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Bile acid 7a-dehydroxylating bacteria accelerate injury-induced mucosal healing in the colon

GSE287080 Mus musculus (mouse) RNA-seq (gene expression) 40 samples Submitted 2025/05/22 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 40 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
40 samples: 11 × WT_control vs 10 × KO_treatment vs 10 × WT_treatment vs 9 × KO_controlGroups 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
Bile acid 7α-dehydroxylating bacteria accelerate injury-induced mucosal healing in the colonEMBO molecular medicine · 2025
Summary (written by the submitters)
Host-microbiome communication is frequently perturbed in gut pathologies due to microbiome dysbiosis, leading to altered production of bacterial metabolites. Among these, 7a-dehydroxylated bile acids are notably diminished in inflammatory bowel disease patients. Herein, we investigated whether restoration of 7a-dehydroxylated bile acids levels by Clostridium scindens, a human-derived 7a-dehydroxylating bacterium, can reestablish intestinal epithelium homeostasis following colon injury.
Read the full summary ↓
Gnotobiotic and conventional mice were subjected to chemically-induced experimental colitis following administration of Clostridium scindens. Colonization enhanced the production of 7a-dehydroxylated bile acids and conferred prophylactic and therapeutic protection against colon injury through epithelial regeneration and specification. Computational analysis of human datasets confirmed defects in intestinal cell renewal and differentiation in ulcerative colitis patients while expression of genes involved in those pathways showed a robust positive correlation with 7a-dehydroxylated bile acid levels. Clostridium scindens administration could therefore be a promising biotherapeutic strategy to foster mucosal healing following colon injury by restoring bile acid homeostasis.
Published in
Bile acid 7α-dehydroxylating bacteria accelerate injury-induced mucosal healing in the colon
Jalil A, Perino A, Dong Y et al. · EMBO molecular medicine 2025 · PMID 40065134 · doi:10.1038/s44321-025-00202-w
This dataset
Open GSE287080 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 GSE287080_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 PRJNA1211096 and SRA study SRP557753. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40065134) ↗
Study design
11 × WT_control vs 10 × KO_treatment vs 10 × WT_treatment vs 9 × KO_control

Supports a between-group comparison across 40 samples.

How we read this: 4 replicated groups read from 40 sample titles; they account for 40 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.