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Old 08-21-2015, 11:39 AM   #2
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Location: Purdue University, West Lafayette, Indiana

Join Date: Aug 2008
Posts: 2,317

The 200 vs 600 bp result, I would tend to blame on different buffer/salt concentrations in the marker( 1KB ladder -- my favorite) and the samples.

Okay, for the high molecular weight stuff visible on the bioanalyzer chip, but not your gel -- I would have to reach into deep speculation, so be forewarned... How about, that material is genomic DNA, single stranded after many cycles of denaturation during in PCR. Very poor visibility of single stranded DNA with the ethidium bromide in your gel, but a high sensitivity chip will visualize it just fine.

Irritatingly, when I originally asked whether single-stranded DNA/RNA would be visible on a high sensitivity chip, Agilient tech support answer that I should not use it for that purpose. Thanks Agilent.
Later experimentation showed that single stranded molecules were visible and migrated aberrantly with respect to their actual length. See here for more details.
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