(A) Flow-cytometric analysis of KI67-expressing cells at week four following treatment with anti-RANKL and an age-matched isotype control mouse (two pooled thymi per replicate, n = 4 replicates for treatment, n = 5 for controls). Plots show absolute number of cells that are KI67+, KI67+AIRE+, and KI67+AIRE- in anti-RANKL treated and isotype control samples (data are mean ± s.d.). (B) Analysis for this figure was restricted to the persistent TAC-TEC population of all samples (511 total cells), highlighted on the UMAP of all cells. (C) Percentage of cycling cells within the TAC-TEC population, colored by sample. (D) Normalized log expression of Aire, Ccl21a, and Fezf2, across TAC-TECs in each sample. Color represents sample, black dot is median expression. (E) UMAP visualization and clustering of TAC-TEC reanalysis. Each point represents a cell in the TAC-TEC population, color represents new cluster identity (labeled 0, 1, or 2). (F) Normalized log expression of Aire, Ccl21a, and Fezf2 in the TAC-TEC population across cells in each cluster. Color represents sample, black dot is median expression. (G) Proportions of cells in each cluster in each sample. Color represents cluster. See also Figure 5—figure supplements 1 and 2.