Expression profile of Gastro-Entero-Pancreatic Neuroendocrine Tumors (GEP-NET)

Expression profile of human GEP-NET tumors, including 113 fresh frozen biopsies of primary and metastatic tumours originating from pancreas (P-NET, 83 primary and 30 metastasis), 81 from small intestine (SI-NET, 44 primary and 37 metastasis), and 18 from rectum (RE-NET, 3 primary and 15 metastasis). Overall design: 212 GEP-NET samples with cellularity >70% were analyzed. Total RNA was isolated and RNA integrity assayed by a 2100 Bioanalyzer (Agilent Technologies). High-quality total RNA samples, with RIN (RNA integrity number) above 7, were processed by TruSeq library preparation for RNA-Seq profiling (Illumina). For each sample, a minimum of 30 million 100bp single-end reads or 90 million 100bp paired-end reads were sequenced on the Illumina HiSeq2500 platform. RNA-Seq reads were mapped to the Homo sapiens assembly 19 reference genome, using Bowtie. Reads mapping to known genes, based on Entrez Gene identifiers, were then counted using the GenomicFeatures R-system package (Bioconductor).