The thymus contains a population of CX3CR1 ⁺ tDC. (A) scRNA-seq of CD11c⁺ and CD11b⁺ FACS-sorted cells from the thymus of 7-wk-old C57BL/6 mice. Cells were bioinformatically filtered and displayed as described in Fig. 3 A. DC2, CX3CR1⁺ DC2, and pDC are marked by color-coded lines. (B) UMAP plots showing the distribution of filtered DC2, CX3CR1⁺ DC2, and pDC thymic populations defined in A. (C) Violin plots displaying the normalized expression of signature genes associated with cell clusters defined in B. (D) Representative flow cytometry plots showing the normalized expression of MHCII, CD11b, Ly6C, SiglecH, TCF4, CX3CR1, and CD14 in thymic DC populations defined in B and gated according to the Fig. S4 A. (E) Frequency of tdTomato⁺ thymic DC populations (gated as in Fig. S4 A) in Ms4a3^Cre ROSA26^tdTomato (Ms4a3^tdTomato) mice; n = 9 mice from three independent experiments, and moDC are used as control. (F) Frequency of eYFP⁺ thymic DC populations (gated as in Fig. S4 A) in hCD2^iCre ROSA26^eYFP (hCD2^eYFP) mice; n = 5 mice from three independent experiments. (G) Numbers of thymic populations (gated as in Fig. S4 A) in Itgax^CreTcf4^fl/fl mice, shown as KO/WT ratio of cell numbers; n = 3 mice from two independent experiments, and Itgax^Cre− mice were used as controls. 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, and n.s., not significant.