Extended Data Fig. 7: Analysis of the FB5P-seq data for all cells from uninfected and infected mice.

a, UMAP dimensionality reduction of the gene expression data for DC types isolated from the spleens of eight ZeST mice (3 uninfected, 3 MCMV-infected for 36 h and 2 infected for 48 h, see graphical legend). Cells were index sorted into the 5 DC types studied (see Fig. 3b), and used for single cell RNA sequencing. After quality controls, 951 cells were kept for the analysis. b, Projection onto the UMAP space of the 13 Seurat clusters obtained (see graphical legend). c, Projection onto the UMAP space of the phenotype of cells based on their belonging to the Rphenograph clusters (color code) obtained upon re-analysis of the fluorescent signals for 10 of the phenotypic markers acquired during index sorting as listed in panel d. d, Annotation of the Rphenograph clusters for DC type identity based on mean fluorescent intensities per marker and cluster as shown on the heatmap. e, Number of cells belonging to the intersections between Seurat (rows) and Rphenograp (column) clusters. Seurat clusters were annotated for cell types based on analysis of their marker genes (see Supplementary Table 2). f, Heatmap showing sgCMAP scores of individual cells (rows) for the DC type-specific sgCMAP signatures (columns) generated from the analysis of the data focused on cells from uninfected mice (see Extended Data Fig. 6). Hierarchical clustering was performed, using the Pearson’s minus one metric for signatures (columns), and the Euclidian distance for individual cells (rows), with annotation of individual cells (rows) for i) belonging to Seurat clusters, ii) belonging to Rphenograph clusters, iii) sorting phenotype, and iv) final cell type assignment. 851 cells were assigned a cell type identity based on consistency between their belonging to Seurat and Rphenograph clusters (panel e), which was well corroborated by the sgCMAP scores. 100 cells were left non-annotated (NA).