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Regional encoding of enteric nervous system responses to microbiota and type 2 inflammation [Neuron SmartSeq2]

GSE302208 Mus musculus (mouse) RNA-seq (gene expression) 169 samples Submitted 2025/10/30 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 169 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
169 samples: 44 conditions, mostly in duplicateGroups 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
Regional encoding of enteric nervous system responses to microbiota and type 2 inflammationScience (New York, N.Y.) · 2025
Summary (written by the submitters)
Enteric neurons are essential regulators of intestinal physiology, yet their responses to varying microbial and immune environments along the intestinal tract and or during challenges remain poorly understood. Here, we regionally profile enteric neurons across gnotobiotic, allergic and parasite-infected mice.
Read the full summary ↓
We demonstrate that timing and complexity of microbial perturbations and type 2 inflammation result in motor neuron state shifts and alter multiple functionally distinct sensory neurons, including IL-13- and leukotriene-responsive Nmu-hi cells and Grp-hi neurons, which expand in germ-free colonic tissue and interact with Grpr+ interstitial cells of Cajal. Leveraging AAV-based Perturb-seq to define genetic controllers of inhibitory motor neuron state transition, we identified Edf1 and Mitf as controllers of this program and of gastrointestinal transit time, directly linking enteric neuron states to physiology.
Published in
Regional encoding of enteric nervous system responses to microbiota and type 2 inflammation
Tan P, Jaiswal A, Murphy SP et al. · Science (New York, N.Y.) 2025 · PMID 41166460 · doi:10.1126/science.adr3545
This dataset
Open GSE302208 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 GSE302208_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 PRJNA1289207 and SRA study SRP599733. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41166460) ↗
Study design
44 conditions, mostly in duplicate
B20_OVAc_F65_ileum ×4 B22_SPF_M1_ileum ×4 B10006_GF_Col_M3631 ×4 B28_OVAc_F65_DJ ×4 B10007_Btheta_M3807_colon ×4 B10008_ASF_M3805_colon ×4 B12_HPneg_M1_ileum ×3 B17_OVA_M3 ×3 +96 more

Supports a between-group comparison across 109 samples.

How we read this: 44 replicated groups read from 169 sample titles; they account for 109 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

+ 129 more — browse all 169 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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