Compatibility between standard titanium and rapid libraries

[Coyk]

Hi all,
We are slated to do some 454Junior sequencing runs for some colleagues. They prepared the library from cDNA mostly following the Roche standard Titanium protocol but they used their own adaptors. We have a 454Junior and Lib-L and Lib-A emPCR kits in house. I suspect there is a compatibility issue but I'm not sure if we have to add Rapid library adaptors to the library to make it compatible wit the 454Junior chemistry or if we have to buy different emPCR and sequencing kits altogether. Anyone run standard Titanium libraries on a Junior? Thoughts?

[ajthomas]

I haven't ever used a Jr., but I've done a fair number of runs on a FLX. As I understand, the chemistry is the same; only the instrument/plate is different, right? You use the same library and emPCR kits, don't you? If so, then I can't see how the instrument should make a difference. As long as your colleagues used the right sequence for their adapters, it should work fine. It would be a good idea to double check that and make sure. Get the sequences from them and make sure they match the Lib-L or Lib-A sequences and use the appropriate kit.

If they followed the older standard library prep protocol, they will have made a single-stranded library, meaning that you couldn't add Rapid library adapters to the ends anyway.

[pmiguel]

Titanium and Titanium Rapid libraries sequence using the same lib L emPCR and sequencing primer. You should be fine unless you try to mix them in the same region. They have non-compatible keys, if I recall correctly.

Rapid libs must be strand denatured prior to emPCR. (They have Y adapters. So each strand is a different amplicon.) Not required for non-rapid libraries.
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Phillip