Gene expression profiling study by RNA-seq in PDX model based diffuse type gastric cancers.

We established PDX lines from diffuse type gastric cancers (DGCs). Using these cells, we carried out RNA-seq based transcriptome profiling using 15 stomach samples including three PDX lines (HGC-3, HGC-8, and HGC-20) and normal-looking surrounding tissues. Via comparative analysis between cells and tissues, we identified significant gene set associated with each cell and observed that genes involved in AKT signalling pathway were commonly associated with all PDX lines. RNA-seq data of 15 gastric samples were generated. Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light. Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR. Sequencing was performed in paired end reads (2x75 bp) using Hiseq-2500 (Illumina).