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Indigenous gut microbes modulate neural cell state and neurodegenerative disease susceptibility [mono-colonized_RNA-seq]

GSE289591 Mus musculus (mouse) RNA-seq (gene expression) 29 samples Submitted 2026/02/03 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 29 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
29 samples: 8 conditions, mostly with about 4 replicates eachGroups 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
Indigenous gut microbes modulate neural cell state and neurodegenerative disease susceptibilityCell systems · 2026
Summary (written by the submitters)
The native microbiome influences a plethora of host processes, including neuroimmune function. However, the consequences of individual gut microbes on neuroinflammatory tone remain largely unexplored. In the present dataset, we investigated the consequences of four bacterial type strains representing prevalent genera within the mammalian gut microbiome (Bacteroides thetaiotaomicron (B.
Read the full summary ↓
theta), Clostridium celatum, Lactobacillus johnsonii, and Escherichia coli) on the transcriptional profile of CD11b+ brain myeloid cells. After 2 weeks of mono-colonization with the bacteria species of interest, it was found that each bacterial type had distinct effects on brain myeloid cell gene expression, highlighting the bacterial dependent consequences of the microbiome for neuroinflammatory outcomes.
Published in
Indigenous gut microbes modulate neural cell state and neurodegenerative disease susceptibility
Blackmer-Raynolds L, Lipson LD, Kozlov A et al. · Cell systems 2026 · PMID 41638211 · doi:10.1016/j.cels.2025.101481
This dataset
Open GSE289591 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 GSE289591_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1223796 and SRA study SRP564077. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41638211) ↗
Study design
8 conditions, mostly with about 4 replicates each
L. johnsonii mono-colonized, female, ×4 E. coli mono-colonized, male, ×4 Germ-free, female, ×4 L. johnsonii mono-colonized, male, ×4 C. celatum mono-colonized, male, ×4 E. coli mono-colonized, female, ×3 B. thetaiotaomicron mono-colonized, male, ×3 Germ-free, male, ×3

Supports a between-group comparison across 29 samples.

How we read this: 8 replicated groups read from 29 sample titles; they account for 29 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
Datasets on a similar topic

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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.