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Single cell approaches define neural stem cell niches and identify microglial ligands that enhance precursor-mediated remyelination

GSE266690 Mus musculus (mouse) Single-cell RNA-seq 33 samples Submitted 2024/12/19 Platform GPL17021Platform GPL33896Platform GPL31217
At a glance

Single-cell RNA-seq · mouse · 33 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Mus musculus (mouse)
Samples
33 samples: 9 conditions, mostly in duplicateGroups 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
Single cell approaches define neural stem cell niches and identify microglial ligands that can enhance precursor-mediated oligodendrogenesisCell reports · 2025
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
Single cell approaches define neural stem cell niches and identify microglial ligands that can enhance precursor-mediated oligodendrogenesis
Willis A, Jeong D, Liu Y et al. · Cell reports 2025 · PMID 39823226 · doi:10.1016/j.celrep.2024.115194
This dataset
Open GSE266690 in finder → Find more 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 GSE266690_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 PRJNA1108280 and SRA study SRP510503. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39823226) ↗
Study design
9 conditions, mostly in duplicate
Adult_BSAInfused_Xenium ×6 Adult_Control_NoRecovery_Xenium ×3 Adult_CupRap_NoRecovery_Xenium ×3 Adult_OSMInfused_Xenium ×3 Adult_Control_Forebrain_MERFISH_Biol ×2 Adult_CupRap_Forebrain_MERFISH_Biol ×2 Adult_Control_Forebrain_Xenium_Biol ×2 Adult_CupRap_Forebrain_Xenium_Biol ×2 +9 more

Supports a between-group comparison across 25 samples.

How we read this: 9 replicated groups read from 33 sample titles; they account for 25 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
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