title: GSM7509997: BCX-080.P1; Homo sapiens; RNA-Seq
library_construction_protocol: Frozen fragments of breast tumors from patients (BCX P0) and corresponding breast cancer xenografts (BCX P1) were placed in lysis buffer, homogenized, and RNA was isolated using Norgen BIOTEK Total RNA Purification Plus Kit.  RNA quality was assessed with an Agilent Bioanalyzer. Genomic RNA was quantified by Picogreen (Invitrogen) and quality was then assessed using 2200 Tapestation (Agilent).  RNA was converted to doubled stranded complementary DNA (cDNA) using Ovation RNA-Seq System V2 Kit (Nugen).  Libraries of cDNA were made using KAPA kits and capture was performed using Nimblegen whole exome V3 probes.  Libraries were then sequenced on a HiSeq 2000 (Illumina) via a version 3 TruSeq paired end flowcell per manufacturer's instructions.  FASTQ files are aligned to the reference genome (human Hg19) using STAR 64, and HTSeq 65 was used to obtain the read counts of genes.  Qualities of raw reads were assessed using FastQC 66. The read counts were normalized with DESeq2 67.