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Effect of CD154:CD11b blockade on antigen-specific CD8 T cell response to murine Epstein-Barr virus infection

GSE293467 Mus musculus (mouse) RNA-seq (gene expression) 10 samples Submitted 2025/04/11 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 10 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
10 samples: 5 × Mm Spleen, p79/Kb CD8 T cells, Day 10-Post MHV68 Infection, No Treatment, Biol vs 5 × Mm Spleen, p79/Kb CD8 T cells, Day 10-Post MHV68 Infection, cM7 Treatment, BiolGroups 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
CD154:CD11b blockade enhances CD8+ T cell differentiation during infection but not transplantationJCI insight · 2025
Summary (written by the submitters)
CD154 is a promising target for immunosuppression in transplantation, autoimmunity, and inflammatory diseases. We previously identified CD11b as a novel alternate receptor for CD154 during alloimmunity. However, the impact of specific CD154:CD11b blockade on immune responses to infection has not been well characterized.
Read the full summary ↓
Here, we have shown that in contrast to its immunosuppressive effect on graft-specific CD8+ T cells, CD154:CD11b blockade unexpectedly improved both the quantity and quality of murine herpesvirus-68 (MHV)-specific CD8+ T cells as measured by an increase in tetramer-positive KLRG1loCD127hi memory precursor effector cells (MPECs). RNAseq of antigen-specific CD8+ T cells identified using an MHV68-specific MHC tetramer reveals specific pathways altered following cM7 treatment during MHV68 infection, including transcripts associated with T cell activation and survival. The differential effect of CD154:CD11b blockade on graft-vs. virus-specific CD8+ T cells was underpinned by differences in phospho-S6 downstream of mTORC1, however differential expression of key transcription factors Eomes and TCF-1 was dictated by the type of antigen stimulus. These data demonstrate that priming conditions play an important role in determining the outcome of immunotherapy and suggest that specific inhibition of CD154:CD11b interactions could be effective for suppressing alloimmune responses while maintaining protective immunity to minimize infectious complications following transplantation.
Published in
CD154:CD11b blockade enhances CD8+ T cell differentiation during infection but not transplantation
Alexander KL, Bennion KB, Liu D et al. · JCI insight 2025 · PMID 40485581 · doi:10.1172/jci.insight.184843
This dataset
Open GSE293467 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 GSE293467_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 PRJNA1244744 and SRA study SRP575780. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40485581) ↗
Study design
5 × Mm Spleen, p79/Kb CD8 T cells, Day 10-Post MHV68 Infection, No Treatment, Biol vs 5 × Mm Spleen, p79/Kb CD8 T cells, Day 10-Post MHV68 Infection, cM7 Treatment, Biol

Supports a between-group comparison across 10 samples.

How we read this: 2 replicated groups read from 10 sample titles; they account for 10 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
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