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Dynamic fibroblast-immune interactions shape recovery after brain injury [snRNASeq_Timecourse]

GSE254162 Mus musculus (mouse) Single-nucleus RNA-seq 12 samples Submitted 2025/06/30 Platform GPL24247
At a glance

Single-nucleus RNA-seq · mouse · 12 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).
Organism
Mus musculus (mouse)
Samples
12 samples: 12 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
Dynamic fibroblast-immune interactions shape recovery after brain injuryNature · 2025
Summary (written by the submitters)
Fibroblasts and immune cells coordinate tissue regeneration and necessary scarring after injury. In the brain, fibroblasts are border-enriched cells whose dynamic molecular states and immune interactions after injury remain unclear. We used single nuclear RNA sequencing at multiple timepoints to profile stromal and immune responses to sterile (photothrombotic, PT) injury. We find that early pro-fibrotic myofibroblasts transition into several states, including meningeal and lymphocyte-interactive fibroblasts.
Published in
Dynamic fibroblast-immune interactions shape recovery after brain injury
Ewing-Crystal NA, Mroz NM, Larpthaveesarp A et al. · Nature 2025 · PMID 40903576 · doi:10.1038/s41586-025-09449-2
This dataset
Open GSE254162 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 GSE254162_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 PRJNA1068657 and SRA study SRP485736. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40903576) ↗
Study design
12 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 12 sample titles: 12 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

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