← BioTransfer GEO Dataset Finder
GEO series

Astrocyte-enriched murine cortical and white matter transcriptional profiles after stroke in spatially-defined zones of post-stroke reactivity

GSE263986 Mus musculus (mouse) RNA-seq (gene expression) 82 samples Submitted 2025/08/21 Platform GPL17021
At a glance

RNA-seq (gene expression) · mouse · 82 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
82 samples: 18 conditions, mostly with about 5 replicates eachGroups 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.
Summary (written by the submitters)
Zones of reactive astrocytes after stroke were defined in both white matter and cortical stroke models using a combination of phenotyping and morphology. These zones were then excised via laser capture microscopy in mGFAP-77.6-Cre/Ribotag mice and astrocytic ribosomes were immunopreciptated to generate astrocyte-enriched zone-specific transcriptomic profiles.
Read the full summary ↓
RNA extracted from cleared lysate (input) was used to assess astrocytic enrichment in white matter and cortex in both the uninjured brain and in the combined first three zones of reactivity after stroke, comparing expression profiles to matched immunoprecipitated ribosome-associated RNA.
This dataset
Open GSE263986 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 GSE263986_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 PRJNA1100502 and SRA study SRP501956. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
18 conditions, mostly with about 5 replicates each
White matter, uninjured, input RNA, ×5 White matter, uninjured, immunoprecipitated R… ×5 Cortex, uninjured, input RNA, ×5 Cortex, uninjured, immunoprecipitated RNA, ×5 White matter, stroke zone 1, immunoprecipitat… ×5 White matter, stroke zone 2, immunoprecipitat… ×5 White matter, stroke zone 3, immunoprecipitat… ×5 White matter, stroke zone 4, immunoprecipitat… ×5 +10 more

Supports a between-group comparison across 82 samples.

How we read this: 18 replicated groups read from 82 sample titles; they account for 82 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

+ 42 more — browse all 82 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.