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Old 09-11-2012, 03:19 AM   #4
TonyBrooks
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Location: London

Join Date: Jun 2009
Posts: 298
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SMARTer all the way for us.
We had some strange mapping results from the NuGen kit with lots of intronic mappings. In the end we ignored them and the results did correlate well with array data (from the same total RNA), but it's a waste of sequencing capacity. I think there are other posts on here where people mention they had similar problems with intronic reads. I suspect the kit may be very sensitive to any (DNA) contamination due to the use of random priming.

http://seqanswers.com/forums/showthread.php?t=12373

The SMARTer kit on the other hand produced very clean data, even from a single cell - so it's very sensitive. The downsides are the protocol isn't as user friendly as NuGen and it's much more expensive. It also requires a bit of expertise to optimise the library prep post amplification. There was also greater disparity between the array data and the SMARTer data, but we expected this from single cell work.
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