Integrative omics analysis in HCC samples [lncRNA expression]

38 paires of tumor tissues and adjacent non-tumor tissues from HCC patients The number of known lncRNAs increased sharply upon the tiling microarrays and RNA-sequencing were applied to identify lncRNAs. However, only about a dozen of lncRNAs have been well characterized and demonstrated to be tightly associated with development and progression of HCC. A major challenge remains to identify functional lncRNAs associated with HCC. Previous reports mainly selected differentially expressed lncRNAs in cancer tissue or cell lines as candidates for further validation and characterizing. Here, based on mRNA and lncRNA gene expression profiles data collected from tumor and adjacent normal tissues of thirty-eight HCC patients, we adapted integrative omics strategy to identify HCC-associated lncRNAs. To systematically discover functional lncRNAs in HCC, we recruited tumor tissues and paired adjacent non-tumor tissues from thirty-eight patients of primary HCC undergoing surgery and acquired the protein-coding genes and lncRNAs expression profiles through microarray assay. Particular attention was paid to obtain the “core” part of the tumor mass to avoid the adjacent non-tumor tissues, each specimen was reviewed by a board-certified pathologist to confirm that the frozen sections was histological consistent with tumor or non-tumor tissues, and tumor sections had to contain more than 70% tumor cell nuclei and less than 20% necrosis. Tissues were kept frozen in liquid nitrogen immediately after separation until they were used for molecular studies. This study was performed with the approval of the Medical Ethical Committee of Beijing Institute of Radiation Medicine (Beijing, China). Please note that total RNAs of 38 adjacent non-tumor tissues were mixed with equal amount and used as the common reference labelled with cy5.