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Class switch recombination regulation by extracellular vesicles mediated intercellular epigenomic signaling

GSE242731 Mus musculus (mouse) RNA-seq (gene expression) 48 samples Submitted 2025/02/05 Platform GPL16417Platform GPL17021
At a glance

RNA-seq (gene expression) · mouse · 48 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
48 samples: 16 conditions, mostly in triplicateGroups 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
Intercellular Epigenomic Signalling via Extracellular Vesicles During B Cell MaturationJournal of extracellular vesicles · 2025
Summary (written by the submitters)
B cell maturation is crucial for effective adaptive immunity and requires a complex signaling network to control gene expression and protein function to mediate antibody diversification. B cells also rely on extracellular signaling queues from other cells within the germinal center. Recently, a novel class of intercellular signaling mediated by extracellular vesicles (EVs) has emerged.
Read the full summary ↓
Studies have shown B cell EVs mediated signaling is involved in immune response regulation, infection control, and tumorigenesis. However, the mechanistic role of B cell EVs in B cell maturation is not yet established. We herein study the biological properties and physiological function of B cell EVs in the context of B cell maturation. We use novel technologies to characterize B cell EVs surface marker signatures, molecular cargo and physiological roles in B cell maturation. A new specialized nanoparticle analyzer was used to profile B cell EVs at the single particle level and characterize their surface markers and sub-populations at various maturation stages. EV ncRNA cargo was characterized by RNA-seq and bioinformatic analyses identified an EVs mediated regulatory network for B cell maturation. A previously uncharacterized micro-RNA (miR-5099) in combination with a set of long non-coding RNA carried within B cell EVs is shown to be important for antibody diversification signaling. The physiological role of EVs in B cell maturation is investigated using EV blockade assays and complementation studies using diverse EV sources further confirmed the physiological role and mode of action of EVs in B cell maturation.
Published in
Intercellular Epigenomic Signalling via Extracellular Vesicles During B Cell Maturation
Yim KHW, Al Hrout A, Chahwan R · Journal of extracellular vesicles 2025 · PMID 39868437 · doi:10.1002/jev2.70040
This dataset
Open GSE242731 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 GSE242731_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 PRJNA1014428 and SRA study SRP459302. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39868437) ↗
Study design
16 conditions, mostly in triplicate
Primary B EVs_Day1_small RNA_exp ×3 Primary B EVs_Day1_long non-coding RNA_exp ×3 Primary B EVs_Day4_small RNA_exp ×3 Primary B EVs_Day4_long non-coding RNA_exp ×3 Primary B cells_Day1_small RNA_exp ×3 Primary B cells_Day1_long non-coding RNA_exp ×3 Primary B cells_Day4_small RNA_exp ×3 Primary B cells_Day4_long non-coding RNA_exp ×3 +8 more

Supports a between-group comparison across 48 samples.

How we read this: 16 replicated groups read from 48 sample titles; they account for 48 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

+ 8 more — browse all 48 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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