scRNA-seq reveals heterogeneity in thymic DCs. (A) scRNA-seq of CD11c+ and CD11b+ FACS-sorted cells from the thymus of 7-wk-old C57BL/6 mice. UMAP plots show the analysis of 11,586 transcriptome events, with dashed lines representing clusters expressing Flt3, Csf1r, and Csf3r. (B) Feature plots showing the normalized expression of Flt3, Csf1r, and Csf3r in the clusters defined in A. (C) UMAP plots show the analysis of 8,514 transcriptome events and identify 16 clusters of thymic myeloid cells. Violin plots show the normalized expression of signature genes in these clusters. (D) Representative flow cytometry gating strategy for pre-gating thymic myeloid cells. (E) Representative gating strategy for identifying thymic neutrophils (Ly6G/SiglecF+Ly6C+CD11c−) and eosinophils (Ly6G/SiglecF+Ly6C−CD11c+). The graph shows the total numbers of neutrophils and eosinophils per thymus in 7-wk-old C57BL/6 mice; n = 3 mice. Data are shown as mean ± SD.
Figure S1.

scRNA-seq reveals heterogeneity in thymic DCs. (A) scRNA-seq of CD11c+ and CD11b+ FACS-sorted cells from the thymus of 7-wk-old C57BL/6 mice. UMAP plots show the analysis of 11,586 transcriptome events, with dashed lines representing clusters expressing Flt3, Csf1r, and Csf3r. (B) Feature plots showing the normalized expression of Flt3, Csf1r, and Csf3r in the clusters defined in A. (C) UMAP plots show the analysis of 8,514 transcriptome events and identify 16 clusters of thymic myeloid cells. Violin plots show the normalized expression of signature genes in these clusters. (D) Representative flow cytometry gating strategy for pre-gating thymic myeloid cells. (E) Representative gating strategy for identifying thymic neutrophils (Ly6G/SiglecF+Ly6C+CD11c−) and eosinophils (Ly6G/SiglecF+Ly6C−CD11c+). The graph shows the total numbers of neutrophils and eosinophils per thymus in 7-wk-old C57BL/6 mice; n = 3 mice. Data are shown as mean ± SD.

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