Transcriptome profiling of human bladder cancer cell line RT112 infected with lentivirus expressing either an shRNA targeting ELOVL6 (shE6) or a scrambled shRNA (shCtrl)

ELOVL6 is a member of mammalian fatty acid elongase family responsible for converting C16 saturated and monounsaturated fatty acids into C18 species. To investigate the role of ELOVL6 in human bladder cancer, we generated RT112 cells (a human bladder cancer cell line) infected with lentivirus expressing either an shRNA targeting ELOVL6 (shE6) or a scrambled shRNA (shCtrl). The aim of this experiment was to assess the effects of ELOVL6 knockdown on the transcriptome of human bladder cancer cells. Total RNA was extracted from RT112 cell lines stably expressing shControl (shCtrl, n=3), shELOVL6#1 (shE6#1, n=3), or shELOVL6#2 (shE6#1, n=3) that were cultured in E-MEM supplemented with 5% FBS for 48 hours. RNA amplification and RNA sequencing were outsourced to Takara Bio, Inc (Shiga, Japan). Mapped reads per gene (raw tag counts) were quantified as gene expression levels, and between-sample normalization of gene expression was performed on the raw count data using Genedata Profiler Genome software (Genedata).