Many DNA extraction protocols warn against vortexing during sample preparation as it tends to shear DNA into smaller fragments. This makes sense if the downstream application requires high molecular weight DNA - but vortexing is really handy. Illumina sequencing doesn't require high molecular weight DNA (shearing is part of the library preparation) - but I notice people still taking pains to avoid vortexing during extractions that are intended for Illumina sequencing. Is there a compelling reason to do so, or is it more likely a case of not customizing a generalized protocol to the specific needs of the situation.
Hi Eric,
Your instinct is correct and no, you do not need to avoid shearing during DNA preparation for samples that will be used for Illumina sequencing.
Those are steps that you should take if your DNA samples are intended to be sequenced using long read platforms, such as PacBio and Nanopore.
Best,
Sheng
Hi Eric,
I think usually people avoiding shearing the DNA during extraction as more for record-keeping/troubleshooting purposes. I like to keep DNA intact during extracton so that i can QC my extraction and make sure I have good quality DNA yield/starting material. Downstream, yes I shear for library prep but there is a record that you chose to shear and that your starting material/extraction went well. If you accidentally shear during DNA extraction and need to troubleshoot later if your library happens not to be of good quality, you can't tell if your extraction yielded degraded DNA or did you accidentally start shearing your DNA. It's jst another factor you can rule out for troubleshooting, in my opinion.
Best,
Angela
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