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

GSE312880 Mus musculus (mouse) Single-nucleus RNA-seq 35 samples Submitted 2026/01/08 Platform GPL34290
At a glance

Single-nucleus RNA-seq · mouse · 35 samples

What it is
Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue). Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Mus musculus (mouse)
Samples
35 samples: 35 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)
Single Nuclei RNA seq was used to examine gene expression of all spinal cord cell types from rostral and caudal spared regions of the injured spinal cord in a mouse model of incomplete spinal cord injury (iSCI, lateral hemisection) at multiple timepoints after injury (3, 7, 28 dpi). A focus of this study was to characterize spatiotemportal lesion-remote astrocyte gene expression via integration with paired spatial transcriptomics data.
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 GSE312880 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 GSE312880_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 PRJNA1377547 and SRA study SRP653429. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41407858) ↗
Study design
35 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 35 sample titles: 35 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
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.