I'm going to use abcam's ChIP assay protocol. At the sonication step it just talk about times. (5-10-15 min. etc.) But there's nothing about power or cycle. What do you prefer for 500-600 bp dna fragments? Thank you.
I agree with the above (30s on 30s off pulse 10 times), but you will probably need to optimisatise this further as it will change depending on cell line, cell number and volume of buffer. It will also depend on your sonicator.
It really depends on the sonicator type (probe/cup), tube material, volume, concentration, etc. In general though, keep the power low and cycle short, especially with probe type sonicators (eg. 50%, 1s/1s). This will minimize heating and aeration. However, I've used a cup type before with circulating, chilled water, and I used 100% power for several seconds at a time.
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