Hi all,
I would like to test the effect of my treatment in the cell by assessing DNA methylation pattern. I would like to assay the alteration of DNA methylation of a specific gene set contains about 30 genes before (ctrl) and after the treatment (expt). whole genome methylome analysis may help me but that would be out of budget in my case. can anyone suggest me any technique which would be cost effective as well as reliable?
thanks and regards.
As you want to perform loci specific DNA methylation analysis i would recommend you three alternatives, BisPCR2 (NGS based targeted bisulfite sequencing) , Target enrichment bisulfite sequencing and finally EpiHRMAssay (qRT-based analysis of dna methylation changes.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4522100/
https://epigeneticsandchromatin.biomedcentral.com/articles/10.1186/s13072-016-0105-1
https://academic.oup.com/biomethods/article/2/1/bpw008/2957405/EpiHRMAssay-in-tube-and-in-silico-combined
There are different possibilities by mean of PCR based techniques.
Please, see my paper for this specif question:
https://www.ncbi.nlm.nih.gov/pubmed/24107250
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