← BioTransfer GEO Dataset Finder
GEO series

Pericytes and perivascular fibroblasts contribute to central nervous system fibrosis in a region dependent manner

GSE229916 Mus musculus (mouse) RNA-seq (gene expression) 832 samples Submitted 2024/05/10 Platform GPL17021
At a glance

RNA-seq (gene expression) · mouse · 832 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
832 samples: 256 × Spinal cord, Uninjured, P6981 vs 144 × Spinal cord, Injury , P6981Groups 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
Distinct origin and region-dependent contribution of stromal fibroblasts to fibrosis following traumatic injury in miceNature neuroscience · 2024
Summary (written by the submitters)
Fibrotic scar tissue formation is conserved throughout the central nervous system in humans and mice, and impairs tissue regeneration and functional recovery. However, the origin of scar-forming stromal fibroblasts is controversial. Here, we show that stromal fibroblasts found after spinal cord injury derive from two populations of perivascular cells that are anatomically and transcriptionally defined as pericytes and perivascular fibroblasts.
Read the full summary ↓
We identify two distinct perivascular cell populations, which activate and transcriptionally converge on the generation of stromal myofibroblasts after injury. Our results suggest potential targets to improve tissue regeneration and functional recovery after central nervous system injuries.
Published in
Distinct origin and region-dependent contribution of stromal fibroblasts to fibrosis following traumatic injury in mice
Holl D, Hau WF, Julien A et al. · Nature neuroscience 2024 · PMID 38849523 · doi:10.1038/s41593-024-01678-4
This dataset
Open GSE229916 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 GSE229916_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 PRJNA956577 and SRA study SRP433039. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38849523) ↗
Study design
256 × Spinal cord, Uninjured, P6981 vs 144 × Spinal cord, Injury , P6981

Supports a between-group comparison across 400 samples.

How we read this: 2 replicated groups read from the first 400 of 832 sample titles; they account for 400 of them. 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

+ 792 more — browse all 832 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.