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Old 07-08-2011, 11:51 AM   #1
SageSigh
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Question 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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Old 07-09-2011, 09:17 AM   #2
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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

http://seqanswers.com/forums/showthread.php?t=12523

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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Old 07-09-2011, 10:50 AM   #3
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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.

Gary
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Old 07-19-2011, 06:18 PM   #4
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we would be interested in RNA cassettes
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Old 07-19-2011, 06:32 PM   #5
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Quote:
Originally Posted by msheldon View Post
we would be interested in RNA cassettes
So would I!
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Old 07-19-2011, 10:11 PM   #6
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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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Old 07-22-2011, 04:41 AM   #7
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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.
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Old 07-22-2011, 10:42 AM   #8
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Default 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. - Gary
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Old 07-23-2011, 07:41 AM   #9
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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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