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APOE4 expression causes distinct effects on meningeal immunity, brain lipid composition, and cognition in male and female mice

GSE295612 Mus musculus (mouse) Single-cell RNA-seq 16 samples Submitted 2026/03/23 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 16 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
16 samples: 8 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
Sex-specific APOE4-dependent innate immunity regulates meningeal lymphatics, brain lipids, neuroinflammation, and cognitionNeuron · 2026
Summary (written by the submitters)
This experiment was designed to understand the distinct effects of sex and APOE genotype on the transcriptome of meningeal dural vascular and resident immune cells. After transcardiac perfusion with a buffered saline solution containing heparin and actinomycin D, meningeal dural whole mounts were immediately dissected from the skulls of 12-month-old male and female mice expressing APOE3 or APOE4 and digested into a single-cell suspension.
Read the full summary ↓
After enrichment for CD31+ cells via positive selection using MACS, the cells were counted and approximately 5000 cells per sample were used to obtain single-cell gene expression libraries using 10x Genomics equipment and reagents, namely the Chromium Single Cell 3' Reagent Kits. The generated libraries were sequenced in 2 lanes of a NovaSeq 6000 S4 PE100 flow cell.
Published in
Sex-specific APOE4-dependent innate immunity regulates meningeal lymphatics, brain lipids, neuroinflammation, and cognition
Delivanoglou N, Todd KT, Almeida F et al. · Neuron 2026 · PMID 41895266 · doi:10.1016/j.neuron.2026.02.030
This dataset
Open GSE295612 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 GSE295612_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 PRJNA1255476 and SRA study SRP581244. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41895266) ↗
Study design
8 conditions, mostly in duplicate
scRNAseq of Mus musculus, meningeal dura, APO… ×2 scRNAseq of Mus musculus, meningeal dura, APO… ×2 scRNAseq of Mus musculus, meningeal dura, APO… ×2 scRNAseq of Mus musculus, meningeal dura, APO… ×2 scRNAseq of Mus musculus, meningeal dura, APO… ×2 scRNAseq of Mus musculus, meningeal dura, APO… ×2 scRNAseq of Mus musculus, meningeal dura, APO… ×2 scRNAseq of Mus musculus, meningeal dura, APO… ×2

Supports a between-group comparison across 16 samples.

How we read this: 8 replicated groups read from 16 sample titles; they account for 16 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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