Fig. 4: ScRNA-seq confirmed proper identification of pDCs, pDC-like cells and tDCs in ZeST mice.

a, UMAP dimensionality reduction for DC types isolated from the spleens of eight ZeST mice (three uninfected, three MCMV infected for 36 h and two infected for 48 h; Extended Data Fig. 7a). Cells were index sorted into the five DC types studied (Fig. 3b) and used for scRNA-seq. As indicated by the color code, 851 individual cells were reassigned by deduction to a DC-type identity (cDC1s, cDC2s, pDCs, pDC-like cells or CD11c^high tDCs), based on combined analysis of their phenotypic and transcriptomic characteristics, as assessed, respectively, by Rphenograph clustering (Extended Data Fig. 7c) and Seurat clustering (numbers on the UMAP; Extended Data Fig. 7b), with confirmation via a single-cell enrichment analysis for DC-type-specific signatures generated from prior analysis of the cells from uninfected mice only (Extended Data Figs. 6 and 7); 100 cells were left nonannotated (NA). b, Violin plots showing expression of phenotypic markers across DC types. c, Heatmap showing messenger RNA expression levels of selected genes (rows) with hierarchical clustering using Euclidean distance, across all 951 cells (columns) annotated for (1) cell type final annotation as shown in a, (2) sorting phenotype, (3) time point after MCMV infection, (4) belonging to Rphenograph clusters and (5) belonging to Seurat clusters. Six gene groups are shown: (1) genes specifically expressed at high levels in pDCs, (2) genes with shared selective expression in pDCs and pDC-like cells, (3) cDC1-specific genes, (4) genes previously reported to be expressed at higher levels in pDC-like cells over pDCs, (5) cDC2-specific genes and (6) genes expressed selectively at higher levels in CD11c^high tDCs and cDC2 or cDC1 or pDC-like cells. d, Violin plots showing mRNA expression levels of selected genes across DC types. e, Violin plots showing tdT expression across DC types.