scRNAseq of thymic myeloid APCs. (A) Quality control contour plots showing the expression level of TdTOMATO in sorted TdTOMATO⁻ and TdTOMATO⁺ thymic myeloid cells. (B) UMAP of scRNAseq of all sorted and annotated thymic myeloid cells. Items in red font mark subsets that were excluded from the analysis. DC = conventional DC; aDC = activated DC; Gran = granulocytes; Mac = macrophages; Mono = monocytes; pDC = plasmacytoid DC; T-APC d. = doublets of T cells and APCs; T B NK = T, B, and NK cells; prolif = proliferating. (C) UMAP featureplots showing the expression of marker genes of cell subsets that were excluded from scRNAseq analysis. (D) Heat map showing up to 25 of the top marker genes of each subset from scRNAseq annotated in Fig. 1 B. The heat map color scale depicts average log₂ fold change. For better discernibility of the expression profile across all subsets annotated in Fig. 1 B, the selected marker genes are highlighted by arrows and underlined with a white line. (E) Heat map showing up to 15 of the top marker genes of each aDC subset from scRNAseq. The heat map color scale depicts average log₂ fold change. (F) Violin plots show the expression of selected marker genes of subsets annotated in Fig. 1 B. All mice were bred on the B6 background. Littermates were used. Age-matched WT B6 mice from JAX were used as TdTOMATO⁻ controls to set the TdTOMATO positivity threshold.