Originally posted by ikripp
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But native DNA electrophoresis hides a critical issue we see with some substantial fraction of amplicon pools submitted to us. We see cases where strand-denatured assays (eg, heat denature the sample and run it on an RNA pico chip) show lots of short fragments that barely show up on a non-denaturing (DNA High Sensitivity). So I presume the short fragments are annealed to full-length fragments.
We mainly decided to start using pico chips to check libraries for NovaSeq runs -- index hopping being potentiated by primers/primer-dimers -- or at least that is what we are told. But then we saw that this assay could predict bad amplicon pool runs we started using it for that purpose as well.
I don't see why you couldn't develop the same denatured DNA run on an RNA assay for the multiNA. We just heat the DNA to 96oC for 2 minutes in a thermal cycler with a heated lid to prevent evaporation. Then we "snap cool" the DNA in a wet ice bath before loading.
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Phillip
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Phillip
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