Extended Data Fig. 7: Trajectories in viral gene expression space upon perturbation of viral factors.

a, Cartoon explaining the analytical workflow for comparing viral trajectories across the different sgRNA targets. b, Heatmaps of viral gene expression for all cells with virus-targeting sgRNAs, corresponding to the middle panel of the workflow cartoon. For each sgRNA target, cells were grouped in bins of 10% of viral RNA fraction, and the expression of viral genes plotted relative to a corresponding bin defined by cells with host-directed, safe-targeting sgRNAs (similar to Supplementary Fig. 4b), representing the unperturbed, dominant trajectory. Both the columns (viral sgRNA targets) as well as the rows (expressed viral genes) are ordered by genome position. This facilitates the distinction of gene expression effects in cis, that is the immediate effect of cutting on genes adjacent to the cut site, as opposed to in trans, which are reflecting an altered trajectory of infection. Pink boxes indicate the sgRNA target genes. c, Mapping the sgRNA targets onto the phenotypic landscape of the HCMV genome, indicating genome position and phenotype in the CRISPRn tiling screen.