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Type 2 cytokines act on enteric sensory neurons to regulate neuropeptide-driven host defense [RNA-Seq 2]

GSE292634 Mus musculus (mouse) RNA-seq (gene expression) 41 samples Submitted 2025/06/25 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 41 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
41 samples: 6 conditions, mostly with about 7 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
Type 2 cytokines act on enteric sensory neurons to regulate neuropeptide-driven host defenseScience (New York, N.Y.) · 2025
Summary (written by the submitters)
Enteric nervous system (ENS)-derived neuropeptides modulate immune cell function, yet our understanding of how inflammatory cues directly influence enteric neuron responses during infection is considerably lacking. Here, we characterize a primary enteric sensory neuron (PSN) subset that produces the neuropeptides neuromedin U (NMU) and calcitonin gene-related peptide beta (CGRPβ) and co-expresses receptors for the type 2 cytokines IL-4 and IL-13.
Read the full summary ↓
Type 2 cytokines were sufficient to upregulate NMU and CGRPβ expression in PSNs, in vitro and in vivo, which was abrogated by PSN-specific Il13ra1 deletion. Importantly, PSN-specific Il13ra1 deletion impaired host defense to the gastrointestinal helminth H. polygyrus, diminished enteric sensory neuron populations, and blunted muscularis immune responses. Co-administration of NMU23 and CGRPβ rescued helminth clearance deficits and restored anti-helminth immunity. Mechanistically, we show that CGRPβ signaling synergizes with IL-4 in intestinal macrophages, inducing alternatively-activated macrophage defense responses, altogether illustrating the critical role of bi-directional neuro-immune crosstalk in regulating intestinal type 2 immunity.
Published in
Type 2 cytokines act on enteric sensory neurons to regulate neuropeptide-driven host defense
Barilla RM, Berard C, Sun L et al. · Science (New York, N.Y.) 2025 · PMID 40403128 · doi:10.1126/science.adn9850
This dataset
Open GSE292634 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 GSE292634_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 PRJNA1240347 and SRA study SRP572276. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40403128) ↗
Study design
6 conditions, mostly with about 7 replicates each
Enteric neuro-glial culture; IL-13 (24h); ×9 Enteric neuro-glial culture; Control (media o… ×7 Enteric neuro-glial culture; IFNg (24h); ×7 Enteric neuro-glial culture; IL-4 (24h); ×7 Enteric neuro-glial culture; IL-13 + IFNg (24… ×6 Enteric neuro-glial culture; IL-13 + IL-4 (24… ×5

Supports a between-group comparison across 41 samples.

How we read this: 6 replicated groups read from 41 sample titles; they account for 41 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

+ 1 more — browse all 41 samples with per-sample file links →

Datasets on a similar topic

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