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Old 07-23-2014, 08:48 AM   #4
Location: Missoula, MT

Join Date: Jan 2014
Posts: 19

nucacidhunter - I did not see any DNA in the wells while looking at the gel on our UV transilluminator, but it would have been a bit difficult to see as I added so little sample to each well and the well indentations make it difficult to visualize remaining DNA. I was thinking that the quantification could have been inaccurate which could have resulted in over dilution of some of the samples, or perhaps they are so degraded that the smear is difficult to visualize when only using 100 ng. Thinking about it now, though...the high agarose gel percentage seems more likely to have been the problem. My mistake! Thanks for posting your thoughts on this!

I'll be running the rest of our samples (and rerunning these) on a new TapeStation that our Genomics Core just installed, so hopefully those results will be a bit more informative. I will post the results in case there is any current or future interest. We are waiting for Genomic DNA Screen Tapes to arrive so results will not be posted for at least a couple of days.

WhiteSeal - Thanks for your input! Very helpful. Do you perform DNA repair on your samples? (Assuming you don't because it wasn't mentioned, but want to double check.) What is your target insert size? Have you run your degraded gDNA samples on a gel / do they look similar to the samples that we can see on our gel? I have never worked with FFPE samples and am not familiar with how FFPE storage affects / damages DNA.
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