GEO series

Immunoglobulin A controls intestinal virus colonization to preserve immune homeostasis [ZE303]

GSE289554 Mus musculus (mouse) RNA-seq (gene expression) 60 samples Submitted 2025/03/24 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 60 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: 60 samples
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: Immunoglobulin A controls intestinal virus colonization to preserve immune homeostasisCell host & microbe · 2025

Summary (written by the submitters)

Immunoglobulin A (IgA) is the predominant immunoglobulin isotype in mammals, primarily secreted at type I mucosal surfaces. Despite its abundance, the precise role of secretory IgA in the intestinal lumen, where it coats a diverse array of commensal microbiota, has remained elusive. Our study reveals that germinal center IgA responses are essential for preventing chronic colonization of the gut by specific viruses.

Read the full summary ↓

In absence of IgA, chronic viral colonization triggers an antigen-driven expansion of CD8αβ+ intraepithelial lymphocytes (IELs). Although, these IELs are unable to clear the virus, they contribute to maintaining homeostasis by regulating its load and type-I interferon responses. Consequently, IgA deficiency increases susceptibility to colitis in genetically susceptible host or following chemical induction, but only in presence of viral pathobionts requiring IgA for their clearance. These findings underscore the potential vulnerability of IgA deficient individuals to immunopathology when exposed to selective viral pathobionts.

Published in

Immunoglobulin A controls intestinal virus colonization to preserve immune homeostasis

Lisicka W, Earley ZM, Sifakis JJ et al. · Cell host & microbe 2025 · PMID 40154490 · doi:10.1016/j.chom.2025.03.004

This dataset

Open GSE289554 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 GSE289554_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 PRJNA1223416 and SRA study SRP563757. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40154490) ↗

Samples in this study

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+ 60 more — browse all 60 samples with per-sample file links →

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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.