Actually, our interpretation of the strange bioanalyzer traces after Pippen prep (the old one and with EthBr gel cassettes) was that the ethidiumbromide bound to the DNA leads to aberrant migration and reduced staining with the BA dye. After an additional PCR the the products produce the more or less the expected smears on a BA. We found that the Pippen prep fragments are amazingly accurate even for PCR libraries, despite the Y-adapters. We have not tried long 600 bp fragments, though. We are only using 2% cassettes at the moment.
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