tDCs represent transendothelial cells. (A) Representative flow cytometry gating strategy of thymic myeloid cells. Cells were pre-gated as shown in Fig. S1 D. The gating strategy identifies pDCs (B220⁺CD11c⁺), moDCs (B220⁻Ly6C⁺CD11b⁺CD11c⁺), aDCs (CD11c⁺MHCII⁺CCR7⁺), DC1 (CD11c⁺MHCII⁺CCR7⁻XCR1⁺), DC2 (CD11c⁺MHCII⁺CCR7⁻SIRPα⁺CD11b⁺), and tDCs (CD11c⁺MHCII⁺CCR7⁻SIRPα⁺CD11b^lowCX3CR1⁺). (B) Representative flow cytometry plots showing the normalized expression of MHCII, CD80, CD86, CD40, and PD-L1 in thymic DC populations. Cells were gates as shown in A. (C) Violin plot displaying the normalized expression of gene associated with Hallmark IFN response mouse in clusters defined in Fig. 4 B. (D) Feature plot showing the normalized expression of Ccr2 in clusters identified in Fig. 1 A. (E) Representative flow cytometry plot showing normalized expression of CCR2 in thymic myeloid cell populations. Graph shows gMFI of CCR2 expression by thymic myeloid cells; n = 2 from two independent experiments. Data are shown as mean ± SD. (F) Representative flow cytometry plots showing analysis of ex vivo anti–CD11c-PE-Cy7 and i.v. anti–CD11c-PE labeling in thymic populations of moDCs and DCs. Statistical analysis was performed by a Wilcoxon run-sum test; ****P ≤ 0.0001.