RNA-Seq of Pt10: Tumor
RNA was extracted from FFPE sample  using a Qiagen FFPE RNeasy Kit, respectively. RNAseq libraries were prepared using Illumina's TruSeq RNA Access Library Prep Kit. Total RNA was quantified using a Quant-iT RiboGreen RNA Assay Kit and normalized to 5 ng μ l−1. An RNA transcriptome capture method was used. Using Illumina's TruSeq RNA Access Library Prep Kit, a stranded cDNA library was prepared from isolated RNA which was then hybridized to a set of DNA oligonucleotide probes to enrich the library for mRNA transcript fragments. The transcriptome capture targeted 21,415 genes, representing 98.3% of the RefSeq exome (and was the same bait set as the Rapid Capture Exome). Flowcell cluster amplification and sequencing were performed according to the manufacturer's protocols. Data were analysed using the Broad Picard Pipeline which includes de-multiplexing and data aggregation.