GBS

Service Description

GBS (Genotype By Sequencing) is a cost effective, high throughput service that helps in the discovery of single nucleotide polymorphisms (SNP) for plant and animals along with genotyping studies. If your species does not have a known enzyme combination for GBS, we offer optimization/restriction enzyme selection! We have also improved our GBS prep by adding a post-PCR normalization step.

We offer single and dual enzyme digest
ddRAD and RADseq can be done with the inclusion of a size selection step
Cost-effective sequencing with out novel Shared NovaSeq 6000 offering
UWBC Bioinformatics Resource Center has vast experience with downstream analysis
Licensed service provider*
Sequencing of customer prepared GBS libraries

*The University of Wisconsin-Madison Biotechnology Center
– DNA Sequencing Facility is a Licensed Service Provider,
for internal and external clients, providing GBS services under license from Keygene N.V. which owns patents and patent applications protecting its Sequence Based Genotyping technologies.

**KeyGene license fee will be applied to any client-prepared libraries

Optimization of Species

Species’ genomes respond differently to combinations of restriction enzymes, this can all be impacted by the G/C content, methylation status, or complexity amongst other conditions. If the enzyme combination is not known yet, species will need to have optimization/restriction enzyme selection performed to determine which enzymes to proceed with for GBS. We have worked with a variety of different species and are open to working with new species. Please contact us at nextgen-seq@biotech.wisc.edu to discuss your project.

Advantages

We have updated our GBS prep protocol to now include post-PCR Normalization! Post-PCR normalization provides data with a more even distribution of reads across a 96 well plate. This ensures that low concentration samples get even coverage. A comparison of the number of reads per GBS samples with or without post-PCR normalization can be seen in two different plates of samples in Figure 1 and 2.

GBS Data Figures 1 & 2

Getting Started

To discuss a project or acquire a quote, please contact us! For new clients, please set up an account (see New Lab or Customer Access below). All projects must be discussed before samples are submitted.

If you would like to initiate a project or get more information, please use the following contact information, and a member of our group will get in touch with you directly.

Next Generation Sequencing: nextgen-seq@biotech.wisc.edu

New Lab or Customer Access

We MUST have this information before we can proceed with your request.

Adding a new lab:

- Name, address, phone number, UW NetID and email of the Principal Investigator (PI) or Primary scientific contact person.
- Name, address, phone number, FAX number and email of he financial contact person.
- Name, UW NetID, phone number and email of all individuals who will be using our service.
- Payment information: For campus users this should be a direct charge number, e.g. a 144 or 133 prefixed account (please send the whole string of characters). For off campus users you can set up a PO or we can send the financial contact person a bill — your choice. Non-UW system users are charged an additional institutional overhead.

Adding a member to an existing lab:

- Name of the PI whose lab you are joining.
- Your name, UW NetID, phone number and email.

Sample Submission

Please contact nextgen-seq@biotech.wisc.edu to arrange all sample submissions. Samples and submission forms must be submitted before a project can be entered into our queue.

Submission Forms and Guidelines

Please check the service page guidelines for specific Submission Forms and Guidelines that need to be included with your samples.

Submitting Samples/ Shipping Instructions

After setting up a customer account, filling out submission form, and reviewing submission guidelines, you can now submit or send samples. *We require customers to submit electronic Submission Forms!*

In Person Submission

Please give advance notice of submission date and time so staff can be prepared to receive samples. Schedule a time for drop off with a staff member at nextgen-seq@biotech.wisc.edu

Shipping Submission

Please send the tracking information to:

Next Generation Sequencing: nextgen-seq@biotech.wisc.edu

*Samples that are being shipped must have a hard copy of the submission form and guidelines in the package! This way we know what the samples are and where they are from.*

If shipping samples from outside UWBC, ship via express shipping carrier on dry ice to the address below:

Next Generation Sequencing
UW DNA Sequencing Facility Attn: Next Generation Sequencing 425 Henry Mall 1250 Biotechnology Madison WI, 53706

Submission Forms and Guidelines

- Illumina Submission Form (required with every extraction submission)
- Guidelines and Sample Sheet (required with every submission)

GBS Submission Guidelines

Follow general guidelines listed (See above).

Success in GBS is determined primarily by the quantity and quality of the submitted DNA. Please submit the following quality control metrics with EACH project.

Lyophilized DNA is also acceptable, but we would prefer to have DNA suspended in 10 mM Tris or nuclease-free water. Please avoid EDTA.

Figure 1. Gel image example for gDNA and HindII Digest (Gel Image Provided by Mockler Lab).

Questions?

Sample Storage

All input DNA submitted after 9/12/19, along with any intermediate and/or derived products (to include undiluted stock libraries), will be stored for 6 months and then disposed of.

All customer prepared libraries submitted after 4/23/18 will be stored for 6 months and then disposed of.

Library Preparation Pricing

MiSeq Pricing

NovaSeq Pricing

EXTERNAL RATES: Clients not affiliated with UW Madison or the University of Wisconsin system are charged a 55% surcharge for all labor and incidentals provided; prices are as listed above. This surcharge is subject to change.

Illumina pricing is broken into two components: library preparation and run cost. Library preparation is charged on a per sample basis and varies by type. Run charges are based on the length of the sequencing run and whether it is single or paired end. Prices are subject to change due to increasing reagent costs.

Unless otherwise specified, all data and reagents distributed by the University of Wisconsin Biotechnology Center DNA Sequencing Facility are intended for research purposes only. They are not intended nor certified for diagnostic or clinical use. Clinical services are provided through our collaboration with the UW Collaborative Genomics Core.