GEO series

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

GSE254161 Mus musculus (mouse) Spatial transcriptomics 4 samples Submitted 2025/06/30 Platform GPL24247

At a glance

Spatial transcriptomics · mouse · 4 samples

What it is: Spatial transcriptomicsGene activity measured with its position in a tissue section.
Organism: Mus musculus (mouse)
Samples: 4 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI.

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 spatial transcriptomics (10X Visium) to spatiotemporally profile CNS wound healing responses, including stromal and immune responses, after photothrombotic (PT) injury.

This dataset

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Download · which file do I need?

Direct links to NCBI, 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.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE254161_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

What the files usually look like: Spatial studies usually ship Space Ranger style folders (count matrix plus tissue images). Look for them among the supplementary files.

Also filed as BioProject PRJNA1068655. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40903576) ↗

Samples in this study

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+ 4 more — browse all 4 samples with per-sample file links →

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GSE227189 Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [mouse] 28 samples shares dynamic, injury

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