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Old 05-08-2013, 06:46 PM   #1
Biomicrogen
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Default cDNA sequencing on IONTorrent PGM

Greetings all,

I will be doing some single cell transcriptomics soon. I am going to extract RNA from small numbers of bacterial cells (<10) and then circularize (after rRNA depletion) and subject this to MDA using phi29. The resulting cDNA should be able to be shunted into the MuSeek Library Prep kit workflow right? I mean, cDNA can be treated just like sheered gDNA can't it? I can't think of a reason I wouldn't get good reads doing it this way.

I would appreciate any insight you all might have!

Thanks,
Brandon @ASU
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Old 05-09-2013, 07:26 PM   #2
IonTorrent
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Hi Brandon,

While there's not an official supported protocol to do that with MuSeek, you're absolutely correct - full length ds cDNA can generally be treated like gDNA for most library prep methods and I would suspect it will work fine. You might also consider checking in with the Thermo tech support team for further tips: ts.molbio@thermofisher.com
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Old 05-13-2013, 05:21 PM   #3
jonathanjacobs
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Should work fine - but you'll loose strandedness information if you have any overlapping ORFs on opposite strands.
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Old 11-12-2013, 01:45 AM   #4
Proksima
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We did library sequencing of cDNA using MuSeek. But cDNA have to be ds for transpose to fragment it.
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