Extended Data Fig. 5: Correlation of viral gene expression with dose of infection and cell cycle.

a, Comparison of virus stock-derived RNA (virion-associated RNA) and old RNA levels of CMV genes. Mean levels obtained from four independent virus stock vials and mean expression levels in the CMV-infected cells (n = 2 replicates, 49 cells) are compared. The colours indicate viral genes of different kinetic classes. TL, true late. Pearson’s correlation coefficient and P values determined by a t-test on Pearson’s correlation coefficient are indicated. b, As in a but normalized for the total expression levels of the respective genes in the CMV-infected cells. Pearson’s correlation coefficient and P values are indicated. c, Scatter plot comparing the predicted extent of viral gene expression per individual cell (n = 2 replicates, 49 cells) on the basis of the dose of infection with the observed expression. P value determined by likelihood ratio test. d, Distribution of viral reads for cells in G1 (n = 9 cells), S (n = 20 cells) or G2/M (n = 20 cells) phases at the beginning of infection. P value determined by two-sided Wilcoxon test. e, Extent of cell-cycle disruption on the basis of cell-cycle projections derived from old and total RNA of uninfected (mock, n = 2 replicates, 45 cells) and CMV-infected (n = 2 replicates, 49 cells) cells for G1, S and G2/M phases. Individual cells are shown as dots. P values determined by two-sided Wilcoxon tests. f, Unbiased pathway and gene set overdispersion analysis (PAGODA)¹² revealed Gene Ontology (GO) terms associated with mock- and CMV-infected cells. The fraction (total, new or old) in which each signature was found is indicated. g, h, The NF-κB (g) and IFN (h) response signature score for each cell (n = 2 replicates, 49 cells) is plotted against its viral RNA content. The linear regression fit (line), 95% credible interval (shading), Spearman’s ρ values and P values determined by t-test on Spearman’s ρ are indicated. i, j, Distribution of the extent of the NF-κB (i) and IFN (g) responses for cells in G1 (n = 9 cells), S (n = 20 cells) or G2/M (n = 20 cells) phase at the beginning of infection. P values determined by two-sided Wilcoxon tests. All box plots are as in Fig. 4c. Dots represent outliers.