Fig. 3
The HPV16 transcriptome in EPE6 and AAE6 organotypic rafts. a Linear viral gene map. Viral RefSeq ([GenBank: AF125673], HPV16 W12E genome) alignment from each individual raft culture was visualized using IGV [50]. The y-axis (coverage) is log2 scaled. Total number of viral reads are given on the right-hand side of each track. b Heatmap & clustering analysis of viral transcriptome on DESeq normalized counts: viral genes vs sample replicates. Two distinct sample clusters matched EPE6 and AAE6 replicates respectively, clustering independently of each other. Within the high-variability EPE6 cluster, replicate 1 and 3 were clustered together. Within the low-variability AAE6 cluster, replicate 1 and 2 were clustered together. As well, AAE6 epithelia converged on consistently high viral transcription (specifically E6/E7). From the viral gene perspective, two distinct clusters were identified: E6, E7, E1, and L1 in one, and E2, E4, E5, and L2 in another. Within the first primary cluster, E6 and E7 cluster close together, as expected given they are expressed together as a multi-cistronic transcript. E1 and L1 also cluster together, constituting the truncated transcripts on the periphery of the non-transcribed region within AAE6 samples. In the second primary cluster, E5 and L2 cluster together, independent of E2 and E4 which is transcribed only in EPE6 samples. E2 and E4 expression unsurprisingly clusters together given that E4 is contained within the E2 ORF. c Scatterplot of average viral gene expression for EPE6 samples (x-axis) and AAE6 samples (y-axis). The axes (DESeq normalized gene counts) are log10 scaled. Significant differential gene expression is denoted by marker colour. Dashed line represents equal expression