I was wondering if any used a Mandel to optimize their sonication settings for ChIP assay on stem cells. If so, what conditions do you suggest?
1 reply to this topic
Posted 21 September 2004 - 03:15 PM
You have to determine it empirically. Do a preliminary study using same number of cells and get the lysate after crosslinking, try different settings for sonication. then reverse crosslink and recover DNA and run an agarose gel to see what is the dominant size of sheared DNA. I do it for 4x10 s at a power setting of 3-4 using a Fisher 500 Sonic Dismembrator.