I'm trying to optimize sonication as part of my ChIP protocol. Instead of seeing a smear after sonication, I consistently see a single band (perhaps spread over only 200bp) sometimes at 200-400bp and once at 600-800bp. I just did a test to check the chromatin before sonication, and then after every burst, and interestingly I found that before sonication my DNA is only 300-400bp, and sonication (up to 10 bursts) has made no difference. Any suggestions??
I've uploaded a pic of the chromatin before sonication, and then after 1 burst, 2 bursts, etc.