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We are trying to troubleshoot contamination issues that we are having in our ChIP-seq experiments. It seems that recently we have been sequencing constructs that have been cloned in the lab in other experiments in our IPd samples. We are trying to decided how to proceed, how many precautions to take. We are interested in hearing what others do. Do you have a designated area, designated equipment, etc.? At what point in the procedure do you begin to use this designated area? As early as the IP or just at the amplification step? Any and all of your thoughts and suggestions would be greatly appreciated!
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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