GEO series

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]

GSE278804 Mus musculus (mouse) Single-cell RNA-seq 12 samples Submitted 2025/02/21 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 12 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: 12 samples: 3 × gex_gp33 vs 3 × gex_np396 vs 3 × vdj_gp33 vs 3 × vdj_np396Groups 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: 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. In this experiment, the transcriptome and TCR-sequences of endogenous gp33 or np396 specific CD8 T-cells were analyzed on day 30 post infection to assess the role of TCR-affinity and antigen-specificity in the formation of the different CD8 T-cell precursors.

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 GSE278804 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 GSE278804_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 PRJNA1168957 and SRA study SRP536634. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39778709) ↗

Study design

3 × gex_gp33 vs 3 × gex_np396 vs 3 × vdj_gp33 vs 3 × vdj_np396

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

GSM8555143 gex_gp33_2 gex_gp33
GSM8555144 gex_gp33_3 gex_gp33
GSM8555145 gex_gp33_5 gex_gp33
GSM8555146 gex_np396_2 gex_np396
GSM8555147 gex_np396_3 gex_np396
GSM8555148 gex_np396_5 gex_np396
GSM8555149 vdj_gp33_2 vdj_gp33
GSM8555150 vdj_gp33_3 vdj_gp33
GSM8555151 vdj_gp33_5 vdj_gp33
GSM8555152 vdj_np396_2 vdj_np396
GSM8555153 vdj_np396_3 vdj_np396
GSM8555154 vdj_np396_5 vdj_np396

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 tcf-1, lcmv, precursor, armstrong
GSE278806 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] 1 samples shares tcf-1, lcmv, 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, precursor, armstrong
GSE329359 Single cell RNA sequencing of gp33 tetramer-positive CD8 T cells sorted from the SI-LP and spleen of germ-free and SPF mice 16 days after LCMV Docile infection [scRNA-Seq 10x] 12 samples shares lcmv, gp33
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
GSE301961 Pan organ and time course analysis of T cells in acute LCMV (armstrong) infection (day 60) [I40] 30 samples shares lcmv, armstrong
GSE44322 Gene expression profile analysis of mouse whole spleen following infection by lymphocytic choriomeningitis virus (LCMV), comparing LCMV-Armstrong and LCMV-Clone 13 expression patterns at 0, 5, 9, and 30 days 26 samples shares lcmv, armstrong

Search all mouse RNA-seq datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.