RNA Seq of HPV+ head and neck cancers after transoral robotic surgery
Tumor tissue samples were macrodissected by a pathologist from FFPE blocks for each patient to maximize tumor purity for each sample, and RNA was isolated using the Mag-Bind RNA FFPE kit (Omega Bio-tek). RNA sample quality was assessed by RNA TapeStation (Agilent Technologies) and quantified by AccuBlue® Broad Range RNA Quantitation assay (Biotium). Total RNA libraries were created using Illumina Stranded with RiboZero plus kit. Final library quantity was estimated by Qubit 2.0 (ThermoFisher) and quality was assessed by TapeStation HSD1000 ScreenTape (Agilent Technologies). Final library size was ~350bp with an insert size of about 200bp based on Illumina® 8-nt unique dual-indices. Libraries were pooled in equimolar proportions and sequenced on an Illumina® Novaseq platform.