4.2. RNA Sequencing

RNA sequencing (RNA-seq) data for 29 of the 37 gastric cancer cell lines were previously reported [14]. Total RNA from the eight remaining gastric cancer cell lines were extracted with a RNeasy Plus Mini Kit (Qiagen, Hilden, Germany). RNA-seq libraries were then generated with a TruSeq RNA Sample Prep kit v2 (Illumina, San Diego, CA, USA) and sequencing with the HiSeq 2500 platform. The TopHat-Cufflinks pipeline was used to align reads to the reference genome and to calculate normalized values in FPKM (fragments per kilobase of exon per million fragments mapped).