The issue with using a sonicator for chromatin shearing is with reproducibility of settings with different cell lines. All shearing conditions have to be optimized for each cell line which can be quite a laborious task in itself. Thermal damage is a major issue when dealing with smaller shearing sizes. Thermal denaturation of the the proteins, non-specific and biased shearing, thermal acetlyation issues are commonly noticed.
Have you heard of the Covaris AFA technology for non-contact, isothermal chromatin shearing? Here are some protocols using the Covaris technology http://covarisinc.co...a-shearing.html. Let me know if you need further details. Good luck.
I have a dumb question, in terms of sonication efficiency what is the difference between 30 sec on/30 sec off cycles and smaller cycles, like 15 sec on/15 sec off?
Back when I had access to a Misonix 3000 I remember watching the power output reading during sonication and noticed that power decreased from the beginning to the end of a pulse. It seemed the longer the pulse the lower the average power output (since there was more time for the power to decrease). I used 5 second pulses after that since the power output stayed around 100% of what I set it to. I don't know if this is the case with all sonicators though.