Fig. 3

Antisense expression using phosphonoacetic acid (PAA) and knockout viruses. a Simplified phylogenetic tree showing the analyzed herpesviruses. b Nanostring nCounter profiling with the replication inhibitor PAA. RNA was collected from HFF cells at different timepoints post-infection with or without the HSV-1 replication inhibitor PAA. Infection and host cell shutoff were tracked using selected HSV-1 transcripts and housekeeping genes (top panels). A subset of antisense transcripts and corresponding host genes (all 12 antisense transcripts in Additional file 1: Figure S3) are shown in the two lower panels. Experiments were performed with one measurement each from two biological replicates and scaled to the 2 hpi timepoint after normalization using the provided control spike-ins. Error bars represent standard deviations. All values are scaled to the largest value for the same transcripts. Antisense and sense transcripts are sorted by expression profile. c Nanostring nCounter profiling using ICP0 and ICP4 knockout viruses. RNA was collected from HFF cells at different timepoints post-infection with wild-type (WT), ∆ICP0, or ∆ICP4 virus. Infection and host cell shutoff were tracked using selected HSV-1 transcripts and housekeeping genes (top panels). A subset of antisense transcripts and corresponding host genes (all 12 antisense transcripts in Additional file 1: Figure S3) are shown in the two lower panels. Experiments were performed with one measurement each from two biological replicates and scaled to the 2 hpi timepoint after normalization using the provided control spike-ins. Error bars represent standard deviations. All values are scaled to the largest value for the same transcripts. Antisense and sense transcripts are sorted by expression profile