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Divergent cytokine and transcriptional signatures control functional T follicular helper cell heterogeneity (RNAseq)

GSE302862 Mus musculus (mouse) RNA-seq (gene expression) 104 samples Submitted 2025/08/25 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 104 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
104 samples: 47 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
Divergent cytokine and transcriptional signatures control functional T follicular helper cell heterogeneityNature immunology · 2025
Summary (written by the submitters)
CD4+ T follicular helper (Tfh) cells support tailored B cell responses against multiple classes of pathogens. To reveal how diverse Tfh phenotypes are established, we profiled Tfh cells in response to viral, helminth and bacterial infection. We identified a core Tfh signature that is distinct from CD4+ T follicular regulatory and effector cells and identified pathogen-specific transcriptional modules that shape Tfh function.
Read the full summary ↓
Cytokine-transcriptional Tfh programming demonstrated that type I interferon and TGFbeta signaling direct individual Tfh phenotypes to instruct B cell output. Cytokine-directed Tfh transcriptional phenotypes are shared within human germinal centers (GCs), but distinct Tfh phenotypes dominate between donors and following immune challenge or in antibody-mediated disease. Finally, we identified novel cell surface markers that align with distinct Tfh phenotypes. Thus, we provide a comprehensive resource of Tfh diversity in humans and mice, to enable immune monitoring during infection and disease and to inform the development of context-specific vaccines.
Published in
Divergent cytokine and transcriptional signatures control functional T follicular helper cell heterogeneity
Dalit L, Tan CW, Sheikh AA et al. · Nature immunology 2025 · PMID 40926076 · doi:10.1038/s41590-025-02258-9
This dataset
Open GSE302862 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 GSE302862_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 PRJNA1292709 and SRA study SRP601465. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40926076) ↗
Study design
47 conditions, mostly in duplicate
Run1, Teff, Citrobacter, ×3 Run1, Tfr, Citrobacter, ×3 Run1, IL21+ Tfh, Citrobacter, ×3 Run1, IL21- Tfh, Citrobacter, ×3 Run2, Teff, Citrobacter, ×3 Run2, Tfr, Citrobacter, ×3 Run2, IL21+ Tfh, Citrobacter, ×3 Run2, IL21- Tfh, Citrobacter, ×3 +41 more

Supports a between-group comparison across 102 samples.

How we read this: 47 replicated groups read from 104 sample titles; they account for 102 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

+ 64 more — browse all 104 samples with per-sample file links →

Datasets on a similar topic

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