Hi,
In general, two pairs of primers are designed. One of these pairs that allows for amplification of the methylated DNA, and the second one promotes the amplification of the unmethylated DNA. Next, two qPCR reactions, such as the SYBR green based method or the Taqman probe method, are performed for each sample, and the relative methylation of the gene promoter is measured based on the difference of their Ct values.
Hi there,
have you considered targeted methyl sequencing? You can get preconfigured as well as custom panels that will give you base-specific and quantitative information tailored to your particular needs:
https://www.qiagen.com/us/products/discovery-and-translational-research/next-generation-sequencing/dna-methylation-analysis/qiaseq-targeted-methyl-custom-panels/
Best, Peter