GEO series

RNA sequencing data of leptomeningeal/perivascular CAMs 8 weeks after repopulation.

GSE294773 Mus musculus (mouse) Single-cell RNA-seq 12 samples Submitted 2026/03/01 Platform GPL30172

At a glance

Single-cell RNA-seq · mouse · 12 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
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: Distinct origins and niches determine the cellular responsiveness of CNS macrophages after repopulationNature immunology · 2026

Summary (written by the submitters)

Perivascular and leptomeningeal macrophages are non-parenchymal macrophages summarized as central nervous system (CNS)-associated macrophages (CAMs) that mediate immune responses at brain boundaries. Both, CAMs and juxtaneuronal microglia are derived from prenatal yolk sac (YS) precursors, long-living and maintain their populations by homeostatic self-renewal without input from the periphery.

Read the full summary ↓

Whereas microglia have been shown to be repopulated by CNS endogenous remnants of the same lineage following depletion, the renewal biology of CAMs is still poorly understood. Here, by combining multilineage myeloid fate mapping, bulk and single-cell profiling and high resolution confocal imaging, we show that the repopulation is strikingly different between CAMs and microglia. In contrast to microglia, CAMs do not renew exclusively cell-autonomously, but transiently utilize CCR2+Ly-6C+ monocytes after niche induction in an integrin-dependent manner. Remarkably and unlike repopulated microglia, replenished monocyte-derived CAMs remain transcriptionally and functionally distinct from their YS-derived counterparts. Finally, we established a protocol that allows to selectively exchange CAMs modulating disease response without functionally affecting parenchymal microglia. These new insights into the biology of the CNS immune system offer completely new therapeutic avenues for diverse neuroinflammatory and neurodegenerative diseases.

Published in

Distinct origins and niches determine the cellular responsiveness of CNS macrophages after repopulation

Fliegauf M, Levard D, Cardamone F et al. · Nature immunology 2026 · PMID 41851525 · doi:10.1038/s41590-026-02457-y

This dataset

Open GSE294773 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 GSE294773_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 PRJNA1251586 and SRA study SRP579032. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41851525) ↗

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

GSM8919324 F1_CTL
GSM8919325 F2_CTL
GSM8919326 M1_CTL
GSM8919327 M2_CTL
GSM8919328 M1_neg
GSM8919330 M1_pos
GSM8919331 M2_neg
GSM8919332 M2_pos
GSM8919333 F1_neg
GSM8919334 F1_pos
GSM8919335 F2_neg
GSM8919337 F2_pos

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GSE295334 RNA sequencing data of leptomeningeal/perivascular CAMs and MG following LPS stimulation 8 weeks after repopulation 54 samples shares leptomeningeal, perivascular, repopulation, weeks, cams
GSE318159 RNA sequencing data of fate-mapped leptomeningeal/perivascular CAMs 8 weeks after repopulation and 1 day after MCAo 23 samples shares leptomeningeal, perivascular, repopulation, weeks, cams
GSE295335 RNA sequencing data of leptomeningeal/perivascular CAMs 8 weeks after repopulation. [scRNA-Seq] 8 samples shares leptomeningeal, perivascular, repopulation, weeks, cams
GSE318071 RNA sequencing data of dural CAMs 8 weeks after repopulation stimulated with LPS 20 samples shares repopulation, weeks, cams
GSE318386 scATAC sequencing data of subdural, dural CAMs and MG 8 weeks after repopulation 8 samples shares repopulation, weeks, cams
GSE318650 scRNA sequencing data of cells from leptomeninges, cortex and dura mater from CTL, 5d and 8 weeks after macrophage deletion 20 samples shares weeks
GSE297835 Single Cell RNA Sequencing of C57BL6 mouse whole aortas after 8 weeks of L-NAME treatment 22 samples shares weeks
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