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Whole transcriptome sequencing of UPEC-infected testis and epididymis (5d) following depletion of CX3CR1+ macrophages

GSE309348 Mus musculus (mouse) RNA-seq (gene expression) 18 samples Submitted 2026/03/11 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 18 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
18 samples: 6 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
Depletion of CX3CR1(+) macrophages results in disrupted functionality and immune surveillance within epididymis and testisMucosal immunology · 2026
Summary (written by the submitters)
A finely tuned immune regulation within the epididymis and testis—balancing tolerance towards sperm with effective defense against infections—is essential for maintaining male fertility. This balance is especially critical in the epididymis, where sperm mature and where it is often disrupted during ascending urogenital infections. While testicular inflammation is typically reversible, the epididymis undergoes irreversible tissue remodeling, particularly in distal regions, whereas proximal regions remain mostly unaffected despite bacterial presence.
Read the full summary ↓
We previously identified that each epididymal region has a unique immunological landscape, distinct from that of the testis. Notably, CX3CR1⁺ macrophages are the dominant immune cell type and appear central to maintaining homeostasis and orchestrating immune responses in a region-specific manner. To assess their functional role, we used a transgenic mouse model to deplete CX3CR1⁺ macrophages under steady-state and infected conditions. Whole-transcriptome analysis following E. coli infection revealed downregulation of genes linked to innate immunity and cytokine regulation, indicating that CX3CR1⁺ macrophages restrain excessive inflammation—particularly in proximal regions. Combined with histological and cellular phenotyping, our data highlight a key role for CX3CR1⁺ macrophages in preserving epithelial integrity and modulating immune responses during infection.
Published in
Depletion of CX3CR1(+) macrophages results in disrupted functionality and immune surveillance within epididymis and testis
Ai D, Kreyling L, Battistone MA et al. · Mucosal immunology 2026 · PMID 41621662 · doi:10.1016/j.mucimm.2026.01.011
This dataset
Open GSE309348 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 GSE309348_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 PRJNA1335220 and SRA study SRP628099. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41621662) ↗
Study design
6 conditions, mostly in triplicate
UPEC Distal regions Tam+Dtx ×3 UPEC Distal regions Tam only ×3 UPEC Proximal regions Tam+Dtx ×3 UPEC Proximal regions Tam only control ×3 UPEC Testis Tam+Dtx ×3 UPEC Testis Tam only control ×3

Supports a between-group comparison across 18 samples.

How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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
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