Analysis of gene expression in primary human foreskin keratinocytes +/- HPV16 E7 or PTPN14 knockout

This RNA-seq study in primary human forekin keratinocytes was to define genes that are differetially expressed in the presence or absence of HPV16 E7 or several HPV16 E7 variants. We also generated and conducted RNA-seq on primary human foreskin keratinocytes that were CRISPR-Cas9 edited with nontargeting sgRNA or sgRNA targeting PTPN14. mRNA profiles in primary HFK were generated for the following samples (# of replicates): empty vector (3), HPV16 E7 (3), HPV16 E7 ∆21-24 (also known as ∆DLYC) (2), Cas9 + nontargeting sgRNA (2), Cas9 + sgRNA targeting PTPN14 (2). Retroviral vectors are MSCV-IP N-HA empty or MSCV-P C-FlagHA for E7 expression. CRISPR-Cas9 vectors are LentiCRISPR v2 with sgRNA sequences from Brunello sgRNA library (Doench et al (2016) Nature biotechnology 34, 184-191.)