cDNA sequencing on IONTorrent PGM

[Biomicrogen]

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

[IonTorrent]

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: [email protected]

[jonathanjacobs]

Should work fine - but you'll loose strandedness information if you have any overlapping ORFs on opposite strands.

[Proksima]

We did library sequencing of cDNA using MuSeek. But cDNA have to be ds for transpose to fragment it.