I need to run a gel before sequencing it. What percent gel should I run it on, and what size ladder is adequate?
Dear O. Marte,
You have to pay attention for the scientific jargon used in your question as it is so critical for scientists to understand you question aim when reading it: Genomic DNA is run on a gel and not the inverse case. Also, it is the DNA that is targeted for sequencing and not the gel!!!
Anyway, usually the genomic DNA ranges from ~30 to 50 kb in size. For this, a low agarose gel concentration will do (i.e 0.8 %), you may even use 1 % or 1.5 %. It will not really matter for such kind of electrophoretic migration, unlike smaller DNA fragment when you have to increase the gel concentration (restriction fragments analyses for example). Personally, I don't use the marker for the case of Genomic DNA, but this will be necessary for PCR products (quality assessing). However, if you feel the necessity of ladder use, you may include a molecular weight markers from 10 kb to 50 bp in length.
Good luck!
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