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University of Wisconsin–Madison

DNA Sequencing Facility

The UW-Madison Biotechnology Center is currently open and following the university's COVID-19 Response regarding campus operations.

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Index PCR

Service Description  

Our index PCR service supplements customer amplified products with an Illumina TruSeq adapter. The samples will then be quantified, pooled, QC’d and diluted for Illumina sequencing on either the MiSeq or NovaSeq. 

Index PCR Pic PPT

Index PCR Workflow

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This service is ideal for customers who are looking for a cost-effective way to sequence their region of interest and are comfortable performing the initial PCR reactions. 

Clients who would like to use this service must ensure that their products contain the necessary portion of the Illumina TruSeq Universal Adapter Sequence.

Our submission form has a tab to concatenate sequences with your region-specific primers to ensure that the correct primers are ordered for the initial PCR; utilizing these primers is critical to the success of the index PCR reaction we perform. We highly recommend customers order primers that are HPLC purified.

To keep costs low, we do not perform upfront QC prior to index PCR; therefore, you are responsible of ensuring that the initial amplification was efficient, and the final product is clean. Please contact us with any questions and see the guidelines tab for the specifics of the submission process.

General Guidelines

  • Getting Started

  • New Lab or Customer Access

  • Sample Submission

Library Preparation Pricing
Index PCR Pricing
MiSeq Pricing (Effective 5/1/21)
MiSeq Runs Pricing Table
NovaSeq Pricing (Effective 5/1/21)
NovaSeq Runs Pricing Table

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.

Please visit our Personnel Tab
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.