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Old 04-05-2012, 07:46 AM   #2
ajthomas
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Location: Utah

Join Date: Mar 2010
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I imagine any normal gel purification method should work just fine. One caution I would offer, however, is to be sure you use SYBR Safe and a blue light box rather than a UV light box. Using UV for the gel cut will cause a lot of damage that may severely impact your sequencing results. I imagine you already are as it seems that many labs have already switched over, so this advice is just in case you haven't.

You could do it either before or after pooling your samples. The advantage of doing it after pooling is that it is much less work, as you state. The only problem that might arise is if you're trying to pool your samples stoichiometrically and you get a lot more primer dimers from some samples than others. In that case, samples that produce a lot of primer dimers will end up underrepresented in the final pool because the primer dimers will make up a larger fraction of the total from those samples before pooling. So, as long as you get similar results from all of your samples I would say do it after pooling.
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