Input reverse cross linking - (Apr/21/2012 )

I am performing a ChIP assay using the R&D kit. According to the manufacturers protocol, the samples (antibody IP and IgG IP) are washed after the antibody incubation and then boiled with a Chelating Resin solution for 10 minutes. This basically is the final step before DNA purification using a kit. I am assuming this boiling step involves reverse cross linking for the samples. My question is, how do I reverse cross link the input DNA that I have set aside previously? The kit nowhere says anything about the processing of input DNA. Can I add Chelating Resin solution to the input and treat likewise or do I follow a traditional 65 degrees treatment (though I am reluctant to use different methods for the input and samples).

Any help or experience with a such a problem will be welcome....

In my experience, boiling in either chelex or high pH Tris-EDTA buffers (they're essentially equivalent) is sufficient for reversal of crosslinking of input samples.