WGS, long read DNA-sequencing, RNA-seq, ChIP-seq, ATAC-seq, and HiC-seq of HPV-associated Oropharyngeal cancer (HPVOPC)

To determine human-viral hybrid extrachromosomal DNA (hybrid ecDNA) status, we performed WGS and RNA-seq on 2 HPVOPC cell lines, HMS001 and SCC154, and 2 patient-derived xenograft (PDX) tumors from clinical tumor samples of HPVOPC patients, described here as PDX_A and PDX_C. In addition, long read sequencing for HMS001 and PDX_A that had hybrid ecDNA were also performed.To elucidate chromatin status of hybrid ecDNA, we performed ChIP-seq for H3K27ac (activation mark), H3K4me1 (enhancer mark), and H3K4me3 (promoter mark), and ATAC-seq on HPVOPC cell lines and PDX tumors. To elucidate enhancer and HPV DNA interactions in hybrid ecDNA, HiC-seq was performed using the same cell lines and PDX tumors. Comparison between DMSO and JQ1 treatment of ChIP-seq data or HiC-data are included.