GEO series

Indigenous gut microbes modulate neural cell state and neurodegenerative disease susceptibility [5xFAD_CD11b+_Bulk_RNA-seq]

GSE289590 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2026/02/03 Platform GPL34290

At a glance

RNA-seq (gene expression) · mouse · 12 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: 12 samples: 3 × 5xFAD_E. coli_1mo vs 3 × 5xFAD_vehicle_1mo vs 3 × 5xFAD_E. coli_2wk vs 3 × 5xFAD_vehicle_2wkGroups 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 neurological function. We have shown that colonization by Escherichia coli induces a distinct adaptive immune and neurogenerative disease-associated cell state in wildtype mice, suggesting increased disease susceptibility. Further, E. coli exposure in the 5xFAD mouse model results in exacerbated cognitive decline and amyloid pathology, demonstrating its sufficiency to worsen Alzheimer’s disease-relevant outcomes.

Read the full summary ↓

Here, we performed bulk RNA-seq of CD11b+ brain myeloid cells from E. coli or vehicle treated 5xFAD mice to understand how E. coli modulates neuroimmune responses in the context of amyloid pathology. We demonstrate that E. coli exposed animals have a subtle decrease in genes associated with the disease associated microglia phenotype after 1 month of enrichment, perhaps helping to explain why these animals displayed worsened 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 GSE289590 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 GSE289590_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 PRJNA1223797 and SRA study SRP563960. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41638211) ↗

Study design

3 × 5xFAD_E. coli_1mo vs 3 × 5xFAD_vehicle_1mo vs 3 × 5xFAD_E. coli_2wk vs 3 × 5xFAD_vehicle_2wk

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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

GSM8794719 5xFAD_E. coli_1mo_rep1 5xFAD_E. coli_1mo
GSM8794720 5xFAD_E. coli_1mo_rep2 5xFAD_E. coli_1mo
GSM8794721 5xFAD_vehicle_1mo_rep1 5xFAD_vehicle_1mo
GSM8794722 5xFAD_vehicle_1mo_rep2 5xFAD_vehicle_1mo
GSM8794723 5xFAD_vehicle_1mo_rep3 5xFAD_vehicle_1mo
GSM8794724 5xFAD_E. coli_1mo_rep3 5xFAD_E. coli_1mo
GSM9125440 5xFAD_E. coli_2wk_rep1 5xFAD_E. coli_2wk
GSM9125441 5xFAD_E. coli_2wk_rep2 5xFAD_E. coli_2wk
GSM9125442 5xFAD_E. coli_2wk_rep3 5xFAD_E. coli_2wk
GSM9125443 5xFAD_vehicle_2wk_rep1 5xFAD_vehicle_2wk
GSM9125444 5xFAD_vehicle_2wk_rep2 5xFAD_vehicle_2wk
GSM9125445 5xFAD_vehicle_2wk_rep3 5xFAD_vehicle_2wk

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