Transcriptomic analysis of human gastric cancer and normal epithelial tissues

Small nucleolar RNAs (snoRNAs) are a highly conserved category of non-coding RNAs that play emerging roles in tumorigenesis and aggressiveness. However, the functions and underlying mechanisms of snoRNAs in regulating gastric cancer progression remain elusive. We identify SNORA37 as a driver of alternative splicing and gastric cancer progression. To explore the expression profiles of snoRNAs, we employed the Illumina HiSeq X Ten as a discovery platform to analyze the transcriptome profiling in three pairs of gastric cancer and corresponding normal epithelial specimens. The results showed 15 differentially expressed snoRNAs in gastric cancer tissues, including 9 up-regulated and 6 down-regulated snoRNAs. Meanwhile, 2204 alternative splicing events were also discovered in gastric cancer tissues compared to those in adjacent normal epithelial tissues. Furthermore, we validated the RNA-seq results by real-time RT-PCR with high identity. Overall, our results provided fundamental information about the transcriptomic changes in human gastric cancer tissues, and these findings will help us understand the pathogenesis of cancer progression. Total RNA of tissues was extracted using the TRIzol® reagent according to the manufacturer's instructions. RNA concentration was measured using a Qubit® RNA Assay Kit with a Qubit® 2.0 Fluorometer (Life Technologies, Inc.), and integrity was assessed using the RNA Nano 6000 Assay Kit with a Bioanalyzer 2100 system (Agilent Technologies, CA). Library preparation and transcriptome sequencing on an Illumina HiSeq X Ten platform were performed by Wuhan SeqHealth Technology Co., Ltd. (Wuhan, China), and 100 bp paired-end reads were generated. HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. Alternative splicing events were detected by using rMATS (version 3.2.5) with a FDR value less than 0.05.