GEO series

Single nucleus analysis of post-mortem brain tissues from Adult-onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP) patients

GSE295854 Homo sapiens (human) Single-nucleus RNA-seq 29 samples Submitted 2025/08/13 Platform GPL24676

At a glance

Single-nucleus RNA-seq · human · 29 samples

What it is: Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue). Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Homo sapiens (human)
Samples: 29 samples: 29 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: Mutations in the human CSF1R gene impact microglia's maintenance of brain white matter integrityNature immunology · 2025

Summary (written by the submitters)

Microglia, the brain's resident macrophages, depend on interleukin 34 (IL-34) and colony-stimulating factor 1 (CSF1) for their development and maintenance, engaging the CSF1 receptor (CSF1R). Adult-onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP), a neurodegenerative disorder affecting the brain's white matter, is caused by heterozygous pathogenic mutations in the CSF1R gene.

Read the full summary ↓

Neuropathological studies of postmortem ALSP brains have shown widespread depletion of microglia, demyelination of cerebral white matter, axonal swellings, and pigmented glial cells. In this study, we investigated how individual brain cell populations respond to microglia depletion and contribute to ALSP progression. To do this, we analyzed post-mortem specimens from patients wirth ALSP using single-nucleus RNA-seq (snRNA-seq).

Published in

Mutations in the human CSF1R gene impact microglia's maintenance of brain white matter integrity

Du S, Zhou Y, Li D et al. · Nature immunology 2025 · PMID 40571738 · doi:10.1038/s41590-025-02195-7

This dataset

Open GSE295854 in finder → Find more human 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 GSE295854_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 PRJNA1249385 and SRA study SRP577974. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40571738) ↗

Study design

29 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 29 sample titles: 29 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

GSM8958752 Control1_OC
GSM8958753 Control2_CB
GSM8958754 Control2_FC
GSM8958755 Control2_WM
GSM8958756 Control3_CB
GSM8958757 Control3_FC
GSM8958758 Control3_WM
GSM8958759 ALSP1_CB
GSM8958760 ALSP1_FC
GSM8958761 ALSP1_OC
GSM8958762 ALSP1_WM
GSM8958763 ALSP2_CB
GSM8958764 ALSP2_FC
GSM8958765 ALSP2_OC
GSM8958766 ALSP2_WM
GSM8958767 Control13_OC
GSM8958768 ALSP3_FC
GSM8958769 ALSP3_temporal
GSM8958770 ALSP3_parietal
GSM8958771 ALSP3_BG
GSM8958772 ALSP4_FC
GSM8958773 ALSP5_FC
GSM8958774 ALSP5_SC
GSM8958775 ALSP5_WM
GSM8958776 ALSP5_OC
GSM8958777 ALSP6_FC
GSM8958778 ALSP6_SC
GSM8958779 ALSP6_WM
GSM8958780 ALSP6_OC

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