Illumina HiSeq 4000 sequencing; Transcriptome profiling of human urothelial carcinoma cell lines RT-112, VM-Cub-1, SW1710, UMUC3 and a benign urothelial control HBLAK engineered to stably express HDAC5 against their vector control
Transcriptome profiling of human urothelial carcinoma cell lines RT-112, VM-Cub-1, SW1710, UMUC3 and a benign urothelial control HBLAK engineered to stably express HDAC5 against their vector control
To study the effect of HDAC5 overexpression on selected cell lines, quadruplicates from individual culture dishes were prepared from RT112, VM-Cub-1, SW1710, and UM-UC-3 cells expressing HDAC5 and vector controls as well as corresponding and HBLAK vector-only cells.  Cells were harvested with Qiazol (Qiagen, Hilden, Germany) and lysates were stored at −80 °C. Total RNA was then isolated by the Qiagen RNeasy Mini Kit (Qiagen, Hilden, Germany). RNA quality was checked by spectrophotometry. Total RNA samples used for transcriptome analyses were quantified (Qubit RNA HS Assay, Thermo Fisher Scientific) and quality measured by capillary electrophoresis using the Fragment Analyzer and the Total RNA Standard Sensitivity Assay (Agilent Technologies, Santa Clara, CA, USA). All samples in this study showed high quality RNA Quality Numbers (RQN; mean = 9.8). The library preparation was performed according to the manufacturer's protocol using the 'TruSeq Stranded mRNA Library Prep Kit' from Illumina®. Briefly, 250 ng total RNA were used for mRNA capturing, fragmentation, the synthesis of cDNA, adapter ligation and library amplification.
Experimental Factor: cell line
VM-Cub-1
Experimental Factor: genotype
empty vector