GEO series

Cell-type-specific contributions to impaired blood-brain barrier and altered cerebral metabolism in prodromal 5XFAD mice

GSE295077 Mus musculus (mouse) Single-nucleus RNA-seq 16 samples Submitted 2025/07/30 Platform GPL24247

At a glance

Single-nucleus RNA-seq · mouse · 16 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: Mus musculus (mouse)
Samples: 16 samples: 4 × 5xFAD.All vs 4 × WT.All vs 4 × 5xFAD.Vas vs 4 × WT.VasGroups 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: Cell type-specific contributions to impaired blood-brain barrier and cerebral metabolism in presymptomatic 5XFAD micebioRxiv : the preprint server for biology · 2025

Summary (written by the submitters)

Single-nucleus RNA sequencing (snRNA-Seq) further revealed cell type-specific transcriptomic changes in the hippocampus of prodromal 5XFAD mice, including downregulation of synaptogenesis and synaptic transmission genes in the CA1 and dentate gyrus excitatory neurons, impaired endothelia gene expression linked to brain barrier function and angiogenesis, altered innate immune response genes in astrocytes, as well as upregulation of cholesterol biosynthesis and metabolism genes in the CA1 excitatory neurons.

Published in

Cell type-specific contributions to impaired blood-brain barrier and cerebral metabolism in presymptomatic 5XFAD mice

Yao M, Sun N, Linville R et al. · bioRxiv : the preprint server for biology 2025 · PMID 40635873 · doi:10.1101/2025.04.23.650260

This dataset

Open GSE295077 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 GSE295077_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 PRJNA1252762 and SRA study SRP579785. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40635873) ↗

Study design

4 × 5xFAD.All vs 4 × WT.All vs 4 × 5xFAD.Vas vs 4 × WT.Vas

Supports a between-group comparison across 16 samples.

How we read this: 4 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

GSM8941775 5xFAD.All.1 5xFAD.All
GSM8941776 WT.All.1 WT.All
GSM8941777 5xFAD.Vas.1 5xFAD.Vas
GSM8941778 WT.Vas.1 WT.Vas
GSM8941779 5xFAD.All.2 5xFAD.All
GSM8941780 WT.All.2 WT.All
GSM8941781 5xFAD.Vas.2 5xFAD.Vas
GSM8941782 WT.Vas.2 WT.Vas
GSM8941783 5xFAD.All.3 5xFAD.All
GSM8941784 WT.All.3 WT.All
GSM8941785 5xFAD.All.4 5xFAD.All
GSM8941786 WT.All.4 WT.All
GSM8941787 5xFAD.Vas.3 5xFAD.Vas
GSM8941788 WT.Vas.3 WT.Vas
GSM8941789 5xFAD.Vas.4 5xFAD.Vas
GSM8941790 WT.Vas.4 WT.Vas

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