sonication for ChIP - protocols for sonication in a water bath for ChIP (Nov/01/2004 )
I would like to sonicate eukaryotic cells in order to perform chromatin immunoprecipitation. Our sonicator is a warter bath- sonicator. Regulation of the amplitude or any other parameters is not possible. I can set only the time of the sonication (not the rests between them). I would like to receive advises about sonication protocols for ChIP with sonicators of that type. Thank you!
I have not worked with that type of sonicator. However, no matter what machine you use, you should run a preliminary experiment to determine the optimal condition. You can use the same number of cells you would use for formal experiment and do the sonication with different settings, then reverse crosslink the DNA, phenol/chloroform purify it and run a gel to see which setting give the best result.
During the sonication, keep your sample in a ice-water bath to reduce heat.
The sonicator you have is mainly used for cleaning. It will most likely not be strong enough to shear DNA to the base pair range you need. If you find that this is the case, you may want to check out actual sonicators as opposed to ultrasonic cleaning baths. The following is a link to Misonix, who sells sonicators for this application and can provide a lot of support for doing ChIP assay.