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Old 07-16-2011, 12:32 PM   #21
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Location: Purdue University, West Lafayette, Indiana

Join Date: Aug 2008
Posts: 2,315

Hi Eli,
In principle it should be possible to skip amplification altogether if you do qPCR on the unamplified library.
We got post-amplification yields in some cases that were less than pre-amplification. (These were DNA libraries.) Probably an issue with the ampure reaction clean-up. The libraries went on to produce plenty of sequence and none of them looked "bottomed out".
This is all just stuff to be aware of, in my opinion. The Illumina protocol should be fine in many cases. Might even be worth using their spike in controls. I personally an not yet able to get over the horror of adding extraneous DNA during library construction. But that is just me...

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