Expression of marker and antigen presentation–associated genes by thymic DCs. (A) Flow cytometry gating strategy of thymic DCs based on scRNAseq of thymic myeloid cells. DCs were gated as B220⁻CD11c⁺MHCII⁺ and further distinguished into XCR1⁺CCR7⁻ DC1 and XCR1⁺CCR7⁺ aDC1a. XCR1⁻CCR7⁺ DCs were further separated into SIRPA^HighIL7R^Low aDC2a, SIRPA^LowIL7R^High aDC2b, and SIRPA⁻IL7R⁻ aDC1b. XCR1⁻CCR7⁻ cells were then gated as SIRPA⁺MGL2⁺CD14⁻ DC2. The color code of thymic DC subsets defined here is used across all figures. (B) Frequencies of DC subsets within parent populations (left panel) and within all B220^–CD11c⁺MHCII⁺ cells (right panel) (mean ± SEM, n = 45–49 mice from seven independent experiments) gated as in Fig. S2 A. (C) Histograms depicting the protein expression of DC markers in DC subsets as defined in Fig. S2 A. (D) MFI z scores of DC markers within DC subsets related to Fig. S2 C (mean ± SEM, n = 29–33 mice from five independent experiments). (E) Violin plots show the expression of MAT ON genes taken from Ardouin et al. (2016) within cell subsets annotated in Fig. 1 B. (F) Violin plots show the expression of genes involved in MHCII presentation within cell subsets annotated in Fig. 1 B. All mice were bred on the B6 background. Littermates were used.