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Effector differentiation by stem-like intraepithelial γδ T cells is required for host defense against infection

GSE309993 Mus musculus (mouse) RNA-seq (gene expression) 25 samples Submitted 2026/04/13 Platform GPL28457Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 25 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
25 samples: 11 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
Effector differentiation by stem-like intraepithelial γδ T cells is required for host defense against infectionImmunity · 2026
Summary (written by the submitters)
Intraepithelial γδ T cells (γδIELs) are crucial for maintaining intestinal homeostasis, yet their functional regulation remains incompletely understood. Here, we identified two distinct γδIEL subsets: CD160+TCF1+BCL6+ stem-like and granzymeB+BLIMP1+ effector-like cells; the latter exhibited cytotoxic activity. Stem-like γδIELs differentiated into effector-like cells in response to microbiota and pathogen infection.
Read the full summary ↓
IL-12, in cooperation with IL-15 and TCR signaling, activated a STAT4-BLIMP1 pathway to induce effector differentiation, and IL-12 signaling was required for their cytotoxic function. Tcf7 deletion significantly reduced stem-like but not effector-like γδIELs, while Bcl6 deficiency increased effector-like γδIELs selectively. In contrast, the absence of Prdm1 not only abolished the development of effector-like γδIELs but also impaired the clearance of enterogenous pathogens. Taken together, these findings define two functionally distinct γδIEL subsets with a hierarchical regulatory program linking microbial signals and cytokine pathways to their cytotoxic function in the gut.
Published in
Effector differentiation by stem-like intraepithelial γδ T cells is required for host defense against infection
Xie S, Xing Q, Zhang Q et al. · Immunity 2026 · PMID 41747734 · doi:10.1016/j.immuni.2026.01.006
This dataset
Open GSE309993 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 GSE309993_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 PRJNA1357327 and SRA study SRP641196. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41747734) ↗
Study design
11 conditions, mostly in duplicate
SI_gd_Bcl6n ×3 SI_gd_Bcl6p ×3 LI_gd_Bcl6p ×2 CD160p_gd_Bcl6_WT ×2 CD160p_gd_Bcl6_KO ×2 total_gd_Prdm1_WT ×2 total_gd_Prdm1_KO ×2 CD160p_gd_Tcf7_WT ×2 +4 more

Supports a between-group comparison across 24 samples.

How we read this: 11 replicated groups read from 25 sample titles; they account for 24 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
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