Checked DNA integrity of the Crassostrea virginica mantle gDNA I isolated on 20181114 in preparation for MBD enrichment. Detailed sample info and sample processing (including calculations for MBD enrichment using the MethylMiner Kit) are here (Google Sheet):
Loaded 100ng of each sample on a 0.8% agarose, 1X Low TAE gel with ethidium bromide. Each sample was mixed with 3uL of 6x loading dye and brought up to 18uL with nuclease-free H2O. Gel was run for ~2hrs @ 100V. Used two ladders in a (failed) attempt to accurately assess gDNA size:
The idea being that the HighRange ladder would handle high integrity gDNA molecular weight, while the DNA Ladder Mix would handle any degraded DNA and/or RNA present.
Wish I had wiped the dust off of the protective UV screen before snapping the pic…
Almost all of the samples look pretty good. The exceptions are:
These three samples appear to be degraded (evidenced by lack of prominent, high molecular weight band).
Also, just to add info regarding the ladders, the HighRange ladder’s smallest band is ~10kbp and the largest is ~48kbp.
The DNA Ladder Mix’s smallest band is ~100bp and the largest is ~10kbp.
The DNA Ladder Mix ran from the upper lane into the lane below it, giving the appearance of a continuous ladder; however, it is just overlapping the DNA Ladder Mix in the lane below. Additionally, the HighRange ladder did not have sufficient time to separate out in to defined bands - probably needed a couple of more hours!
Will proceed with shearing tomorrow morning and then MBD enrichment.