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.
I agree with the other Kevin. It greatly depends on the sonication device you use, so which one is it?
For probe sonicators (tip width 2-3mm) I used a Bandelin Sonopuls GM70 for 15 sonication cycles (with cooling on ice in between) of 15s at 90% cycle (90% of the 15s are actual sonication), 40% power output. With this I obtained 200-300 bp fragments in a suspension of 1µg/µL chromatin in 1% SDS. So, I guess, 10-12 cycles would be enough for you. As Poppy said, you need to optimise the sonication duration.
For the Diagenode Bioruptor NextGen, I used about 12 cycles of 30s ON/30s OFF at 4 deg.C with a water change every 4 cycles.
If you need a detailed protocol, let me know.
Best,
Kevin
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