Fig. 2

Analysis of CD8⁺ antigen-specific T cells sampled from Donor 1. a Unsupervised clustering with k = 8 clusters, p-value = 0.01, AUROC = 0.8. Epitope species specificity, the four largest TCR clones, surface protein expression levels, and the percentage of mitochondrial genes are annotated. b t-SNE coloured by the results of clustering, epitope species, TCR clone and genes of interest (CCR7, CMC1, LEF1), with point size corresponding to highest tetramer read count of each cell, CD45RO TotalSeq expression, and genes of interest (GZMH, CST7, TCF7), show that clustering is preserved, and that clonally expanded T cells dominate the major clusters. Genes of interest reveal further sub-clusters of cells. c Pseudo-time plots reveal a naïve to effector phenotype transition, with cluster preservation at the extremes of each state and a clear trajectory for influenza specific T cells