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Pippin Prep for RNA?
For those of you familiar with the Pippin Prep, currently used for automated DNA size selection and band capture, your thoughts on whether or not Sage Science should commercialize a series of cassettes for RNA too? What RNA applications are of greatest interest? Thanks for your thoughts and help!
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If these were denaturing gels that would work on strand denatured DNA as well, I think they would be very useful.
Subtext of a recent thread
is that short ssDNA/adapters may be annealing to longer library products -- preventing their removal via size-selection on dsDNA products. If the size selection were done on ssDNA there is no where for these short contaminants to "hide" and they should be removed.
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Phillip -
Phillip - We can manufacture any standard precast gel chemistry, including denaturing gels that should enable this. Thanks for the link and the idea. I will discuss it with our team.
GaryComment
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we would be interested in RNA cassettesComment
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Seems like you have a ready-made list of beta testers right here in this very thread!
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I agree with pmiguel. We see effects similar to the ones in the cited thread, and I think a denaturing gel to size select ssDNA fragments would be very helpful.Comment
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RNA on Pippin Prep
Sounds good everyone. I will discuss this application with the team and Sage. Thanks for your thoughts, interest and willingness to test RNA cassettes. - GaryComment
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Yes, send them to Purdue and we will test them on our Pippin prep.
I think there are lots of otherwise perfectly good libraries that are getting hosed by small "hitchhiker" amplicons that can't be removed with double-stranded size-selection methods. Maddening!
Well, there is always normal denaturing PAGE. But it always seems like such a hassle to extract the sample from polyacrylamide gels.
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PhillipComment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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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...
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