Next, we aimed to identify probes demethylated as a result of treatment in all experiments. Prolonged AZA and DAC treatment reduced the number of CHIR-99021 methylation high and medium probes by half. Principal component analysis indicated that AZA and DAC treatments had a global effect on CGI methylation with treated samples clustered away from those in mock-treated controls. Since DNMT inhibition results in a decrease in methylation across the genome it is possible that this may affect the accuracy of array-based estimates of methylation through implicit or explicit normalisation procedures. A comparison of log2-ratios for treated and control samples indicated that a reduction in methylation occurs at the vast majority of methylated regions and that AZA and DAC have very similar effects. However, probes with low log2-ratios in the control samples generally showed higher log2-ratios in treated samples. To determine the cause of this, we performed bisulfite sequencing for all 12 samples for regions showing an increase, and ones showing a decrease in methylation after treatment. This indicated that increases in log2- ratios after treatment at regions hypomethylated in control samples do not represent increases in methylation, and are likely caused by inappropriate normalization. More pleasingly however, this analysis shows a strong linear relationship between percent methylation and log2-ratios for regions with more than 10 of methylation. Importantly this relationship is identical across all samples thus validating our primary data. From the selected 52915 probes, only 2217 CGI probes had log2-ratios higher than 1.0 in control samples. Of these, a total of 880 and 803 probes were demethylated by at least one of, or both, drugs respectively. Probes representing promoter CGIs were over-represented whereas probes associated with gene bodies were underrepresented in the identified sets. In summary, our result shows that low-dose AZA and DAC treatment can effectively induce CGI demethylation at promoters, while methylation is maintained within gene bodies. We next examined the correlation between expression and methylation levels. We performed transcriptome analyses for both mock and drug treated SKM-1 cells. The level of methylation in individual islands was 944118-01-8 distributor summarised by t
