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Hi all,
I've been trying to validate results from MBD-Seq. I noticed that in some of my bound fractions (none of the corresponding inputs) there is a slight shift in the melt curve, maybe .7 degrees. I did phenol-chloroform clean up and etoh precipitation after MBD pulldown, but my best guess is that something is still bound to the DNA. Has anyone else experienced this (we see it sometimes in ChIP qPCR too, especially the Igg fraction) and what have you done to resolve it.
I've been trying to validate results from MBD-Seq. I noticed that in some of my bound fractions (none of the corresponding inputs) there is a slight shift in the melt curve, maybe .7 degrees. I did phenol-chloroform clean up and etoh precipitation after MBD pulldown, but my best guess is that something is still bound to the DNA. Has anyone else experienced this (we see it sometimes in ChIP qPCR too, especially the Igg fraction) and what have you done to resolve it.