Liang et al. BMC Genomics 2011, 12:231 http://www.biomedcentral.com/1471-2164/12/231 Page 3 of 16 Scaled log2 ratio CpG island Transcript Transcript Start Liver 1 Liver 2 ES 1 ES 2 Testis 1 Testis 2 Sequenom Methylation Analysis 0 100% Not analyzed Liver 1 Liver 2 ES 1 ES 2 Testis 1 Testis 2 Methylated Testis Stk31 Figure 1 Comparison of methylation data between MeDIP/NimbleGen Promoter + CpGi Array and Sequenom MassArray: Stk31 CpGi promoter region. The Stk31 gene region with a CpGi promoter region that is methylated in the liver, but not in ES or testis cells. The box indicates the position of the methylation peak in the liver that overlaps with the CpGi promoter region analyzed by Sequenom. In the epigram of Sequenom methylation analysis shown at the bottom panel, the blue circles indicate 100% methylation, green circles indicate around 50% methylation and yellow circles indicate 0% methylation. The results from biological duplicate samples are shown. The bottom lane (Sequenom Methylation Analysis) shows the results of analysis of testis DNA after in vitro methylation using M. Sss1 methylase (New England Biolabs). almost 5,000 adult T-DMRs that are present in one or more of the examined adult tissues but are absent in one or more tissues, whereas there are only 460 methy- lated regions that are common to all four tissues. There are a relatively high number of T-DMRs unique to testis (1,294) and a relatively low number unique to brain (285). Most of the T-DMRs (69.3%) are located within non-CpGi promoter regions, but 30.7% are within CpGi regions, among which 13.7% are within CpGi promoter regions and 17% are in non-promoter CpGi regions (intragenic and intergenic CpGi regions). Within the dif- ferent tissues there are some notable differences. For