Got different size PCR products from chIP - (Jul/26/2006 )

Does any one know why I got different size of input and antibody PCR products from chIP?

Can we see your gel? Can it be you have your product and primer dimers?

This is my gel. All the input bands are smaller than antibody added bands.

which one is of expected size?

It looks like the ChIPed DNA migrates slower than the input or retarded by something. They may have the same size. Have you purified your ChIP DNA using either phenol extraction and ethanol precipitation or using a kit?

Do you have an idea of which is the size of the band you are supposed to amplify? As pcrman said: didi you purify your DNA? I would suggest you to use the kit I'm using because it gives me very good results (Qiagen DNeasy tissue kit)

Thank you so much for all your suggestions.
Acturally,I purified my ChIP DNA using phenol extraction and ethanol precipitation .I will try Qiagen DNeasy tissue kit.

Qiagen PCR purification kit also works well for ChIP DNA. After reverse crosslinking and digestion with proteinase K and RNase A, then apply your samples to the kit.