Fig. 1: Overview of the pan-disease single-cell TCRαβ repertoire reference atlas.

a Pan-disease and population-level data collection of scRNA/TCR-seq data. b UMAP of the integrated datasets colored by T cell subtypes. c Kernel density estimation plot of expression of key marker genes for T cell subtypes. d UMAP of the unique clonotypes displaying corresponding single-cell transcriptome information colored by the T cell types. e Sankey plot illustrating the enriched TRAV/TRAJ, TRAV/TRBV, and TRBV/TRBJ pairing and joining preferences in major T cell types. f Violin plot showing the preference for amino acids with different physicochemical properties in the CDR3 middle region (mr) of CD4⁺ T_reg, CD4⁺ T_conv, and CD8⁺ T cells. Each gray dot in the plot represents data from one individual, while lines connecting gray dots indicate amino acid usage differences in different cell types within each individual, considering support from at least 100 cells. White dots within the violin plot represent the average percentage of amino acid usage. Letters within colored dots represent the various physicochemical properties of amino acids. g UMAP view of relative cell density plot of clonotypes either using CD4⁺ T_conv (left) or CD8⁺ T (right) preferential TRAV/TRBV. The blue and orange dashed lines outline the CD4⁺ T_conv and CD8⁺ T cells defined by gene expression. ***P < 0.001, **P < 0.01, *P < 0.05, paired t-test; N.S., not significant.