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Old 11-05-2012, 07:29 AM   #2
Location: USA

Join Date: Nov 2011
Posts: 17
Default PCR clean-up for sequencing

Originally Posted by alpinedna View Post
Hi All-

I am generating PCR product of DNA sampled from water (environmental DNA). The amplicons range in size from 650-790 bp. This is the input DNA I would like to use for the Nextera XT sample prep kit from Illumina. I have asked their tech support with out much help on this topic...

If I have a nice clean and tight PCR band on a gel, is there any reason why one can not use exo and sap to "clean" the PCRs before diluting the DNA to 1 ng/uL?

I have over 600 PCRs and doing gel extraction or even a magnetic bead clean up is too much time and money.

Given how much money you are about to spend sequencing these samples, and the potential precious nature of them, I would not risk it. Do the magnetic bead clean-up! If you do it in a 96-well plate it shouldn't take too much time at all. A simple clean-up with 0.6x bead volume would suffice.
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