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The MAIT cell response to controlled oral enterotoxigenic E. coli challenge

GSE276378 Homo sapiens (human) RNA-seq (gene expression) 28 samples Submitted 2025/05/20 Platform GPL18573
At a glance

RNA-seq (gene expression) · human · 28 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
Homo sapiens (human)
Samples
28 samples: 28 samples, each with a distinct title — no replicated groupsGroups 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
The MAIT cell response to controlled oral enterotoxigenic E. coli challengeJournal of immunology (Baltimore, Md. : 1950) · 2025
Summary (written by the submitters)
Mucosa-associated invariant T (MAIT) cells recognize conserved microbial antigens presented by the non-polymorphic MR1 molecules and play important roles in barrier immunity. Enterotoxigenic E. coli (ETEC) is a major cause of diarrheal disease especially among children in lower-income countries. Here we investigate the potential role of MAIT cells in ETEC infection using samples from a human experimental ETEC challenge study.
Read the full summary ↓
MAIT cells were activated with elevated function and proliferation in blood on day 7 after challenge, reflected both at protein and transcript levels, a pattern most evident among individuals who developed mild to severe diarrhea (MSD). The MSD-positive group had elevated expression of CCR9 and α4β7 on MAIT cells and experienced expansion of the peripheral MAIT cell pool at day 28 after challenge. Finally, the size of the MAIT cell pool correlated with MSD disease severity score. These findings indicate that MAIT cells respond to ETEC infection in a way associated with the development of symptomatic disease.
Published in
The MAIT cell response to controlled oral enterotoxigenic E. coli challenge
Lal KG, Kim D, Creegan M et al. · Journal of immunology (Baltimore, Md. : 1950) 2025 · PMID 40713903 · doi:10.1093/jimmun/vkaf143
This dataset
Open GSE276378 in finder → Find more human 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 GSE276378_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 PRJNA1156802 and SRA study SRP530768. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40713903) ↗
Study design
28 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 28 sample titles: 28 distinct titles with little repetition. 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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