Simul-seq:LCM tumor RNA
Nucleic acids were extracted using the RNeasy Mini kit (Qiagen:74104) per manufacturer's instructions, except the optional DNase I treatment was not performed. Ribosomal RNA sequences were depleted from the total nucleic acid mixture using Ribo-Zero gold (Illumina:MRZG126), with the standard 70 °C hybridization step changed to 65 °C. Simul-seq library preparation was performed as described in Reuter, JR, Spacek, DV, Pai, RK and Snyder MP (2016). Simul-seq: combined DNA and RNA sequencing for whole-genome and transcriptome profiling. Nat Methods. doi: 10.1038/nmeth.4028. Subsequent libraries were then sequenced using the Illumina HiSeq 2000 platform.