Filamentous pellet when you sonicate in ChIP assay - (May/23/2007 )

what is that pellet? is it insoluble chromatin, is it protein?

im using a misonix S3000 sonicator with the cup horn, following the standard upstate ChIP kit protocol.

thanks

alvin

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Is the pellet, after sonication, close to the same size as your nuclear pellet before sonication? If so, this probably means your sonication isn't very efficient. It probably consists of minimally fragmented nuclei and associated cytoskeleton.

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no the pellet is somewhat smaller, i would say 30% of the original size (pre-sonication).

I sonicate in a cup horn, 15s on (power at 7.5 on a misonix S3000), with 2mins off, for 5 cycles (total sonication time of 1m15s).

It's strange because i see the same filamentous pellet floating during sonication whether i use a cup horn or a microtip probe (have to use the tip probe at 2.0, anything above that and you get instant foaming in 500ul of sonication buffer).

thanks for the reply, does anyone else see this pellet. Im using homogenized animal tissue BTW.

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