GEO series

Single nucleus transcriptomics to study sex differences during murine E. coli pyelonephritis

GSE296327 Mus musculus (mouse) Single-nucleus RNA-seq 18 samples Submitted 2026/02/18 Platform GPL24247

At a glance

Single-nucleus RNA-seq · mouse · 18 samples

What it is: Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue). Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
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: Single-nucleus transcriptomics illuminates sex differences during murine Escherichia coli pyelonephritisResearch square · 2025

Summary (written by the submitters)

This project employs models of urinary tract infection (UTI) in female, androgen-exposed female, and male mice to determine molecular mechanisms by which host androgen exposure promotes Escherichia coli pyelonephritis as well as renal scarring, a common sequela of upper-tract UTI. Our prior findings indicated that the influence of sex, including androgen exposure, on these common bacterial infections is more complex than previously appreciated.

Read the full summary ↓

Specifically, male sex was associated with increased risk for chronic cystitis and high-titer pyelonephritis, as well as formation of renal abscesses. These snRNA-seq experiments were designed to interrogate the fundamental sex differences impacting the host-pathogen interaction and cellular responses in E. coli pyelonephritis, thereby influencing pathogenicity and outcome of infection.

Published in

Single-nucleus transcriptomics illuminates sex differences during murine Escherichia coli pyelonephritis

Hunstad D, Hreha T, Manson A et al. · Research square 2025 · PMID 41282075 · doi:10.21203/rs.3.rs-6976359/v1

This dataset

Open GSE296327 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 GSE296327_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 PRJNA1182331 and SRA study SRP543644. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41282075) ↗

Study design

6 conditions, mostly in triplicate

Androgen-exposed female mice, inoculated with… ×3 Androgen-exposed female mice, inoculated with… ×3 Female mice, inoculated with PBS (control), b… ×3 Male mice, inoculated with PBS (control), biol ×3 Female mice, inoculated with UTI, biol ×3 Male mice, inoculated with UTI, biol ×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

GSM8968633 Androgen-exposed female mice, inoculated with PBS (control), biol rep 1 Androgen-exposed female…
GSM8968634 Androgen-exposed female mice, inoculated with PBS (control), biol rep 2 Androgen-exposed female…
GSM8968635 Androgen-exposed female mice, inoculated with PBS (control), biol rep 3 Androgen-exposed female…
GSM8968636 Androgen-exposed female mice, inoculated with UTI, biol rep 1 Androgen-exposed female…
GSM8968637 Androgen-exposed female mice, inoculated with UTI, biol rep 2 Androgen-exposed female…
GSM8968638 Androgen-exposed female mice, inoculated with UTI, biol rep 3 Androgen-exposed female…
GSM8968639 Female mice, inoculated with PBS (control), biol rep 1 Female mice, inoculated…
GSM8968640 Female mice, inoculated with PBS (control), biol rep 2 Female mice, inoculated…
GSM8968641 Female mice, inoculated with PBS (control), biol rep 3 Female mice, inoculated…
GSM8968642 Male mice, inoculated with PBS (control), biol rep 1 Male mice, inoculated w…
GSM8968643 Male mice, inoculated with PBS (control), biol rep 2 Male mice, inoculated w…
GSM8968644 Male mice, inoculated with PBS (control), biol rep 3 Male mice, inoculated w…
GSM8968645 Female mice, inoculated with UTI, biol rep 1 Female mice, inoculated…
GSM8968646 Female mice, inoculated with UTI, biol rep 2 Female mice, inoculated…
GSM8968647 Female mice, inoculated with UTI, biol rep 3 Female mice, inoculated…
GSM8968648 Male mice, inoculated with UTI, biol rep 1 Male mice, inoculated w…
GSM8968649 Male mice, inoculated with UTI, biol rep 2 Male mice, inoculated w…
GSM8968650 Male mice, inoculated with UTI, biol rep 3 Male mice, inoculated w…

Datasets on a similar topic

GSE263649 Single nucleus RNA sequencing of the cerebral cortex from genetically diverse inbred mouse strains reveals differences in pericyte and endothelial cell composition 16 samples shares differences
GSE236889 Longitudinal scRNA-seq of murine T cell transfer colitis 64 samples shares coli
GSE236385 Longitudinal bulk RNA-seq of murine T cell transfer colitis 62 samples shares coli
GSE281618 Cataloguing the postnatal small intestinal transcriptome during the period of susceptibility to necrotizing enterocolitis 48 samples shares coli
GSE271135 Impact of intestinal ERβ on the colon transcriptome during colitis-induced tumor development 38 samples shares coli
GSE318580 The RNA-binding protein Imp1 promotes a Spdef transcriptional program and mucus fucosylation during necrotizing enterocolitis 32 samples shares coli
GSE267922 Gene Regulatory Programs that Specify Age-Related Differences during Thymocyte Development (RNA-Seq) 31 samples shares differences
GSE255423 Longitudinal scRNA-seq of murine Il10KO colitis 24 samples shares coli

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.