Fig. 3: Cellular state landscape correlates with cell-to-cell variation of HSV-1 infection.

a Cellular state landscape of mock- and HSV-1-infected HeLa cells generated from the high-dimensional cellular state space of 3136 cellular features extracted from the smFISH + 4i experiment projected as UMAP. UMAP colored by time point (left; hpi) or by cell subpopulation (right; 0, mock cells; 1, uninfected cells without infected neighbors; 2, uninfected cells with infected neighbors; 3, infected cells). Arrow, a cluster formed by infected cells at 6–12 hpi. Arrowhead, a cluster formed by uninfected cells with infected neighbors at 9 and 12 hpi. Data are from two (mock) or four (HSV-1 infection) replicate wells per time point, and cell count is indicated in the plot. UMAP of uninfected HeLa cells without infected neighbors (b), uninfected HeLa cells with infected neighbors (c), and infected HeLa cells (d), using the same single-cell features as in a and colored by time point (hpi). Cell counts are indicated in the plots. e UMAP of infected HeLa cells generated from the high-dimensional infection state space (the same cells as in d). Position of single cells within a PC-reduced space of 750 viral features was projected onto a 2-dimensional infection-state landscape using UMAP and colored by time point (hpi). f UMAP of infected HeLa cells (the same cells as in d), colored by cell cycle, size, or local density, or by PML-body presence. Upper panels, UMAP using the same cellular features as in a. Lower panels, UMAP using the same viral features as in e. g Heatmaps of explained variance. A PC-reduced space of the simple phenotypic state (360 single-cell features) or high-dimensional cellular state space (3,136 single-cell features) was used in MLR to predict viral gene expression in infected HeLa cells. Gray, less than 250 cells expressing the corresponding viral marker. h UMAP of infected cells (cellular features) colored by measured or MLR-predicted levels of UL29, UL19, ICP27, or ICP4 in single cells. Scale bar: lower limit is <0.5^th and upper limit is >99.5^th percentile of the values. See also Supplementary Figs. 6 and 7 and Movies 1–3.