GEO series

Microbiota promote enhanced CD39 expression in gamma delta (gd) intraepithelial lymphocytes through the activation of TCR and IL-15 signaling.

GSE292555 Mus musculus (mouse) RNA-seq (gene expression) 16 samples Submitted 2025/08/27 Platform GPL19057

At a glance

RNA-seq (gene expression) · mouse · 16 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: 16 samples: 4 × gdHYP, Vg1 subset, vs 4 × gdHYP, Vg7 subset, vs 4 × WT, Vg1 subset, vs 4 × WT, Vg7 subset,Groups 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: Microbiota promote enhanced CD39 expression in γδ intraepithelial lymphocytes through the activation of TCR and IL-15 signalingMucosal immunology · 2025

Summary (written by the submitters)

Intraepithelial lymphocytes expressing the gd T cell receptor (gd IEL) provide continuous surveillance of the intestinal epithelium. We report that mice harboring a microbiota-specific hyperproliferative gd IEL (gdHYP) phenotype also upregulate the expression of the ectonucleotidase CD39, a marker of regulatory gd T cells. Enhanced TCR and IL-15 signaling correlates with a progression from a naïve-like CD39neg gd IEL to a more mature, tissue-adapted CD39hi IEL population.

Read the full summary ↓

We find that TCRgd activation drives CD122-mediated CD39 upregulation on gdHYP IELs and increased mucosal IL-15 further amplifies CD39 expression in gdHYP IELs. Notably, CD39 induction requires sustained exposure to the gdHYP-associated microbiota. Increased IL-15 signaling prolongs IEL survival and enhances gdHYP IEL bioenergetic potential. Notably, CD39hi gd IELs produce less pro-inflammatory cytokine, which may explain the lack of histopathology in gdHYP mice. Overall, our study identifies a previously unappreciated mechanism by which an altered microbiota amplifies CD39 expression on gdHYP IELs, leading to the expansion of gd IELs with regulatory potential.

Published in

Microbiota promote enhanced CD39 expression in γδ intraepithelial lymphocytes through the activation of TCR and IL-15 signaling

Alonso S, Kaur H, Jia L et al. · Mucosal immunology 2025 · PMID 40683453 · doi:10.1016/j.mucimm.2025.07.005

This dataset

Open GSE292555 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 GSE292555_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 PRJNA1240201 and SRA study SRP572155. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40683453) ↗

Study design

4 × gdHYP, Vg1 subset, vs 4 × gdHYP, Vg7 subset, vs 4 × WT, Vg1 subset, vs 4 × WT, Vg7 subset,

Supports a between-group comparison across 16 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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

GSM8861363 gdHYP, Vg1 subset, rep1 gdHYP, Vg1 subset,
GSM8861364 gdHYP, Vg7 subset, rep1 gdHYP, Vg7 subset,
GSM8861365 gdHYP, Vg1 subset, rep2 gdHYP, Vg1 subset,
GSM8861366 gdHYP, Vg7 subset, rep2 gdHYP, Vg7 subset,
GSM8861367 gdHYP, Vg1 subset, rep3 gdHYP, Vg1 subset,
GSM8861368 gdHYP, Vg7 subset, rep3 gdHYP, Vg7 subset,
GSM8861369 gdHYP, Vg1 subset, rep4 gdHYP, Vg1 subset,
GSM8861370 gdHYP, Vg7 subset, rep4 gdHYP, Vg7 subset,
GSM8861371 WT, Vg1 subset, rep1 WT, Vg1 subset,
GSM8861372 WT, Vg7 subset, rep1 WT, Vg7 subset,
GSM8861373 WT, Vg1 subset, rep2 WT, Vg1 subset,
GSM8861374 WT, Vg7 subset, rep2 WT, Vg7 subset,
GSM8861375 WT, Vg1 subset, rep3 WT, Vg1 subset,
GSM8861376 WT, Vg7 subset, rep3 WT, Vg7 subset,
GSM8861377 WT, Vg1 subset, rep4 WT, Vg1 subset,
GSM8861378 WT, Vg7 subset, rep4 WT, Vg7 subset,

Datasets on a similar topic

GSE317864 The Effector Differentiation of TCRαβ+CD8αα+ Intraepithelial Lymphocytes Is Reciprocally Regulated by BCL6 and BLIMP1 20 samples shares tcr, intraepithelial, lymphocytes
GSE265880 Impact of Sirt2 deficiency on downstream TCR signaling in mouse melanoma tumor-infiltrating T lymphocytes 16 samples shares tcr, lymphocytes
GSE262121 Murine gamma delta intraepithelial lymphocyte response to type I IFN and TCR blockade 13 samples shares tcr, intraepithelial
GSE260895 Lag3 and PD-1 pathways regulate NFAT-dependent TCR signalling programmes during early CD4+ T cell activation 12 samples shares tcr, activation
GSE243972 Gene expression profile at single cell level of lymphocytes extracted from the mesenteric lymph nodes of TCRMOG animals colonized with either Salmonella expressing MOG or OVA 6 samples shares tcr, lymphocytes
GSE323389 Dual Activation of CD8+ and CD4+ T cells by a PD-1 targeted IL-15 Mutein in Viral Infection 4 samples shares il-15, activation
GSE298152 scRNAseq and scTCRseq data from tumor-infiltrating lymphocytes 16 samples shares tcr, lymphocytes
GSE283956 CD8αα+ intraepithelial lymphocytes recruited from peripheral CD4+ and CD8+ T cells represent functionally distinct lineages 12 samples shares intraepithelial, lymphocytes

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.