GEO series

Single cell RNA sequencing of the progeny of PD1hi vs PD1low TCF-1+ P14 precursor cells on day 15 after secondary host infection with LCMV Armstrong [scRNA-Seq BD Rhapsody]

GSE278806 Mus musculus (mouse) Single-cell RNA-seq 1 samples Submitted 2025/02/21 Platform GPL34290

At a glance

Single-cell RNA-seq · mouse · 1 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Mus musculus (mouse)
Samples: 1 samples
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: Precursors of exhausted T cells are pre-emptively formed in acute infectionNature · 2025

Summary (written by the submitters)

T-cell exhaustion limits effector T-cell function in chronic infection and tumors. The development of these hypofunctional T-cells and of their precursors was considered to require stimulatory conditions met only upon persisting exposure to antigen and inflammation. In sharp contrast, we found similar T-cell populations in the early phase of acute infections.

Read the full summary ↓

At that stage early developing TCF1+ precursor population shows an unexpected diversity, which includes precursors of normal memory T-cells but also cells with a phenotype, gene-expression, and epigenetic profile that resembles precursors of exhausted T-cells found in chronic infections. We demonstrate that high ligand affinity promotes, and PD-1 signaling restricts the development of these precursors. While these exhausted precursors are initially frequently found, they decline without being completely lost in infections the immune system resolves. We therefore concluded that precursor T-cells with at least two distinct phenotypes are preemptively generated irrespectively of the outcome of the infection. Here, using adoptively transferred P14 cells, these subsets were isolated early during infection, re-transfered into new hosts that were subsequently infected as well. The entire progeny of the re-transfered cells was analyzed on day 15 pi.

Published in

Precursors of exhausted T cells are pre-emptively formed in acute infection

Chu T, Wu M, Hoellbacher B et al. · Nature 2025 · PMID 39778709 · doi:10.1038/s41586-024-08451-4

This dataset

Open GSE278806 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 GSE278806_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1168960 and SRA study SRP536668. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39778709) ↗

Samples in this study

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+ 1 more — browse all 1 samples with per-sample file links →

Datasets on a similar topic

GSE278803 Bulk RNA sequencing of PD1hi vs PD1low TCF-1+ P14 precursor cells sorted 7 days after infection with LCMV Armstrong [bulk RNA-seq] 10 samples shares pd1low, pd1hi, tcf-1, lcmv, p14, precursor, armstrong
GSE278805 Single cell RNA sequencing of TCF-1+ P14 precursor cells sorted 3.25 days after infection with LCMV Armstrong [scRNA-Seq BD Rhapsody] 1 samples shares tcf-1, lcmv, p14, precursor, armstrong
GSE278804 Single cell RNA sequencing of TCF-1+ precursor cells reacting to LCMV gp33 vs np396 multimers sorted 30 days after infection with LCMV Armstrong [scRNA-Seq + TCR 10x] 12 samples shares tcf-1, lcmv, precursor, armstrong
GSE254211 Analysis of different mouse P14 CD8+T cell subset gene signatures in presence and absence of Tim-3+ Treg during LCMV CL13 infection 18 samples shares lcmv, p14
GSE337539 scRNAseq of LCMV-specific P14 cells: WT, P2RX7-KO and NKG7-KO 8 samples shares lcmv, p14
GSE270606 Single cell analysis of splenic control and ICOS deficient P14 cells from LCMV chronically infected mice 2 samples shares lcmv, p14
GSE301271 Pan organ and time course analysis of T cells in acute LCMV (armstrong) infection (day 7) [I36] 30 samples shares lcmv, armstrong
GSE301960 Pan organ and time course analysis of T cells in acute LCMV (armstrong) infection (day 30) [I38] 30 samples shares lcmv, armstrong

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