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Immunoglobulin A controls intestinal virus colonization to preserve immune homeostasis [ZE309]

GSE289553 Mus musculus (mouse) RNA-seq (gene expression) 88 samples Submitted 2025/03/24 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 88 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
88 samples: 16 conditions, mostly with about 6 replicates eachGroups 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
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 GSE289553 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 GSE289553_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 PRJNA1223415 and SRA study SRP563756. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40154490) ↗
Study design
16 conditions, mostly with about 6 replicates each
Tissue, Ighasec+/-, SPF, Duodenum, ZE ×6 Tissue, Ighasec-/-, SPF, Duodenum, ZE ×6 Tissue, Ighasec+/-, SPF, Jejunum, ZE ×6 Tissue, Ighasec-/-, SPF, Jejunum, ZE ×6 Tissue, Ighasec+/-, SPF, Ileum, ZE ×6 Tissue, Ighasec-/-, SPF, Ileum, ZE ×6 Tissue, Ighasec+/-, SPF, Colon, ZE ×6 Tissue, Ighasec-/-, SPF, Colon, ZE ×6 +8 more

Supports a between-group comparison across 88 samples.

How we read this: 16 replicated groups read from 88 sample titles; they account for 88 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

+ 48 more — browse all 88 samples with per-sample file links →

Datasets on a similar topic

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