Defining the heterogeneity of RORγt-lineage APC subsets. Related to Fig. 2. (A) Expression of Aire and Rorc in adult tdTmt⁺MHCII⁺ scRNA-seq clusters. (B) Heatmap with differential gene expression of cell clusters from scRNA-seq data. (C) tdTomato (left), as well as Aire-GFP and Aire transcript (right) expression levels across RORγt-lineage APC clusters. (D) Distribution of R-eTAC subset clusters found from each sample origin: mLN, spleen, and other LNs (labeled UMAP to reference is Fig. 2 C). (E) Number of cells among R-eTAC subset clusters found in each sample origin. (F) Expression of Itgav, Itgb8, Icosl, and Prdm16 in adult scRNA-seq clusters. (G) Heatmap showing similarities between R-eTAC clusters to other immune cell clusters from ImmGen. (H) Similarity score between adult RORγt-lineage APC clusters and mTECs. (I) Reduced dimensionality representation of scRNA-seq data with annotated cell clusters in 2-wk-old mice. (J) Integrated UMAP of all available RORγt-lineage APC single-cell data, displaying our adult scRNA-seq data (left), as well as expression of Aire and Rorc across the integrated scRNA-seq clusters (middle and right).