I transferred 8ug (136uL) of Crassotrea virginica gDNA (isolated earlier today) to two separate 1.7mL snap cap tubes for sonication/shearing.
I performed shearing at the NOAA Northwest Fisheries Science Center, using the Qsonica Q800R. Mackenzie Gavery assisted me.
Target fragment size was ~500bp.
Samples were run at the same time with the following settings:
- 10 minutes
- 30 seconds on, 30 seconds off
- 25% power
After sonication, fragmentation was assessed using the Seeb Lab’s Bioanlyzer 2100 (Agilent) and the DNA 12000 Chip Kit (Agilent). NOTE: All of the reagents and the chips were past their expiration dates (most in June 2016).
Agilent 2100 Bioanalyzer Expert file (XAD): 2100 expert_DNA 12000_DE72902486_2017-12-11_13-45-31.xad
Fragmentation was successful, and pretty consistent.
Both samples appear to have an average fragment size of ~420bp. Will proceed with MeDIP, once reagents are received.