Since the effect of DNA methylation can be localized (e.g. within 200bp), probe-wise analyses were performed. We adopted a two-consecutive probe analysis (in which two adjacent probes detected the same direction of DNA methylation changes), in parallel with the average DNA methylation analysis, to verify regional changes in DNA methylation. Based on the linear mixed model, 1054 (FDR <30%) two-consecutive probe regions showed a significant difference in DNA methylation between the control and alcohol-treated NSCs during differentiation. Among those genes, alcohol decreased methylation of 681 and increased methylation of 373. These regional changes were also used as the basis for validating regional DNA methylation changes of specific genes using Sequenom.
