CHIP / Is it normal to see pellet after the DNA purification? - (Jul/21/2008 )

Hello

I m doing CHIP assays and during DNA purification and after treatment with 100 % and 70% ethanol and centrifugation I see pellet in all my samples. Is this normal to see the pellet-DNA? I am thinking that maybe I should reduce the amount of chromatin that I incubate with the antibody.

Thanks in advance

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When I used to do ChIP this way I could rarely see a pellet unless I used a carrier like linear acrylamide. You might be using too much or you might have a contaminant (like bicarbonate, if you are using this in your elution buffer).

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I think it's not a big deal. Or you have too much salt in your pellet. Why not wash it again with 70% ethanol? And see what you get.

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Thanks for replying. It must be the salt (although I do a wash with 70% ethanol) because my no antibody sample has the pelet, but I get no zone when I do the PCR.

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