Methylation-specific polymerase chain reaction (MS-PCR) is a more rapid way to detect changes in DNA methylation than is bisulfite sequencing. In addition, by incorporating some basic automation, samples can be prepared and analyzed in a 96-well plate format. The method can be used either quantitatively (qRT-PCR-based MethyLight) or qualitatively (using agarose gels) to detect changes in DNA methylation; both are described in this protocol.
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