title: RNA sequencing results for sample 94334
design: When RNA was simultaneously extracted with the DNA, FFPE sections were deparaffinized using the mineral oil method. Briefly, 800µL mineral oil and 180µL Buffer PKD (Qiagen) were mixed with the sections, Proteinase K was added for tissue digestion, and the sample was incubated at 56°C for 15 minutes. Phase separation was encouraged with centrifugation, and the aqueous phase was chilled 3 minutes to precipitate RNA. After centrifugation 15 minutes at 20,000xg, RNA-containing supernatant was removed for extraction, while DNA remained in the pellet. Nucleic acids were subsequently extracted using the AllPrep DNA/RNA Mini Kit (QIAGEN catalog # 80204) according to the manufacturer's instructions. RNA was eluted in nuclease-free water. Transcriptome sequencing library were made following RiboGreen quantification and quality control by Agilent BioAnalyzer, 0.5-1µg of total RNA with DV200 values ranging from 5% to 68% underwent ribosomal depletion and library preparation using the TruSeq Stranded Total RNA LT Kit (Illumina catalog # RS-122-1202) according to instructions provided by the manufacturer with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 in a PE100 run, using the HiSeq 3000/4000 SBS Kit (Illumina).