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mRNA-seq of AID-expressing cells from mice infected with WT or M2.Stop 73.Bla MHV68

GSE285085 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2024/12/20 Platform GPL17021
At a glance

RNA-seq (gene expression) · mouse · 12 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
12 samples: 3 × AID-cre tdTomato lymphocytes, AID+ MHV68-, 16 dpi WT 73.Bla MHV68, vs 3 × AID-cre tdTomato lymphocytes, AID+ MHV68+, 16 dpi WT 73.Bla MHV68, vs 3 × AID-cre tdTomato lymphocytes, AID+ MHV68-, 16 dpi M2.Stop 73.Bla MHV68, vs 3 × AID-cre tdTomato lymphocytes, AID+ MHV68+, 16 dpi M2.Stop 73.Bla MHV68,Groups 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 germinal center B cells in vivo, we infected AID-cre tdTomato reporter mice with WT or M2.Stop 73.Bla MHV68. At 16 dpi, draining lymph nodes were harvested and treated with CCF4-AM. AID+ and AID+Bla+ lymphocytes were sorted from WT and M2.Stop MHV68 infected tissue and sent for ultra-low input RNA-seq analysis.
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 GSE285085 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 GSE285085_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 PRJNA1201157 and SRA study SRP553001. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39843898) ↗
Study design
3 × AID-cre tdTomato lymphocytes, AID+ MHV68-, 16 dpi WT 73.Bla MHV68, vs 3 × AID-cre tdTomato lymphocytes, AID+ MHV68+, 16 dpi WT 73.Bla MHV68, vs 3 × AID-cre tdTomato lymphocytes, AID+ MHV68-, 16 dpi M2.Stop 73.Bla MHV68, vs 3 × AID-cre tdTomato lymphocytes, AID+ MHV68+, 16 dpi M2.Stop 73.Bla MHV68,

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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
Datasets on a similar topic

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