The thymus contains IFN-activated populations of moDC and moMacs. (A) Feature plot showing the normalized expression of Ly6c2, Fcgr1, Itgam, Itgax, and H2-Aa in clusters identified in Fig. 2 B. (B) Representative flow cytometry plots identifying LYVE-1⁺ macrophages using CD88, CD11c, CD11b, and CD14 antibody staining. (C) Representative flow cytometry plots showing the normalized expression of CD80, CD86, CD40, PD-L1, and CD63 in thymic DCs (Ly6C⁻CD64⁻CD11c⁺MHCII⁺) and thymic monocyte and macrophage populations described in Fig. 2 D. (D) Representative flow cytometry plots comparing the monocyte and macrophage populations between thymus and spleen. (E) Numbers of thymic cells (gated as in Fig. 2 D) in Ifnar1^−/− and Ifnlr1^−/− mice, shown as KO/WT ratio of cell numbers; n = 7–8 mice from at least two independent experiments. Data are shown as mean ± SD. Statistical analysis was performed by a one-sample t test and Wilcoxon test with a theoretical mean of 1; *P ≤ 0.05, **P ≤ 0.01, ****P ≤ 0.0001, and n.s., not significant.