GBS Optimization

If we have not yet genotyped your species or a very close relative, GBS optimization will be required. The optimization process involves making test libraries for determining suitable restriction enzymes for your species and the optimal ratio of adapters to DNA. When your project is reviewed, you will be notified if optimization is required for your species.

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Requirements

Optimization requires 5 µg DNA as measured by intercalating dye or agarose gel. We cannot process samples with concentrations less than 50 ng/µL. The optimization DNA sample may be from one or multiple, pooled individuals or species.  Species with disparate genome sizes cannot be pooled for optimization and must be submitted separately.

We require a test digest of the optimization DNA sample to determine if it is suitable for GBS. Digest 300-500 ng DNA with 3-5U (1U per 100ng DNA) of a restriction enzyme that is NOT methylation sensitive (i.e. HindIII or EcoRI) and run on 0.8-1% agarose gels along with the uncut sample DNA (100ng) and 500ng of λ HindIII size standards.

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Submitting Optimization samples

If Optimization is required, you will be able to upload the optimization sample test digest image using the “Initialize Optimization” button at the bottom of your project page.  Our staff will review your image and if the digest looks good you will receive a shipping address and instructions.  The optimization sample should be shipped in a well-sealed Eppendorf tube at ambient temperature.  Sample tubes should be clearly labeled with the species name.  The optimization sample may be shipped prior to or at the same time as plate submissions.  

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Version 2 updated 2016-02-12