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Old 06-06-2011, 02:14 PM   #4
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Location: St. Louis

Join Date: Dec 2010
Posts: 535

If the PCR works then the adapter ligation had to work to some extent.

Is this an Illumina library prep? I've routinely used 15-30 minute adapter ligations with no issues.

How much starting material did you use? And what manual did you follow? Were there any modifications?

SYBR gold stains single-stranded DNA a lot better than EtBr, I believe, but otherwise I can't think of a reason why it would run differently.
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