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Old 08-02-2011, 04:58 AM   #2
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Location: Purdue University, West Lafayette, Indiana

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This is after PCR "enrichment"? If so, that is the multimeric or hetero-strand dimer product common in TruSeq libraries. It is called, variously, "bird nesting", "daisy chaining", "bubble products", etc. For my formulation of various possibilities, see:

The good news is that it usually is not a problem because most of the time the extra peak disappears after strand denaturation. You could try running a pico RNA chip on the DNA after denaturation. See:

But, should the sample strands re-anneal, you may get confusing results due to single stranded molecules running slower on Agilent chips than double stranded ones:

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