GEO series

mRNA-seq of wild-type or p53-deficient B cells expressing MHV68 M2

GSE225579 Mus musculus (mouse) RNA-seq (gene expression) 17 samples Submitted 2024/12/19 Platform GPL28457

At a glance

RNA-seq (gene expression) · mouse · 17 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: 17 samples: 6 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: Intrinsic p53 activation restricts gammaherpesvirus driven germinal center B cell expansion during latency establishmentNature communications · 2025

Summary (written by the submitters)

Gammaherpesviruses (GHV) are DNA tumor viruses that establish lifelong latent infections in lymphocytes. For viruses such as Epstein-Barr virus (EBV) and murine gammaherpesvirus 68 (MHV68), this is accomplished through a viral gene-expression program that promotes cellular proliferation and differentiation, especially of germinal center (GC) B cells.

Read the full summary ↓

Intrinsic host mechanisms to control virus-driven cellular expansion are incompletely defined. Using a small-animal model of GHV pathogenesis, we identify the B cell-specific latency gene M2, an MHV68 mediator of GC B cell differentiation, as a viral gene product that is sufficient to induce p53 in a manner that is dependent on Src kinase activity. To understand the function of M2 in primary B cells, we performed retroviral transduction of M2 or M2.Stop in wild-type or p53-deficient B cells. Our results reveal p53 and cellular proliferation pathways enriched in M2-expressing B cells.

Published in

Intrinsic p53 activation restricts gammaherpesvirus driven germinal center B cell expansion during latency establishment

Owens SM, Sifford JM, Li G et al. · Nature communications 2025 · PMID 39843898 · doi:10.1038/s41467-025-56247-5

This dataset

Open GSE225579 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 GSE225579_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 PRJNA936439 and SRA study SRP423296. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39843898) ↗

Study design

6 conditions, mostly in triplicate

C57BL/6 B cells, p53-WT, pRetroX_M2.Stop_IRES… ×3 C57BL/6 B cells, p53-KO, pRetroX_M2_IRES_ZsGr… ×3 C57BL/6 B cells, p53-KO, pRetroX_M2.Stop_IRES… ×3 C57BL/6 B cells, p53-WT, pRetroX_LMP1_IRES_Zs… ×3 C57BL/6 B cells, p53-KO, pRetroX_LMP1_IRES_Zs… ×3 C57BL/6 B cells, p53-WT, pRetroX_M2_IRES_ZsGr… ×2

Supports a between-group comparison across 17 samples.

How we read this: 6 replicated groups read from 17 sample titles; they account for 17 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

GSM7050654 C57BL/6 B cells, p53-WT, pRetroX_M2_IRES_ZsGreen, Day 4 #1 C57BL/6 B cells, p53-WT…
GSM7050655 C57BL/6 B cells, p53-WT, pRetroX_M2_IRES_ZsGreen, Day 4 #2 C57BL/6 B cells, p53-WT…
GSM7050656 C57BL/6 B cells, p53-WT, pRetroX_M2.Stop_IRES_ZsGreen, Day 4 #1 C57BL/6 B cells, p53-WT…
GSM7050657 C57BL/6 B cells, p53-WT, pRetroX_M2.Stop_IRES_ZsGreen, Day 4 #2 C57BL/6 B cells, p53-WT…
GSM7050658 C57BL/6 B cells, p53-WT, pRetroX_M2.Stop_IRES_ZsGreen, Day 4 #3 C57BL/6 B cells, p53-WT…
GSM7050659 C57BL/6 B cells, p53-KO, pRetroX_M2_IRES_ZsGreen, Day 4 #1 C57BL/6 B cells, p53-KO…
GSM7050660 C57BL/6 B cells, p53-KO, pRetroX_M2_IRES_ZsGreen, Day 4 #2 C57BL/6 B cells, p53-KO…
GSM7050661 C57BL/6 B cells, p53-KO, pRetroX_M2_IRES_ZsGreen, Day 4 #3 C57BL/6 B cells, p53-KO…
GSM7050662 C57BL/6 B cells, p53-KO, pRetroX_M2.Stop_IRES_ZsGreen, Day 4 #1 C57BL/6 B cells, p53-KO…
GSM7050663 C57BL/6 B cells, p53-KO, pRetroX_M2.Stop_IRES_ZsGreen, Day 4 #2 C57BL/6 B cells, p53-KO…
GSM7050664 C57BL/6 B cells, p53-KO, pRetroX_M2.Stop_IRES_ZsGreen, Day 4 #3 C57BL/6 B cells, p53-KO…
GSM7733012 C57BL/6 B cells, p53-WT, pRetroX_LMP1_IRES_ZsGreen, Day 4 #1 C57BL/6 B cells, p53-WT…
GSM7733013 C57BL/6 B cells, p53-WT, pRetroX_LMP1_IRES_ZsGreen, Day 4 #2 C57BL/6 B cells, p53-WT…
GSM7733014 C57BL/6 B cells, p53-WT, pRetroX_LMP1_IRES_ZsGreen, Day 4 #3 C57BL/6 B cells, p53-WT…
GSM7733015 C57BL/6 B cells, p53-KO, pRetroX_LMP1_IRES_ZsGreen, Day 4 #1 C57BL/6 B cells, p53-KO…
GSM7733016 C57BL/6 B cells, p53-KO, pRetroX_LMP1_IRES_ZsGreen, Day 4 #2 C57BL/6 B cells, p53-KO…
GSM7733017 C57BL/6 B cells, p53-KO, pRetroX_LMP1_IRES_ZsGreen, Day 4 #3 C57BL/6 B cells, p53-KO…

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