Optimizing a Dual Fixation Protocol to Study Protein Complexes Binding to Chromatin in vivo
Here, we tested a Covaris-developed chromatin sample preparation protocol to effectively study the interactions of protein complexes associated with chromatin. An initial crosslinking cocktail was used prior to carrying out the Covaris truChIP® Chromatin Shearing Protocol. Relative to a standard single fixation method, this Covaris-developed protocol enhanced signal over background at known binding sites for members of the BAF complex including the ATPase subunit, BRG1 4. In this application note, we provide shearing profiles, evaluate epitope integrity at each shearing time, and ChIP-qPCR results obtained using the single step formaldehyde fixation and the dual crosslinking protocol.