MiSeq custom libraries

[jhi_pete]

We hope to run some custom Genotyping by Sequencing libraries on the MiSeq which has a paired-end flow cell. Our current libraries work well on the GA/HiSeq, but I understand there may be compatibility issues in moving between platforms, which may require adapter sequence modifications.
Please can comeone provide a definitive set of adapter/primer sequences which will work on the MiSeq?

[kcchan]

The flow cell adapters are the same as the PE flow cells on HiSeq and GA. The MiSeq sequencing primers are HP10, 11 and 12, the same primers that are found in the TruSeq Dual Index sequencing primers box and is compatible with all Illumina adapters. If you're using a custom primer, you can add it in separately in the custom primer wells or spike it into the HP10/11/12 wells.

[jhi_pete]

Thanks kcchan. Its the sequences of the compatible MiSeq adapters I need to check against those we use in the custom libraries.

[GenoMax]

Have you looked at this thread: http://seqanswers.com/forums/showthread.php?t=24119

[jhi_pete]

Thanks GenoMax. The compatible primers are good to know but I also need the adapter sequences outwith the sequencing primers (5'-most) which bind to the PE FC itself to ensure full compatibility.

[kcchan]

The MiSeq uses the same P5 and P7 adapter sequences as the other PE flow cells. Anything that will cluster on the HiSeq/GA flow cell will cluster on the MiSeq. You can also speak with Illumina Tech Support if you need more confirmation.