I've been working on this project on and off for a few months now.  You may remember my previous post about attempting sonication trials.  Unfortunately, things in lab have been busy trying to get a new graduate student started and troubleshooting problems with other experiments so I haven't had as much time to devote to this project as I would like.  I've spent the past month or so trying to optimize my sonication conditions on a sonicator that's in my building, and I've gotten less than spectacular results (I've tested at least 10 different conditions on this machine ex: buffers, cell densities, sonication intensity, sonication duration).  I'm looking to break my DNA up into short 100-300 base pair fragments and previously I was only able to get them down to about 600.  I decided it was time to test other sonicators and here are the results.

It looks like the Fisher 100 is the way to go.  Although it's a completely manual system.  I think I could probably get the Misonix to the same level of sonication and the nice thing about that machine is that it's programmable, there aren't any knobs to turn and I don't have to sit there for an hour manually turning the machine on and off.  I have enough cells left to do one sequencing run (for my 6 proteins), so I think I'm going to do an experiment with the Fisher machine and then on my next set try to get the Misonix working better so I have that extra added level of experimental consistency.  I contacted an old collaborator of mine who used the same Misonix system for his experiments and he has given me his conditions (He used a power level of 7, which could make a huge difference).  I will say that I'm not all that happy with the amount of shearing.  When I did similar trials in graduate school I was able to completely get rid of the high molecular weight DNA and get a nice smear in the 100-500 range.  However, after looking through many sonication protocols, these results are not all that different from what other labs are using as input for their ChIP-seq experiments.  I just wish we had a Covaris available here :(