulatory mechanisms in IBD remain poorly defined. In this study, we demonstrate that mice with intestinal epithelial cell-specific deletion of caspase-3 and -7 (Casp3/7 Tg) exhibit exacerbated colitis, increased mortality, and impaired epithelial regeneration, phenotypes not observed in other cell death-related knockout models.
Read the full summary ↓
These findings highlight a previously unrecognized protective role of caspase-3/7 in controlling inflammation and tissue regeneration following intestinal injury. Mechanistically, caspase-3/7 deficiency negatively affects intestinal stem cell proliferation and promotes GSDMD-dependent pyroptosis, compromising barrier integrity and return to steady state conditions. Together, our results identify caspase-3/7 as key regulators of epithelial integrity and inflammation and suggest their modulation as a promising therapeutic strategy in IBD and colorectal cancer.
Published in
Caspase-3/7 deficiency results in enhanced intestinal inflammation and reduced tumorigenesis
Xie W, Wyckaert L, Vadi M et al. · Science advances 2026 · PMID 41861024 · doi:10.1126/sciadv.adz5906
This dataset
Open GSE297859 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 GSE297859_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 PRJNA1266606 and SRA study SRP587014. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41861024) ↗
Study design
8 conditions, mostly with about 6 replicates each
Tissue - Tg - Day 0 ×6 Tissue - WT - Day 8 ×6 IEC - Wild_type - DSS ×6 IEC - Transgenic - DSS ×6 Tissue - WT - Day 0 ×5 Tissue - Tg - Day 8 ×5 IEC - Wild_type - Control ×4 IEC - Transgenic - Control ×4

Supports a between-group comparison across 42 samples.

How we read this: 8 replicated groups read from 42 sample titles; they account for 42 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

+ 2 more — browse all 42 samples with per-sample file links →

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.