GEO series

Lag3 and PD-1 pathways regulate NFAT-dependent TCR signalling programmes during early CD4+ T cell activation

GSE260895 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2025/03/03 Platform GPL19057

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 × CD4+ T cell, IgG Control vs 3 × CD4+ T cell, anti-PD-L1 vs 3 × CD4+ T cell, anti-Lag3 vs 3 × CD4+ T cell, CombinationGroups 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: Lag3 and PD-1 pathways preferentially regulate NFAT-dependent TCR signalling programmes during early CD4(+) T cell activationImmunotherapy advances · 2025

Summary (written by the submitters)

Here we perform QuantSeq 3' mRNA sequencing of RNA extracted from flow sorted splenic CD4+ T cell from Tg4 Nr4a3-Tocky Tiger mice that been reactivated in the presence of Isotype, anti-PD-L1, anti-Lag3 or combination therapy. Transcriptional analysis reveals strong T cell receptor signalling, T helper cell bias and metabolic priming in response to combination therapy.

Published in

Lag3 and PD-1 pathways preferentially regulate NFAT-dependent TCR signalling programmes during early CD4(+) T cell activation

Sheriff L, Copland A, Lecky DAJ et al. · Immunotherapy advances 2025 · PMID 40351814 · doi:10.1093/immadv/ltaf015

This dataset

Open GSE260895 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 GSE260895_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 PRJNA1083930 and SRA study SRP493427. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40351814) ↗

Study design

3 × CD4+ T cell, IgG Control vs 3 × CD4+ T cell, anti-PD-L1 vs 3 × CD4+ T cell, anti-Lag3 vs 3 × CD4+ T cell, Combination

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

GSM8127674 CD4+ T cell, IgG Control 1 CD4+ T cell, IgG Control
GSM8127675 CD4+ T cell, IgG Control 2 CD4+ T cell, IgG Control
GSM8127676 CD4+ T cell, IgG Control 3 CD4+ T cell, IgG Control
GSM8127677 CD4+ T cell, anti-PD-L1 1 CD4+ T cell, anti-PD-L1
GSM8127678 CD4+ T cell, anti-PD-L1 2 CD4+ T cell, anti-PD-L1
GSM8127679 CD4+ T cell, anti-PD-L1 3 CD4+ T cell, anti-PD-L1
GSM8127680 CD4+ T cell, anti-Lag3 1 CD4+ T cell, anti-Lag3
GSM8127681 CD4+ T cell, anti-Lag3 2 CD4+ T cell, anti-Lag3
GSM8127682 CD4+ T cell, anti-Lag3 3 CD4+ T cell, anti-Lag3
GSM8127683 CD4+ T cell, Combination 1 CD4+ T cell, Combination
GSM8127684 CD4+ T cell, Combination 2 CD4+ T cell, Combination
GSM8127685 CD4+ T cell, Combination 3 CD4+ T cell, Combination

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