Library/ChIP preparation: Is it okay to use frozen samples or is it better to use fresh cells?

There should be no appreciable difference between using frozen vs fresh cells. That being said, since the ChIP method uses fixation to stabilize the DNA-protein interactions, it is advisable to first fix the cells for long term storage. There is the possibility that freeze thaw of frozen tissues or cells may alter interactions. – answered by Tovah Markowitz, Paul Schaughency, Vishal Koparde.