I am trying to shear DNA from PCR using Covaris S2 for NGS lib prep. My amplicons size range from 1 to 4kb and I need to shear them to 400bp. I couldn't find a protocol for this situation. Can anyone out there help?
Sorry for the late response, I haven't check this post for ages.
I did find a solution. I used the microTUBE AFA Fiber Pre-Slit Snap-Cap 6x16mm (25) 520045 http://covaris.corecommerce.com/microTUBE-AFA-Fiber-Pre-Slit-Snap-Cap-6x16mm-25-p23.html
and the Holder microTUBE 500114http://covaris.corecommerce.com/Accessories/S220/Holder-microTUBE-p31.html
I loaded 50 uL of sample in the tube and run on S2 Covaris using the settings below:
Intensity - 5
duty cycle - 5%
cycles per burst - 200
treatment time - 120 seconds
the results look pretty good ( see attached photo).