GEO series

Longitudinal scRNA-seq of murine T cell transfer colitis

GSE236889 Mus musculus (mouse) Single-cell RNA-seq 64 samples Submitted 2026/04/28 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 64 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Mus musculus (mouse)
Samples: 64 samples: 64 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: Spatiotemporal analysis reveals distinct inflammatory programs underlying chronic colitisImmunity · 2026

Summary (written by the submitters)

In order to describe in detail the processes involved in chronic colitis, we performed scRNA-seq at multiple time points in CD45RBhi T cell transfer colitis mouse models. These data were compared to bulk RNAseq and spatial transcriptomics results from the same mice within the same study. scRNAseq data were analyzed by annotating cell clusters and comparing proportions and gene expression programs over time.

Published in

Spatiotemporal analysis reveals distinct inflammatory programs underlying chronic colitis

Fransson J, Sorini C, Castillo F et al. · Immunity 2026 · PMID 42097141 · doi:10.1016/j.immuni.2026.04.005

This dataset

Open GSE236889 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 GSE236889_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 PRJNA992570 and SRA study SRP448105. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42097141) ↗

Study design

64 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 64 sample titles: 64 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

GSM7579128 Colon, W0, Epithelial fraction, gene expression
GSM7579130 Colon, W0, Immune fraction, gene expression
GSM7579131 Colon, W0, Stroma fraction, gene expression
GSM7579132 Colon, W1, Epithelial fraction, gene expression
GSM7579133 Colon, W1, Immune fraction, gene expression
GSM7579134 Colon, W1, Stroma fraction, gene expression
GSM7579136 Colon, W2, Epithelial fraction, gene expression
GSM7579137 Colon, W2, Immune fraction, gene expression
GSM7579138 Colon, W2, Stroma fraction, gene expression
GSM7579139 Colon, W3, Epithelial fraction, gene expression
GSM7579141 Colon, W3, Epithelial fraction, anti-IL-12p40-treated, gene expression
GSM7579142 Colon, W3, Immune fraction, gene expression
GSM7579144 Colon, W3, Stroma fraction, gene expression
GSM7579145 Colon, W4, Epithelial fraction, gene expression
GSM7579146 Colon, W4, Immune fraction, gene expression
GSM7579147 Colon, W4, Stroma fraction, gene expression
GSM7579148 Colon, W5, Epithelial fraction, gene expression
GSM7579150 Colon, W5, Epithelial fraction, anti-IL-12p40-treated, gene expression
GSM7579151 Colon, W5, Immune fraction, gene expression
GSM7579152 Colon, W5, Stroma fraction, gene expression
GSM7579153 Colon, W6, Epithelial fraction, gene expression
GSM7579154 Colon, W6, Immune fraction, gene expression
GSM7579155 Colon, W6, Stroma fraction, gene expression
GSM7579157 Colon, W7, Epithelial fraction, gene expression
GSM7579158 Colon, W7, Epithelial fraction, anti-IL-12p40-treated, gene expression
GSM7579159 Colon, W7, Immune fraction, gene expression
GSM7579160 Colon, W7, Immune fraction, anti-IL-12p40-treated, gene expression
GSM7579161 Colon, W7, Stroma fraction, gene expression
GSM7579163 Colon, W7, Stroma fraction, anti-IL-12p40-treated, gene expression
GSM7579164 Colon, D0, Epithelial fraction, gene expression
GSM7579165 Colon, D0, Immune fraction, gene expression
GSM7579167 Colon, D0, Stroma fraction, gene expression
GSM7579168 Colon, D10, Epithelial fraction, gene expression
GSM7579169 Colon, D10, Immune fraction, gene expression
GSM7579170 Colon, D10, Stroma fraction, gene expression
GSM7579172 Colon, D20, Epithelial fraction, gene expression
GSM7579173 Colon, D20, Immune fraction, gene expression
GSM7579174 Colon, D20, Stroma fraction, gene expression
GSM7579176 Colon, D30, Epithelial fraction, anti-IL-12p40-treated, gene expression
GSM7579177 Colon, D40, Epithelial fraction, anti-IL-12p40-treated, gene expression

+ 24 more — browse all 64 samples with per-sample file links →

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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.