A precipitate appears after 65ºC treatment in ChIP protocol - (Oct/30/2014 )

Hi,

When I treat my samples (DNA Input, and a control for chromatin size, mainly) after sonication at 65ºC for 16 hours, I can see a small layer of "something" that has precipitated. What is that? Is that normal or a bad signal related with the protocol? May I discard it or resuspend it for DNA purification?. I am starting to use Zymo Columns for DNA purification and I don't know if I may keep it by resuspension (it is hard to resuspend).

Thank you very much in advance

I couldn't tell you exactly what that is. Are you treating with proteinase K also? It could just be insoulbe lysate and that's why it's not resuspending. When I purify DNA to check sonication efficiency I usually boil the sample for 10mins, rnase treat for 1 hour at 37c, boil again for 10mins and proteinase K treat for an hour 55c then I would put the sample through a column. This is the only method that really worked nicely for me. It's much faster than decrosslinking overnight but when doing the chips I decroslink overnight at 65c.