Fig. 2

The heterogeneity, development, and clonality of T cells in human organs. a, b t-SNE plots of 7006 CD4⁺ (a, 11 clusters) and 11,256 CD8⁺ (b, 21 clusters) T cells from 15 organ tissues. Each dot represents one cell. Each color-coded region represents one cell cluster, which is indicated on the right. c, d Violin plots showing the normalized expression of marker genes for each CD4⁺ (c) and CD8⁺ (d) T cell cluster as indicated at the bottom. For each panel, the y-axis shows the normalized expression level for a marker gene as indicated on the left. Marker genes were also grouped according to functional cell types. e Pseudo-time trajectory analysis of all CD4⁺ (left panel) and CD8⁺ T cells (right panel) with high variable genes. Each dot represents one cell and is colored according to their cluster above: a for CD4⁺ and b for CD8⁺. The inset t-SNE plot shows each cell with a pseudo-time score from dark blue to yellow, indicating early and terminal states, respectively. f, g Heat maps of the activation scores of each T cell cluster for expression regulated by transcription factors (TFs). T cell clusters are indicated on top, and the scores were estimated using SCENIC analysis. Only shows the top 15 TFs for CD4⁺ T cells (f) and the top 10 for CD8⁺ T cells (g), with the highest difference in expression regulation estimates between each cluster and all other cells, under a Wilcoxon rank-sum test. h Sharing intensity of TCR clones in CD4⁺ (top panel) and CD8⁺ (bottom panel) T cells between different organ samples. Each line represents a sharing of TCR between two organs at the ends, and the thickness of the line represents a migration-index score between paired organs calculated by STARTRAC. The sizes of the dots are shown according to the logarithm to the base 2 of the size of T cell clones in organs with different colors. i Migration- (left panel) and expansion-index (right panel) scores of CD4⁺ and CD8⁺ T cells of each tissue calculated and compared using STARTRAC with a paired Student’s t test