The thymus contains IFN-activated populations of moDC and moMacs. (A) Feature plot showing the normalized expression of Mafb in clusters identified in Fig. 1 A. (B) scRNA-seq of CD11c+ and CD11b+ FACS-sorted cells from the thymus of 7-wk-old C57BL/6 mice. Cells were bioinformatically filtered to include only clusters expressing Mafb. UMAP plots show the analysis of 1,020 transcriptome events, identifying five clusters. (C) Violin plots displaying the normalized expression of signature genes associated with cell clusters defined in B. (D) Representative flow cytometry gating strategy for identifying the four major populations defined in B and C. The gating strategy identifies monocytes (Ly6C+CD11b+MHCII−), moDC (Ly6C+CD11b+MHCII+), macrophages (CD64+CD11c−MHCII−), and moMacs (CD64+CD11c+MHCII+). (E) Representative flow cytometry plots showing normalized expression of CD26, CD11c, CD11b, LY6C, CD64, CX3CR1, F4/80, MERTK, VCAM1, and TIM4 in thymic DCs (Ly6C−CD64−CD11c+MHCII+) and thymic monocyte and macrophage populations described in D. (F) Frequency of tdTomato+ thymic cells (gated as in D) in Ms4a3Cre ROSA26tdTomato (Ms4a3tdTomato) mice; n = 9 mice from three independent experiments. (G) Numbers of thymic DC, monocyte, and macrophage (gated as in D) populations in Zeb2Δ1+2+3 mice, shown as KO/WT ratio of cell numbers; n = 8 mice from three independent experiments. (H) Numbers of thymic and splenic cells (gated as in D), shown as spleen/thymus ratio of cell frequencies; n = 6 mice from three independent experiments. (I) Frequency of eGFP+ thymic cells (gated as in D) in Mx1eGFP mice; n = 5 mice from two independent experiments. (J) Numbers of thymic cells (gated as in D) in Ifnar1−/−Ifnlr1−/−, Cd40l−/−, and Tcra−/− mice, shown as KO/WT ratio of cell numbers; n = 4–17 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 ≤ 0.001, ****P ≤ 0.0001, and n.s., not significant.
Figure 2.

The thymus contains IFN-activated populations of moDC and moMacs. (A) Feature plot showing the normalized expression of Mafb in clusters identified in Fig. 1 A. (B) scRNA-seq of CD11c+ and CD11b+ FACS-sorted cells from the thymus of 7-wk-old C57BL/6 mice. Cells were bioinformatically filtered to include only clusters expressing Mafb. UMAP plots show the analysis of 1,020 transcriptome events, identifying five clusters. (C) Violin plots displaying the normalized expression of signature genes associated with cell clusters defined in B. (D) Representative flow cytometry gating strategy for identifying the four major populations defined in B and C. The gating strategy identifies monocytes (Ly6C+CD11b+MHCII−), moDC (Ly6C+CD11b+MHCII+), macrophages (CD64+CD11c−MHCII−), and moMacs (CD64+CD11c+MHCII+). (E) Representative flow cytometry plots showing normalized expression of CD26, CD11c, CD11b, LY6C, CD64, CX3CR1, F4/80, MERTK, VCAM1, and TIM4 in thymic DCs (Ly6C−CD64−CD11c+MHCII+) and thymic monocyte and macrophage populations described in D. (F) Frequency of tdTomato+ thymic cells (gated as in D) in Ms4a3Cre ROSA26tdTomato (Ms4a3tdTomato) mice; n = 9 mice from three independent experiments. (G) Numbers of thymic DC, monocyte, and macrophage (gated as in D) populations in Zeb2Δ1+2+3 mice, shown as KO/WT ratio of cell numbers; n = 8 mice from three independent experiments. (H) Numbers of thymic and splenic cells (gated as in D), shown as spleen/thymus ratio of cell frequencies; n = 6 mice from three independent experiments. (I) Frequency of eGFP+ thymic cells (gated as in D) in Mx1eGFP mice; n = 5 mice from two independent experiments. (J) Numbers of thymic cells (gated as in D) in Ifnar1−/−Ifnlr1−/−, Cd40l−/−, and Tcra−/− mice, shown as KO/WT ratio of cell numbers; n = 4–17 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 ≤ 0.001, ****P ≤ 0.0001, and n.s., not significant.

This Feature Is Available To Subscribers Only

or Create an Account

Close Modal
Close Modal