Salmon analysis of viral transcripts from RNA-seq on 17syn+- and 17ΔN/H-infected skin.

Viral gene expression in infected human skin was analysed by RNA-seq and quantified by Salmon 0.8.2. Viral transcript abundances are reported as transcripts per thousand (TPT; described in the RNA-seq methods). Some viral transcripts that overlap other viral transcripts have zero values for either or both 17syn+ and 17ΔN/H because their abundances relative to the highest coverage viral transcripts were low. Transcripts US1 and US12 share the exon 1 sequence, which therefore was not counted. LAT and RL2 transcript abundances were evaluated for both the spliced and unspliced species. In addition, three regions were added manually to identify any transcripts from these regions. These were the 5′ end of the LAT locus (5′ LAT) where the 3SEQ10 region hit is located, the 3′ end of the LAT locus (3′ LAT) that was not deleted in 17ΔN/H (118007:118735 in GenBank accession JN555585.1), and the lambda phage DNA insert in the 17ΔN/H genome. (XLSX)