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Atomistic TCR-ligand interactions instruct memory T-cell differentiation and crossreactivity

GSE302856 Mus musculus (mouse) Single-cell RNA-seq 28 samples Submitted 2026/02/18 Platform GPL34290
At a glance

Single-cell RNA-seq · mouse · 28 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Mus musculus (mouse)
Samples
28 samples: 5 conditions, mostly with about 6 replicates eachGroups 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
Atomistic TCR-ligand interactions instruct memory T-cell differentiationbioRxiv : the preprint server for biology · 2025
Summary (written by the submitters)
While memory T-cells provide protective immunity against specific pathogens, their post-encounter differentiation into central (TCM) and/or effector (TEM) subpopulations remains enigmatic. We thus explored the CD8 T-cell receptor (TCR) repertoire of 242 murine TCRαβ clonotypes directed against an immunodominant influenza A virus (IAV) peptide/major histocompatibility complex (pMHC) ligand, the nucleoprotein NP366-374/Db, leveraging single-cell transcriptomics with paired TCR sequencing, mechanosensing metrics, and in vivo memory development plus TCR-pMHC structural analyses.
Read the full summary ↓
Polar TEM and more variegated TCM repertoires as well as bipotential “bipolar” clonotypes (TBP) revealed weak force-dependent bonding parameters associated with heterosubtypic IAV crossreactivities. TCM and TEM polarities manifest pMHC binding skewed to TCRβ- versus TCRα-subunit mechanotransduction, respectively, unlike the more signaling-balanced TBP TCRs. In sum, TCR diversity anticipates pathogen evolution whereas divergent signaling regulates memory fate.
Published in
Atomistic TCR-ligand interactions instruct memory T-cell differentiation
Akitsu A, Tan K, Mallis RJ et al. · bioRxiv : the preprint server for biology 2025 · PMID 41279151 · doi:10.1101/2025.11.05.686789
This dataset
Open GSE302856 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 GSE302856_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 PRJNA1292470 and SRA study SRP601429. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41279151) ↗
Study design
5 conditions, mostly with about 6 replicates each
CD8b+/CD45.1+/+ lymph node T cells bearing th… ×7 CD8b+/CD45.1+/CD45.2+ lymph node T cells bear… ×6 CD8b+/Thy1.1+ lymph node T cells bearing the … ×6 CD8b+/CD45.1+/+ lymph node T cells bearing th… ×4 CD8b+/CD45.1/+CD45.2+ lymph node T cells bear… ×4 CD8b+/CD45.1/+CD45.2+ lymph node T cells bear… ×1

Supports a between-group comparison across 27 samples.

How we read this: 5 replicated groups read from 28 sample titles; they account for 27 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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