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Old 03-07-2014, 05:08 AM   #4
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Location: Oxford, Ohio

Join Date: Mar 2012
Posts: 246

Originally Posted by View Post
Hi I have made an Ampliseq panel for use on the PGM, it has 280 targets of sizes between 250-150bp.
We would like to also sequence these same targets on the MiSeq (we are testing to see how the two platforms compare on our types of targets and may possibly buy the one we like best).
Has anyone before used the Ampliseq primer panel to prepare a library for the MiSeq?
Or have any suggestions about which library prep method would be best?

We have looked at the truseq custom amplicon designer but we would prefer to use the ampliseq primer panel we already have. This is due to the cost of purchasing the full truseq amplicon kits (they only coming in 96sample minimums when we really only want to try on around 10 samples to begin with).
I think bunce is correct. I would probably buy 10 primers that JUST had your target sequence, perform your PCR. Then take the amplicons (seperately) and do five cycles of PCR using barcoded Illumina adaptor primers and then continue on with the MiSeq sequencing. Essentially doing this (Berry et al. (2011)) but with Illumina primers.
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