I am wondering how can I control my converted DNA! I converted my DNA with bisulfite then I amplified the converted DNA with specific primers of BSP and purified my product and finally sequenced the product! In which step should I control my DNA? And what is the protocol? thanks for any advice.

  • $\begingroup$ Wait, so you're looking to retroactively add controls (not feasible) or add controls for future processing? If you already went through the entire process with no controls, I'd be uncertain as to how you're convinced the process went smoothly to begin with. $\endgroup$ – CKM Jun 1 '18 at 21:43
  • $\begingroup$ To initially optimize PCR conditions: Mix 50% methylated bisulphite-converted DNA (50 M) and 50% bisulphite-converted unmethylated DNA (50 U) to test for proportional PCR amplification with bisulphite conversion specific primers and PCR master mix. This is from nature protocol,I dont know how should I control the PCR product because we just have one paired primers and there is no difference between methylated and unmethylated product! should I design another primers that bind to CPG Island? $\endgroup$ – shabnaz Jun 2 '18 at 6:00

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