Crassostrea virginica mantle gDNA that had previously been isolated on 20181114 was evaluated for integrity via agaroase gel yesterday (20190305). Everything looked pretty good, so proceeded with shearing in preparation for MBD enrichment.
Aliquoted 2500ng of DNA in a final volume of 100uL of each sample in 0.5mL snap cap (polypropylene) tubes for shearing in the Seeb Lab sonicator (Diagenode Bioruptor 300) with the following settings:
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30 cycles
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30 seconds on
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30 seconds off
Calculations for DNA dilutions are here (Google Sheet):
Ideally, this will shear DNA to a target size around 300bp.
After shearing, ran all samples on the Bionalyzer 2100 (Agilent) using a DNA 12000 chip according to manufacturer’s protocol.
RESULTS
Date files (XAD - requires Windows and 2100 Expert software):
Electropherograms:
Overall, shearing was decent, albeit, the majority of the resulting fragementation is a tad bit on the larger side (e.g. ~500bp). However, all of these samples will be subjected to bisulfite conversion which should fragment the DNA further, so things should be fine.