Does anyone have a suggestion how to obtain most of information about DNA methylation (prefferably genome wide) from a limited amount of DNA - we're talking about 200 ng. Since this is primary tissue and not cultured cells, I can't have more than that. I was initially planning to do MeDIP-seq (actually MBD-seq, aka MIRA-seq) but after measuring the concentration and concluding I have just a little more than 200 ng total (not per ul), I'm wondering if I'll get enough enrichment to make a library from that. The only options that come to my mind are:
1. do MeDIP (MBD), but amplify the library several cycles more (although this brings the risk of bias)
2. BS-seq??? Is 200 ng enough??
3. Infinium array?? What is the down limit??
Thanks a lot for any suggestions!
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