GEO series

T:B cell cooperation in ectopic lymphoid follicles propagates CNS autoimmunity

GSE279684 Mus musculus (mouse) Single-cell RNA-seq 11 samples Submitted 2025/03/28 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 11 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Mus musculus (mouse)
Samples: 11 samples: 11 samples, each with a distinct title — no replicated groupsGroups 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: T-B cell cooperation in ectopic lymphoid follicles propagates CNS autoimmunityScience immunology · 2025

Summary (written by the submitters)

Meningeal ectopic lymphoid follicle (eLF)-like structures have been described in multiple sclerosis, but their role in central nervous system (CNS) autoimmunity is unclear. Here, we used a T helper 17 (TH17) adoptive transfer experimental autoimmune encephalomyelitis model featuring formation of eLFs. Single-cell RNA sequencing revealed that clusters of activated B cells and B1/marginal zone-like B cells were overrepresented in the CNS and identified B cells poised for undergoing germinal center reactions and clonal expansion in the CNS.

Read the full summary ↓

Using intravital imaging to directly visualize TH17-B cell interactions, we demonstrated that T and B cells form long-lasting antigen-specific contacts in meningeal eLFs that result in reactivation of autoreactive T cells. CNS T cells depended on CNS B cells to maintain a proinflammatory cytokine profile. Our study reveals that extensive T-B cell cooperation occurs in meningeal eLFs, promoting both B cell differentiation and T cell reactivation, and may thereby propagate smoldering inflammation in the CNS.

Published in

T-B cell cooperation in ectopic lymphoid follicles propagates CNS autoimmunity

Kolz A, de la Rosa C, Syma IJ et al. · Science immunology 2025 · PMID 40279405 · doi:10.1126/sciimmunol.adn2784

This dataset

Open GSE279684 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 GSE279684_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1174079 and SRA study SRP539094. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40279405) ↗

Study design

11 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 11 sample titles: 11 distinct titles with little repetition. 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

GSM8578113 B cells, Th17 EAE model, animal 1 [CSP-A1]
GSM8578114 B cells, Th17 EAE model, animal 1 [GEX-A1]
GSM8578115 B cells, Th17 EAE model, animal 1 [VDJ-A1]
GSM8578116 B cells, Th17 EAE model, animal 2 [CSP-A2]
GSM8578117 B cells, Th17 EAE model, animal 2 [GEX-A2]
GSM8578118 B cells, Th17 EAE model, animal 2 [VDJ-A2]
GSM8578119 B cells, Th17 EAE model, animal 3 [CSP-A3]
GSM8578120 B cells, Th17 EAE model, animal 3 [GEX-A3]
GSM8578121 B cells, Th17 EAE model, animal 3 [VDJ-A3]
GSM8578122 B cells, Th1 EAE model [Th1-CSP]
GSM8578123 B cells, Th1 EAE model [Th1-GEX]

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