scRNAseq analysis reveals unique pDC subtypes in St3gal1^MK−/− mice. (A) Flow cytometry diagram for isolating and sorting BM pDCs (Ter119^–, CD11b^–, Gr1^–, B220⁺, CD11c⁺, and CD8^–). (B) Uniform Manifold Approximation and Projection (UMAP) plot displaying clusters from isolated pDCs annotated and matched with data from ImmGen. For complete cell identity assignment see supplemental Figure 4C. (C) UMAP feature plot of Bst2 (dark blue, left panel) and Siglech (green, middle panel) show that annotated pDC clusters express transcripts for classic pDC surface markers. The overlap for both transcripts is shown in light blue (right panel), indicated by the Venn diagram. (D) UMAP feature plot of characteristic pDC genes Ccr9, Klk1, and Ly6d show that high expression concentrated in pDC clusters 1, 2, 11, and 12. (E) UMAP feature plot of Cd4 expression in St3gal1^MK−/− pDCs. (F) Violin plot of Cd4 expression in control vs St3gal1^MK−/− pDC clusters. (G) Quantification calculating percentage of representation in each cell cluster from control (blue) and St3gal1^MK−/− (red) genotypes. (H) UMAP plots differentiating pDC clusters from respective control (black) and St3gal1^MK−/− (red) genotypes. Cluster 5 can be further resolved into distinct control (5a) and St3gal1^MK−/− (5b) subclusters. (I) Subclusters 5a and 5b identified as B cell and pDC-like, respectively, using the ImmGen database as a reference. FSC-A, forward side scatter area.