Fig. 4

Marker genes define subpopulations with different transition probabilities into infection. a Cells were projected on a two-dimensional map using UMAP based on gene expression values, with cells colored by harvesting time point. Main distinguishing features were marked in gray. b Cells colored by amount of HSV-1 transcripts. Cells without HSV-1 transcripts are colored in light gray. c–g Cells colored by expression values of the indicated genes. Color scales are shown to the right of these panels. Areas containing cells with relatively high expression levels were marked with a light green ellipse. The dark green and blue ellipse denote S and G2/M phase cells, respectively. h Correlation of gene expression with NQO1 expression (horizontal axis) and SULF1 expression (vertical axis) in cells harvested at 3 hpi. Every dot represents a gene, colored by the slope of the linear correlation with NQO1. Selected genes were labeled by name. To calculate correlations, only cells with relative normalized expression above a certain threshold were used as for Fig. 2 and viral transcripts (Supplementary Fig. 4c). i Groups of cells according to PAGA were labeled A to Q. The line thickness of the connections (graph edges) between the cell clusters (graph nodes) indicate the likelihood that cells can move from one cluster to the other (right). Probabilities (arbitrary scale) are noted in red. Areas of interest are marked with light green ellipses. j–n Cells colored by RNA velocity values of the indicated genes. Cells for which no value could be calculated were colored in light gray. o RNA velocity arrows projected on the UMAP. Cells containing at least one detected viral transcript were colored in light orange, and all others in light gray