ChIP for a transcriptional coactivator - (Apr/19/2013 )
You need SDS in order to shear your DNA. NP-40 does not do the job. 1% SDS is usually well tolerated in terms of epitope concervation. You should be careful not to over-sonicate, though. This could destroy your epitope and heat the proteins inducing degradation (always perform in ice-cold water). Also, make sure that there are no bubbles when you sonicate, as this could also destroy your epitope due to surface tension.
1. It is possible that 1% formaldehyde may not be able to attache the co-activator to the desired site. To address this problem, you can use protein-protein crossllinkers, which have longer arms, and then perform the 1% FA crosslinking to link the complex to the DNA. Alternatively, I use 4% Paraformaldehyde for 25min at RT and it works fine for me (do NOT exceed 30min).
2. You should use 1% SDS. Do not replace this component of your buffer.