GEO series

Progressively Differentiated Tfh13 Cells are Stabilized by JunB to Mediate Allergen Germinal Center Responses

GSE279058 Mus musculus (mouse) RNA-seq (gene expression) 2 samples Submitted 2024/12/13 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 2 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: 2 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: Progressively differentiated T(FH)13 cells are stabilized by JunB to mediate allergen germinal center responsesNature immunology · 2025

Summary (written by the submitters)

Allergic diseases are common and affect a large proportion of the population. IL-13-expressing follicular T (Tfh13) cells are a newly identified population of Tfh cells that have been associated with high affinity IgE responses. However, the origins, developmental signals, transcriptional programming and precise functions of Tfh13 cells are unknown.

Read the full summary ↓

Here, we examined the developmental signals for Tfh13 cells and found a direct and progressive differentiation pathway marked by the production of IL-21. These two pathways differed in kinetics and extrinsic requirements. However, both pathways converged, forming transcriptionally similar Tfh13 cells that express the transcription factor JunB as a critical stabilizing factor. Using an intersectional genetics-based Tfh13-DTR model to perturb these cells, we found that Tfh13 cells were essential to drive broad germinal center responses and allergen-specific IgG and IgE. Moreover, we found that IL-21 is a broad positive regulator of allergen germinal center B cells and synergizes with IL-13 produced by Tfh13 cells to amplify allergic responses. Thus, Tfh13 cells orchestrate multiple features of allergic inflammation.

Published in

Progressively differentiated T(FH)13 cells are stabilized by JunB to mediate allergen germinal center responses

Chandrakar P, Nelson CS, Podestà MA et al. · Nature immunology 2025 · PMID 39891019 · doi:10.1038/s41590-025-02077-y

This dataset

Open GSE279058 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 GSE279058_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 PRJNA1170275 and SRA study SRP537156. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39891019) ↗

Samples in this study

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+ 2 more — browse all 2 samples with per-sample file links →

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