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Notch-activated basophils support intestinal CD4+ T cell fate and function during helminth infection

GSE297084 Mus musculus (mouse) RNA-seq (gene expression) 14 samples Submitted 2025/08/27 Platform GPL30172

At a glance

RNA-seq (gene expression) · mouse · 14 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: 14 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: Notch-activated basophils support intestinal CD4(+) T cell fate and function during Trichuris muris infectionMucosal immunology · 2025

Summary (written by the submitters)

Helminth infections affect billions of people worldwide and cause substantial morbidity. Intestinal helminth infection provokes Type 2 inflammation orchestrated by CD4+ T helper 2 (Th2) cells. Th2s produce interleukin (IL)-4 and IL-13 that prompt an epithelial “weep and sweep” response to drive parasite clearance. Tissue-specific cues optimize CD4+ T cell responses, but the mechanisms regulating intestinal Th2 responses remain unclear.

Read the full summary ↓

Previously, we identified that the Notch signaling pathway in basophils, rare granulocytes, drove effective parasite clearance and an optimal Th2 response during Trichurismuris infection, a mouse model of human whipworm. Here we report basophil-intrinsic Notch was required for infection-elicited Th2 cytokine responses and a broader IL-4 production program across intestinal CD4+ T cell subsets. In vitro, basophils supported CD4+ T cell cytokine production in a contact-dependent manner, independent of basophil-secreted factors, and was dependent on autocrine IL-4 production from CD4+ T cells. In vivo, basophil-intrinsic Notch mediated basophil-Th2 cell interactions in the cecum during infection. Thus, Notch-programmed basophils act in a contact-dependent manner to optimize intestinal CD4+ T cell function during helminth infection. These findings improve our understanding of the tissue-specific mechanisms regulating intestinal CD4+ T cell responses at inflamed mucosal barriers during Type 2 immunity.

Published in

Notch-activated basophils support intestinal CD4(+) T cell fate and function during Trichuris muris infection

Webb LM, Warner LM, Helm EY et al. · Mucosal immunology 2025 · PMID 40383395 · doi:10.1016/j.mucimm.2025.05.004

This dataset

Open GSE297084 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 GSE297084_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 PRJNA1262485 and SRA study SRP585028. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40383395) ↗

Samples in this study

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+ 14 more — browse all 14 samples with per-sample file links →

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