GEO series

T cell help transiently unlocks a high plasticity state in germinal center B cells during the humoral immune response [ActB_RNA-seq]

GSE298425 Mus musculus (mouse) RNA-seq (gene expression) 15 samples Submitted 2025/10/29 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 15 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: 15 samples: 15 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.

Summary (written by the submitters)

During cellular differentiation, phenotypic plasticity is gradually lost due to the strengthening of epigenetic barriers, although it may be re-acquired upon disease or injury. Here, we report an unprecedented physiological gain of epigenetic plasticity among mature B cells during the humoral immune response. Acquisition of plasticity was strictly dependent on T follicular helper (TFH) cells and restricted to germinal center (GC) but not activated B cells, indicating both non- and cell-autonomous contributions to this phenotype.

Read the full summary ↓

Importantly, GC plasticity was not dependent on proliferation and could not be solely explained by the activation of MYC programs. Instead, GC plasticity was associated with the reciprocal weakening of B cell identity and the de- repression of progenitor and stem cell-like programs induced by NFκB and other signals, downstream of TFH signaling. Therefore, physiological acquisition of GC B cell plasticity is tightly controlled by the affinity maturation positive selection checkpoint. Notably, Histone 1 loss of function, which results in aberrant stem cell gene reactivation through chromatin decompaction, allowed GC B cells to bypass this gatekeeping mechanism. Finally, patients with Diffuse LargeB Cell Lymphoma (DLBCL) that enriched for GC plasticity signatures had significantly worse outcomes, implicating a role for this mechanism in immune regulation and fitness and potential relevance to lymphomagenesis.

This dataset

Open GSE298425 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 GSE298425_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 PRJNA1269441 and SRA study SRP588502. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

15 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 15 sample titles: 15 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

GSM9014108 Nact D5 CD40_A
GSM9014109 Nact D5 CpG_A
GSM9014110 Nact D5 LPS_A
GSM9014111 Nact D5 CD40_B
GSM9014112 Nact D5 CpG_B
GSM9014113 Nact D5 LPS_B
GSM9014114 Nact D5 CD40_C
GSM9014115 Nact D5 CpG_C
GSM9014116 Nact D5 LPS_C
GSM9014117 GC_A
GSM9014118 GC_B
GSM9014119 GC_C
GSM9014120 N_A
GSM9014121 N_B
GSM9014122 N_C

Datasets on a similar topic

GSE298426 T follicular helper cells transiently unlock a plasticity state in germinal centre B cells during the humoral immune response 37 samples shares transiently, plasticity, germinal, humoral, state
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GSE275121 Specific pre-plasma cell states and local proliferation at the dark zone – medulla interface characterize germinal center-derived plasma cell differentiation in lymph node (Figure2) 1 13 samples shares germinal, center, state
GSE275669 RNA binding protein Pcbp1 maintains mitochondria integrity to promote antibody production and germinal center response[RNA-seq] 10 samples shares germinal, rna-seq, center
GSE264164 RNA-seq and ATAC-seq of follicular B cells and germinal center B cells with a conditional deletion of Brwd1 23 samples shares germinal, rna-seq, center
GSE270144 Disabling leading and lagging strand histone transmission results in parental histones loss and reduced cell plasticity and viability [RNA-Seq] 60 samples shares plasticity, rna-seq
GSE309033 Combined BET Bromodomain and DNMT Inhibition Targets Lineage Plasticity in Prostate Cancer [BETi_DNMTi_mouse_RNAseq] 51 samples shares plasticity, state

Search all mouse RNA-seq datasets in GEO →

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.