ChIP sonication Input Agarose gel - (Oct/26/2005 )

Hi,

I'm having an odd experience with Agrose gel electrophoresis. After my ChIP sonication, I aliquot a 100ul out, did the reverse crosslink, phenol extraction, and run a gel. The fragment size look perfect with average 500bp~1kb. Then I went ahead to purified it with Qiaquick kit. After that, I run a gel again. Weird thing happened, the fragment size now looks much bigger, about 2~3kb.
I tried several times with other samples. Even after purification, the size keeps changing. Such as, for same sample, It will look different on the gel from 30' ago on another gel.
Has anyone had the same problem? I'm so frustrated. Help!

Thank!

xyz

Did you treat the samples with RNase? You might be seeing the RNA in once case, and the DNA in the other...just a though...