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Old 11-09-2013, 07:07 AM   #1
MWN
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Default High Mol. Weight Peak from Library on Agilent Bioanalyzer

I made some TruSeq DNA library using Illumina adapter from sonicated FFPE DNA and ran the amplified library after AMPure purification. I have seen the extra high molecular weight peak > 1000 bp. The position of peak looks different from the extra peak described in some earlier posts, which is double and triple in the size of expected peak.
I did not do a size selection. I am going to do hybridization enrichment using the libraries. Just wander about the impact on on-target rate.
Do you have any explanation on the extra peak? Uneven sonication for FFPE DNA even I observed a main 150 bp peak? A running artifact of Bioanalyzer? Concatemer?
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Old 11-09-2013, 07:46 AM   #2
MWN
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I like the idea of ssDNA heterduplex as discussed in
http://seqanswers.com/forums/showthread.php?t=559
Perhaps increasing primer concentrations and/or reducing PCR cycles will help.
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