Monday, February 16, 2009
Invitrogen SequalPrep Normalization plates
Invitrogen has released (May 2008 I think is when they were publicly available) a nifty new trick for those wanting to purify and standardize PCR amplicons for high-throughput sequencing. It is called Invitrogen SequalPrep and ends us being $1/sample compared to the laborious method of Ampure (from Agencourt). We've done a few amplicon LR70s where different labs have used the Invitrogen plates and they seem happy. I'd be curious to hear what amount of variation in sequencing coverage is seen.
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We have tried the SequalPrep plates and found as much as 412% variation in the number of reads per sample. For some studies this may be acceptable, but for our work it is not. I was also not happy with the purity of the samples. It could be that in my hands the plates don't work, but we had three different people prep samples for that run and the variation was consistent across all users. Since then we have gone back to pooling samples one at a time based on Picogreen quantities of cleaned PCR reactions. I will admit, however, the Sequal Prep plates are very convenient and if you don't mind a little variation, they may be right for your particular project.
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