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A temporal map of B cell diversification mechanisms in mice

GSE286215 Mus musculus (mouse) RNA-seq (gene expression) 35 samples Submitted 2026/04/21 Platform GPL19057Platform GPL30172Platform GPL28457
At a glance

RNA-seq (gene expression) · mouse · 35 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
35 samples: 34 distinct titles, 1 of them repeatedGroups 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
A temporal map of B cell diversification mechanisms in miceNature immunology · 2026
Summary (written by the submitters)
Naive B cells diversify via clonal expansion, immunoglobulin isotype switching, phenotypic variation and somatic hypermutation (SHM). Diversity in antigenic targets, functional classes and the production kinetics of antibodies affects immunity to malaria. Here we show that individual clones diversify over time during Plasmodium infection.
Read the full summary ↓
During the first week, amid widespread bystander activation, isotype switching initiates soon after Myc upregulation and overlaps with clonal expansion, resulting in isotype variegation among clones. During the second week, expanded clones seeding germinal centers (GC) bifurcate into extrafollicular plasmablasts, exhibit isotype variegation and initiate SHM, indicating substantial intraclonal diversification. Over the following month, GC clones exhibit SHM at approximately four mutations per week. Antimalarial intervention does not impede SHM, instead exerting quantitative limits on GC size, plasma cell emergence, circulating antibody levels and protection against reinfection. Finally, contemporaneous B cell development relocates from bone marrow to spleen. Thus, multiple temporally overlapping mechanisms combine in vivo to diversify and safeguard humoral immune responses.
Published in
A temporal map of B cell diversification mechanisms in mice
Skinner OP, Asad S, Moreira ML et al. · Nature immunology 2026 · PMID 42297974 · doi:10.1038/s41590-026-02563-x
This dataset
Open GSE286215 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 GSE286215_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 PRJNA1208421 and SRA study SRP556253. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42297974) ↗
Study design
34 distinct titles, 1 of them repeated
Spatial_transcriptomics_day21_spleen ×2

How we read this: Read from 35 sample titles: 34 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
Datasets on a similar topic

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