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power and fragment length: how correlated are they?

ChIP DNA fragment sonication Foaming

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#1 SStamis

SStamis

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Posted 31 August 2012 - 11:56 AM

I'm running ChIP based off of a protocol in Nature Protocols "Fanelli et al, Vol 6. No. 12, 2011. p. 1905-1919" for ChIP of FFPE tissues. I've worked with ChIP before on cell culture, and found that I got horrible foaming unless I did many, many rounds of 10 sec pulses, 20% duty for infinity (probably more like 5 reps but it felt like infinity). This protocol combines MNase and sonication by doing Low power sonication, MNase, then high power sonication.
Well I get bad foaming on high power. I have a Branson 450 sonifier and I'm using a tapered 1/8" tip (though I have a stepped tip as well), 250µl volume in 1.5ml tube, and I can use a max output of 3 without foaming. So what is the advantage of high power sonication? Are the fragment lengths more consistant? Does it favor a larger or smaller fragment size (ie 100bp vs 1,000bp)? Is it just faster?
Like everyone else in the world, sonicating is the bane of my work life.





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