Genome-wide DNA methylation profiling of KYSE180 cells transfected with HOTAIR vector using Illumina HumanMethylation 450 arrays. Homo sapiens

To analysis of the effect of HOTAIR on global DNA methylation in KYSE180 esophageal cancer cell line, genome-scale DNA methylation was analyzed in a pair of esophageal cancer cell lines, KYSE180 cells stably transfected with HOTAIR and control KYSE180 cells. The results from genome-wide DNA methylation analysis indicate that hypermethylation occurs more frequently than hypomethylation after stably ectopic expressing HOTAIR in KYSE180 cells. Overall design: DNA was quantified by Quant-iT PicoGreen dsDNA Reagent (Invitrogen) and the integrity was analyzed in a 1.3% agarose gel. Bisulfite conversion of 600 ng of each sample was perform according to the manufacture's recommendation for Illumina Infinium Assay. Effective bisulphite conversion was checked for three controls that were converted simultaneously with the samples. 4 ul of bisulfite converted DNA were used to hybridize on Infinium HumanMethylation 450 BeadChip, following Illumina Infinium HD Methylation protocol. Chip analysis was performed using Illumina HiScan SQ fluorescent scanner. The intensities of the images are extracted using GenomeStudio (2010.3) Methylation module (1.8.5) software. Methylation score of each CpG is represented as beta value. For pairwise differential methylation analysis, the difference of two biological replicates of the ESCC cell lines KYSE180 and KYSE180_HOTAIR was calculated.