Nextera kits produce dsDNA. Doesn Roche normally recommend loading ssDNA into the emulsion PCR?
• This is not a problem. Roche/454 can use either ssDNA or dsDNA as emPCR input (they currently use dsDNA as input when they sequence amplicons). If there are any concerns, follow the guidelines for sequencing amplicons on the Roche/454 instrument. • Furthermore, the older Roche/454 prep that enriched for A/B fragments with biotin/streptavidin did use ssDNA as the emPCR template. However, Roche/454 is moving away from ssDNA input with the new Y-adaptor preps.
