Extended Data Fig. 6: Developmental relationships between transcriptionally distinct cTregs, eTregs and proliferating Tregs.

a. Heatmap of differentially expressed genes in cTreg, eTreg and proliferating Tregs. b. UMAP of Treg subsets per location, filtering out the subsets with less than 10 cells in a given location (i.e. excluding eTregs_MLN, eTregs_CP, cTregs_LA, cTregs_LP and Prolif-Tregs_CP). Arrows depict summarised scVelo differentiation trajectories (top). Heat map overlay on the Treg UMAP indicating velocity pseudotime, as calculated by scVelo (bottom). c. Velocity analysis of genes that vary across the differentiation trajectory of all Treg subsets. d. Rorc and Gata3 expression of Tregs with Maf expression overlaid in red. e. Heatmap of differentially expressed genes between eTregs in MLN and LP. f. UMAP of the total Treg population with distributions of Treg subsets across locations (top) and overlay of TCR^Hh Tregs (below). g. UMAP overlay of clone size (top) and clone specificity (bottom) of TCR^Hh within total T cell populations. h. Barchart showing the distribution of most expanded TCR^Hh and host clones by location (top) and T cell subset (bottom). i. Heatmap of differentially expressed genes of host LP vs LA eTregs. Blue lines indicate gene expression profile of TCR^Hh eTregs in LP and LA. a-i: Representative of 6 combined mice.