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A single-cell transcriptomic atlas of all cell types in the entire 5xFAD mouse brain in response to dietary inulin supplementation

GSE262881 Mus musculus (mouse) Single-cell RNA-seq 24 samples Submitted 2025/04/28 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 24 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Mus musculus (mouse)
Samples: 24 samples: 8 conditions, mostly in triplicateGroups 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: A single-cell transcriptomic atlas of all cell types in the brain of 5xFAD Alzheimer mice in response to dietary inulin supplementationBMC biology · 2025

Summary (written by the submitters)

Alzheimer’s disease (AD) is a progressive neurodegenerative disease that becomes a major threat to the aging population. Due to lack of effective therapy, preventive treatments are important strategies to limit AD onset and progression, of which dietary patterns have been implicated as a key influencer. Diet with high fiber content is known to have beneficial effects on cognitive decline in AD.

Read the full summary ↓

However, a global survey on brain cell dynamics in response to high fiber intake at single-cell resolution is still missing. Here, we show that dietary inulin supplementation synergized with AD progression to specifically increase the abundance of Akkermansia muciniphila in gut microbiome of the 5x Familial AD (FAD) mice. By performing single-nucleus RNA sequencing on different regions of the whole brain with three independent biological replicates, we reveal region-specific changes in the proportion of neuron, astrocyte and granule cell subpopulations upon inulin supplementation in 5xFAD mice. Intriguingly, such dietary change only marginally alleviated astrogliosis and microgliosis, without affecting the amyloid-beta plaque burden. These results provide a comprehensive overview on the transcriptomic changes in individual cells of the entire mouse brain in response to high fiber intake, which provides a resourceful foundation for future mechanistic studies on related topics

Published in

A single-cell transcriptomic atlas of all cell types in the brain of 5xFAD Alzheimer mice in response to dietary inulin supplementation

Wang X, Zhang H, Wan Z et al. · BMC biology 2025 · PMID 40346662 · doi:10.1186/s12915-025-02230-x

This dataset

Open GSE262881 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 GSE262881_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 PRJNA1070405 and SRA study SRP487505. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40346662) ↗

Study design

8 conditions, mostly in triplicate

Ctrl_FB ×3 Inulin_FB ×3 Ctrl_MB ×3 Inulin_MB ×3 Ctrl_BS ×3 Inulin_BS ×3 Ctrl_CB ×3 Inulin_CB ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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

GSM8181019 Ctrl_FB_1 Ctrl_FB
GSM8181020 Ctrl_FB_2 Ctrl_FB
GSM8181021 Ctrl_FB_3 Ctrl_FB
GSM8181022 Inulin_FB_1 Inulin_FB
GSM8181023 Inulin_FB_2 Inulin_FB
GSM8181024 Inulin_FB_3 Inulin_FB
GSM8181025 Ctrl_MB_1 Ctrl_MB
GSM8181026 Ctrl_MB_2 Ctrl_MB
GSM8181027 Ctrl_MB_3 Ctrl_MB
GSM8181028 Inulin_MB_1 Inulin_MB
GSM8181029 Inulin_MB_2 Inulin_MB
GSM8181030 Inulin_MB_3 Inulin_MB
GSM8181031 Ctrl_BS_1 Ctrl_BS
GSM8181032 Ctrl_BS_2 Ctrl_BS
GSM8181033 Ctrl_BS_3 Ctrl_BS
GSM8181034 Inulin_BS_1 Inulin_BS
GSM8181035 Inulin_BS_2 Inulin_BS
GSM8181036 Inulin_BS_3 Inulin_BS
GSM8181037 Ctrl_CB_1 Ctrl_CB
GSM8181038 Ctrl_CB_2 Ctrl_CB
GSM8181039 Ctrl_CB_3 Ctrl_CB
GSM8181040 Inulin_CB_1 Inulin_CB
GSM8181041 Inulin_CB_2 Inulin_CB
GSM8181042 Inulin_CB_3 Inulin_CB

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