FIG 2.

Extended culturing of HPV16-infected cells increases the number of deregulated genes. (A) Numbers of down- or upregulated genes in WT and E7-TTL mutant HPV16-infected and HPV16-immortalized HFK (p2/3, 27 to 33 dpi; p3/4, 36 to 55 dpi; p4/5, 47 to 63 dpi). All cells were infected and cultured in the absence of Y-27632. (B) TPM values of viral transcript reads in samples from HPV16-infected and HPV16-immortalized cells used for analysis. (C) Heat map analysis of genes altered in HPV16-infected cells. The subgroup of 113 genes identified in Fig. 1 were selected for the analysis and analyzed as sample groups from controls and WT and E7-TTL HPV16-infected cells at different times postinfection. (D) Venn diagram showing the overlap between differentially expressed genes in HPV16-immortalized and -infected cells (p4/5). (E) PCA analysis of RNA sequencing data from control and WT and E7-TTL HPV16-infected cells based on TPM values in the bulk RNA-seq data set.