Index PCR

Index PCR

Service Description

Our index PCR service supplements customer amplified products with an Illumina TruSeq adapter. With a modification to the 5′ end of your template specific primers, the amplicons you generate can be purified and submitted to us! We use the amplicons you provide as template in a PCR to add unique indexes and the remainder of the Illumina TruSeq adapter. We then quantify the resulting libraries and pool, QC, and dilute the pooled libraries in preparation for sequencing on Illumina MiSeq or NovaSeq.

Use the file below to confidently add the appropriate sequence to your oligos and order from your preferred vendor. Please consult with if this if your first time using our service.

Concatenation Tool: Illumina Adapter and Region Specific Primer

Custom Amplicon Workflow


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.

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:

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 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

Shipping Submission

Please send the tracking information to:

Next Generation Sequencing:

*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

Custom Amplicon Submission Guidelines

-Follow the General Guidelines listed (See above)

-This project must be discussed with the UWBC facility prior to submission; we will provide more specific guidelines depending on your project needs

Library Preparation Pricing

MiSeq Pricing (Effective 5/1/21)

NovaSeq Pricing (Effective 5/1/21)

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.