Snap-frozen tumor tissues were sliced into 1-2 mm sized pieces and crushed in an Eppendorf tube with sterile microcentrifuge pestle in the presence of RLT-Plus buffer in the presence ofb-mercaptoethanol. Total RNA was isolated using the RNeasy Micro Plus kit (Qiagen #74034). Total RNA was assessed for quality using an Agilent Tapestation, and all samples had RIN >7.0. RNA libraries were generated from >50 to 100 ng of RNA using Illumina's TruSeq Stranded mRNA Sample Prep Kit following the manufacturer's instructions. RNA libraries were multiplexed and sequenced with 75 base pairs (bp) single-end reads (SR75) or 100 bp paired-end reads to a depth of approximately 30 million reads per sample on an Illumina HiSeq4000 using V4 sequencing chemistry at theUCSD IGM core.