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Effect of Dhps deletion in epithelial cells and Citrobacter rodentium infection on the transcriptome of the colonic mucosa

GSE262899 Mus musculus (mouse) RNA-seq (gene expression) 16 samples Submitted 2024/04/08 Platform GPL17021
At a glance

RNA-seq (gene expression) · mouse · 16 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
16 samples: 5 × Dhps<fl/fl> + C. rodentium vs 5 × Dhps<fl/fl>;Vil1<cre/+> + C. rodentium vs 3 × Dhps<fl/fl>;Vil1<cre/+> vs 3 × Dhps<fl/fl>Groups 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
Hypusination in intestinal epithelial cells protects mice from infectious colitisGut microbes · 2024
Summary (written by the submitters)
We previously reported that hypusination in myeloid cells is required to limit the development of pathogenic bacteria in the gastrointestinal tract, including Helicobacter pylori for the stomach and C. rodentium in the colon. The aim of the present study was to investigate the role of epithelial hypusination on C. rodentium pathogenicity
Published in
Hypusination in intestinal epithelial cells protects mice from infectious colitis
Gobert AP, Hawkins CV, Williams KJ et al. · Gut microbes 2024 · PMID 39673545 · doi:10.1080/19490976.2024.2438828
This dataset
Open GSE262899 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 GSE262899_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 PRJNA1091217 and SRA study SRP497436. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39673545) ↗
Study design
5 × Dhps<fl/fl> + C. rodentium vs 5 × Dhps<fl/fl>;Vil1<cre/+> + C. rodentium vs 3 × Dhps<fl/fl>;Vil1<cre/+> vs 3 × Dhps<fl/fl>

Supports a between-group comparison across 16 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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

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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.