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C. difficile's proline reductase harnesses host and commensal factors to drive efficient metabolism and progression to disease. Mono-association.

GSE252555 Mus musculus (mouse) RNA-seq (gene expression) 26 samples Submitted 2026/06/09 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 26 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
26 samples: 7 × C. difficile WT ATCC43255 20 hours post infection Mouse vs 7 × C. difficile ATCC43255 prdB mutant 24 hours post infection Mouse vs 6 × C. difficile WT ATCC43255 24 hours post infection Mouse vs 6 × C. difficile ATCC43255 prdB mutant 20 hours post infection MouseGroups 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.
Summary (written by the submitters)
Gnotobiotic mice were mono-colonized with either the wild-type Clostridioides difficile ATCC 43255 strain or the proline reductase mutant (ΔprdB) of the ATCC 43255 strain. Cecal contents were collected and underwent RNASeq at the timepoints indicated below for pathway enrichment and transcritpmic analyses. Metatranscriptomic sequence processing was carried out as in Girinathan, et al, 2021 (PMID: 34637781)
This dataset
Open GSE252555 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 GSE252555_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 PRJNA1061165. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
7 × C. difficile WT ATCC43255 20 hours post infection Mouse vs 7 × C. difficile ATCC43255 prdB mutant 24 hours post infection Mouse vs 6 × C. difficile WT ATCC43255 24 hours post infection Mouse vs 6 × C. difficile ATCC43255 prdB mutant 20 hours post infection Mouse

Supports a case/control comparison: 13 samples read as cases, 13 as controls.

How we read this: 4 replicated groups read from 26 sample titles; they account for 26 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

Search all mouse RNA-seq datasets in GEO →

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