We recently collected genomic DNA from a screen.  We did PCR using about 3-5ug of DNA per well on a 96-well plate and got 5ml of PCR product to purify.  So what to do next to purify the 300bp PCR band for Hi-seq?  

Do you do PCR purification followed by gel separation?  I was wondering whether the large amount of genomic DNA (300-500ug) in the PCR mixture will overload the Qiagen columns, which has a binding capacity of 10ug.   Or do you use ethanol/sodium acetate to precipitate both genomic DNA and PCR products, and then do gel separation? 

Any advise would be much appreciated!

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