I treated my cells with 5 Azacytidine, then isolated the DNA and converted it using sodium bisulfite. I have BSP specific primers that i know works because I have used it to amplify regions on bisulfite converted DNA from non 5 Aza treated cells. I have tried designing different BSP primers, used various PCS conditions but nothing is working. I know 5 Aza inhibits DNMT's but are there any other side effects of 5 Aza that affects PCR amplification? If so, any suggestions on how to solve it?
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