A quick update on the side project since I'm procrastinating writing a short fellowship grant...  About a month ago I realized why my sonications were not working.  It turns out that when I moved to Florida from my Graduate work at Iowa, I didn't update my ChIP protocol to reflect a reagent change.  At Iowa, we had been using 16% paraformaldehyde as our crosslinking agent.  Unfortunately, I was throwing 37% formaldehyde in there instead meaning that I was way over crosslinking my samples which explains why I was having such a hard time shearing the DNA.  I practically cemented all of the proteins in the cell together.  Anyway, I had some more downtime this week waiting for a new batch of cells to grow for a massive timecourse experiment involving 3 timepoints and 10 different immunoprecipitations for cool proteins.  I used this waiting period to optimize sonication conditions with the fancy programmable sonicator.

Misonix 4000, power 60, 30s on 1 min off. Numbers above lanes equals the number of cycles

As you can see, I'm getting the accumulation of a nice smear at exactly the right fragment size, 200bp, for a ChIP-Seq experiment.  Maybe in a future post I'll do a write up about how to turn these samples into a multiplexed library for sequencing on a GAIIx or Hi-Seq machine.  I'm really not looking forward to sonicating 30 samples and prepping those libraries...