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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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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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