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Lesion-remote astrocytes govern microglia-mediated white matter repair II

GSE312871 Mus musculus (mouse) RNA-seq (gene expression) 198 samples Submitted 2026/01/08 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 198 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
198 samples: 198 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
Lesion-remote astrocytes govern microglia-mediated white matter repairNature · 2026
Summary (written by the submitters)
RNA sequencing was applied to examine changes in gene expression in astrocytes in spared tissue regions both rostral and caudal to the injury site in a mouse model of incomplete spinal cord injury (ISCI) over multiple post-injury time points. The RiboTag method was used to isolate astrocyte ribosome-associated mRNAs from the spinal cord of wild type mice and mice with astrocyte-specific conditional gene deletion (cKO) of a known transcriptional regulators of reactivity, STAT3 (Stat3 knockout: Stat3-cKO).
Published in
Lesion-remote astrocytes govern microglia-mediated white matter repair
McCallum S, Suresh KB, Islam TS et al. · Nature 2026 · PMID 41407858 · doi:10.1038/s41586-025-09887-y
This dataset
Open GSE312871 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 GSE312871_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 PRJNA1377544 and SRA study SRP653420. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41407858) ↗
Study design
198 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 198 sample titles: 198 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

+ 158 more — browse all 198 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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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.