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A lack of commensal microbiota influences the male reproductive tract intergenerationally in mice

GSE269257 Mus musculus (mouse) RNA-seq (gene expression) 62 samples Submitted 2025/03/02 Platform GPL32159
At a glance

RNA-seq (gene expression) · mouse · 62 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
62 samples: 16 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 lack of commensal microbiota influences the male reproductive tract intergenerationally in miceReproduction (Cambridge, England) · 2025
Summary (written by the submitters)
The microbiome encompasses the array of microorganisms inhabiting various niches in the body and is necessary for numerous physiological processes, including normal metabolism and a functioning immune system. Not only does the absence of a microbiome in mice impact the exposed animals but also inherited phenotypes in successive generations of progeny, suggesting that the absence of a microbiome impacts the germline and gametes.
Read the full summary ↓
Indeed, recent research has identified a role of the gut microbiome in contributing to male fertility, in both healthy and disease states. While this link is beginning to be established, the impact of the microbiome on the male reproductive tract remains understudied. Here, we utilized a germ-free mouse model to examine the influence of the absence of microbes on the male reproductive tract. In contrast to mice with an established microbiome, germ-free mice display decreased testicular weight and the prevalence of an epididymitis-like inflammation phenotype. These histopathological changes are accompanied by transcriptomic dysregulation in the reproductive tract of germ-free mice, particularly in the cauda epididymis. Moreover, such transcriptomic changes are transmitted to the next generation with high correlation of gene expression in the cauda epididymis between germ-free mice and their conventionalized (microbiome-restored) male offspring, when compared to control mice. Ultimately, our findings identify the reproductive sequalae of males without a functional microbiome and additionally in their conventionalized offspring, suggesting that the paternal microbiota is an underappreciated contributor to male reproductive function.
Published in
A lack of commensal microbiota influences the male reproductive tract intergenerationally in mice
Trigg NA, Zhou SK, Harris JC et al. · Reproduction (Cambridge, England) 2025 · PMID 39946159 · doi:10.1530/REP-24-0204
This dataset
Open GSE269257 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 GSE269257_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 PRJNA1120838 and SRA study SRP512231. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39946159) ↗
Study design
16 conditions, mostly in triplicate
caput epididymis, germ free, ×6 cauda epididymis, germ free, ×6 caput epididymis, specific pathogen free, set… ×5 cauda epididymis, specific pathogen free, set… ×5 testis, specific pathogen free, set 2, ×5 testis, germ free, ×4 caput epididymis, specific pathogen free, ×4 cauda epididymis, specific pathogen free, ×4 +8 more

Supports a between-group comparison across 62 samples.

How we read this: 16 replicated groups read from 62 sample titles; they account for 62 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

+ 22 more — browse all 62 samples with per-sample file links →

Datasets on a similar topic

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