GEO series

Single-nucleus RNA-seq analysis of whole brains from 5xFAD mice with microglia-specific CD31 knockdown

GSE331294 Mus musculus (mouse) Single-nucleus RNA-seq 9 samples Submitted 2026/05/23 Platform GPL24247

At a glance

Single-nucleus RNA-seq · mouse · 9 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).
Organism: Mus musculus (mouse)
Samples: 9 samples: 3 × Ctrl mice vs 3 × 5xFAD mice vs 3 × Cx3Cr1CreCD31fl/+5xFAD miceGroups 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)

We performed single-nucleus RNA sequencing (snRNA-seq) on whole-brain tissues from 5xFAD mice with microglia-specific CD31 knockdown to investigate transcriptional alterations associated with Alzheimer’s disease pathology. snRNA-seq analysis identified cell-type-specific transcriptional changes across multiple brain cell populations, including microglia, revealing that CD31 knockdown attenuated disease-associated microglial signatures and inflammatory responses while promoting pathways related to Aβ clearance.

Read the full summary ↓

These findings provide insights into the role of microglial CD31 in regulating neuroinflammation and Alzheimer’s disease progression.

This dataset

Open GSE331294 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 GSE331294_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 PRJNA1467618 and SRA study SRP701701. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

3 × Ctrl mice vs 3 × 5xFAD mice vs 3 × Cx3Cr1CreCD31fl/+5xFAD mice

Supports a between-group comparison across 9 samples.

How we read this: 3 replicated groups read from 9 sample titles; they account for 9 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

GSM9743342 Ctrl mice_1 Ctrl mice
GSM9743343 Ctrl mice_2 Ctrl mice
GSM9743344 Ctrl mice_3 Ctrl mice
GSM9743345 5xFAD mice_1 5xFAD mice
GSM9743346 5xFAD mice_2 5xFAD mice
GSM9743347 5xFAD mice_3 5xFAD mice
GSM9743348 Cx3Cr1CreCD31fl/+5xFAD mice_1 Cx3Cr1CreCD31fl/+5xFAD …
GSM9743349 Cx3Cr1CreCD31fl/+5xFAD mice_2 Cx3Cr1CreCD31fl/+5xFAD …
GSM9743350 Cx3Cr1CreCD31fl/+5xFAD mice_3 Cx3Cr1CreCD31fl/+5xFAD …

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Search all mouse RNA-seq datasets in GEO →

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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.