miRNAs regulated by HDAC6 in HCC

Revealing miRNAs that are regulated by HDAC6 overexpression in hepatocellular carcinoma miRNA expression profiling of 3 Hep3B_Mock and 3 Hep3B_HDAC6 was performed using GenoExplorer Microarray platform. 10 ug of total RNA was isolated from Hep3B HCC cell line that transfected pcDNA3.1_Mock or pcDNA3.1_HDAC6 and then labeled and hybridized to a to microRNA chip for analysis under optimized conditions. The arrays with hybridized targets were scanned using an Axon scanner and the scanned images were analyzed using GenePix® Pro 5.0 software (Axon Instruments) and spots of poor quality determined by visual inspection were also removed from further analysis. The resulting data, the average of 3 mean fluorescence signal intensities for each probe, collected from each array was submitted to the GenePlex 3.0 (Istech Inc. Seoul, Korea) database. Data were normalized using the method of quantile normalization and class-specific filtering.