ChIP Assay and sonicators - ChIP assay question (Sep/21/2004 )
I am about to begin some ChIP assays on muscle tissue and hope to use this assay relatively frequently over the next few years. Thus, I was wondering what type of sonicator do most of you use for such assays. It seems that the standard is the Branson 250? probe sonicator. What about a bath sonicator? Have any of you had much success with the bath style sonicator? I have seen a few published protocols using bath sonicators, but most use probe sonicators for fragmenting the DNA.
Any help would be most appreciated.
We use a Fisher 500 Sonic Dismembrator which is well situated for ChIP sonication.
Here is the link to the product page
Thanks. The one you mention has 500 watts capacity. Do you think that is necessary? There are others that function at 100 watts max. I'm trying to find the best item at the lowest cost.
Again, Thanks very much for the info.
Misonix makes a 100 watt sonicator that can be used for DNA shearing. Here is the product page:
However, the advantage of using a more powerful unit (Misonix also makes a 600 watt model) is that usually, those units are programmable. Reproducibility is very important when doing Chip Assays and the lower units are typically controlled manually.
Normal ultrasonic bath sonicators are not strong enough to fragment DNA. However, cuphorns can be used to sonicated sealed vessels in a similar way as a bath, expect that the sonication is much stronger. The following is a link to the product page for cup horns. DNA shearing has been done in cuphorns before.
We recently purchased a Fisher/Branson 500 sonicator and the cup horn attachment. However, I have been unable to sheer the chromatin with it. What settings do you use? What volume is your DNA in? Do you use eppendorf microfuge tubes? Also, even with the amplitude set at 100%, the graph on the front shows 50% amplitude while it is running. Any advice or assistance would be greatly appreciated! I just spent several thousand dollars on a machine that isn't working for me!