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 then pool, QC, and dilute the pooled libraries in preparation for sequencing on our Illumina MiSeq i100 Plus or NovaSeq X Plus.

Use our Concatenation Tool: Illumina Adapter and Region Specific Primer to confidently add the appropriate sequence to your oligos and order from your preferred vendor. Please consult with nextgen-seq@biotech.wisc.edu if this if your first time using our service.

The illustration below depicts a library created through amplification with targeted primers containing TruSeq adapter modifications.

Advantages

This service is ideal for customers who are looking for a cost-effective way to sequence their region of interest and are comfortable performing initial, targeted amplification. We have a large selection of dual index combinations, which means you don’t have to invest in expensive oligos.

Considerations

Ensure that the oligos you order and the the products you amplify contain the necessary portion of the Illumina TruSeq Universal Adapter Sequence by using the Concatenation Tool: Illumina Adapter and Region Specific Primer. We recommend customers order primers that are HPLC purified, but standard desalting may be acceptable.

To keep costs low, we do not perform upfront QC prior to index PCR; therefore, you are responsible for ensuring that the initial amplification is 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.

Access our Interactive Submission Guidelines and get the exact guidance you need to prepare, label, and deliver your samples.

If you can’t find the information you’re looking for, please contact us at nextgen-seq@biotech.wisc.edu

Illumina Index PCR Pricing

Effective 7/8/24

Service	Details	UW System Setup Rate	UW System Per Sample Rate	External Setup Rate	External Per Sample Rate
Illumina Index PCR	Setup charge for 1-96 concurrent samples + per sample charge	475	3	~$607*	~$4*

* For exact cost, please inquire for a quote.

* For exact cost, please inquire for a quote.

Prices are subject to change without notice. Please email nextgen-seq@biotech.wisc.edu to request a quote. In the absence of a valid quote, prices from our current price books will be applied at the time of the service request. Prices may differ from those listed on this page.

Prices are subject to change without notice. Please email nextgen-seq@biotech.wisc.edu to request a quote. In the absence of a valid quote, prices from our current price books will be applied at the time of the service request. Prices may differ from those listed on this page.

MiSeq i100 Plus Pricing

Effective 3/31/25

Service	Details	UW System Rate	External Rate
5M 300 cycles*	5 million reads**	1150	1610
5M 600 cycles*	5 million reads**	1440	1930
25M 100 cycles*	25 million reads**	1160	1535
25M 300 cycles*	25 million reads**	1760	2280
25M 600 cycles*	25 million reads**	2015	2565

* Cycle count represents the total number of cycles. While typical run configurations produce paired-end reads (100 cycle: 2x50, 300 cycle: 2x150, 600 cycle: 2x300), flow cells may be run as single read and/or custom configurations.
** Read specifications based on Illumina PhiX control library. Output may vary based on library type.

* Cycle count represents the total number of cycles. While typical run configurations produce paired-end reads (100 cycle: 2x50, 300 cycle: 2x150, 600 cycle: 2x300), flow cells may be run as single read and/or custom configurations.

** Read specifications based on Illumina PhiX control library. Output may vary based on library type.

Prices are subject to change without notice. Please email nextgen-seq@biotech.wisc.edu to request a quote. In the absence of a valid quote, prices from our current price books will be applied at the time of the service request. Prices may differ from those listed on this page.

NovaSeq X Plus Pricing

Effective 3/4/25

Service	Details	UW System Rate	External Rate
1.5B 2x50 Full Flowcell	Per Flow Cell (1.5B reads)**	3975	5370
1.5B 2x100 Full Flowcell	Per Flow Cell (1.5B reads)**	4590	6045
1.5B 2x150 Full Flowcell	Per Flow Cell (1.5B reads)**	4845	6320
10B 2x50 Full Flowcell	Per Flow Cell (10B reads)**	10855	12825
10B 2x100 Full Flowcell	Per Flow Cell (10B reads)**	13230	15425
10B 2x150 Shared Lane (10M read increments)	Per 10M reads targeted*	60	66
10B 2x150 Half Lane (450M reads)	Per 450M reads targeted*	924	1139
10B 2x150 10B Full Lane	Per Lane (1.25B reads)**	1848	2278
10B 2x150 10B Full Flowcell	Per Flow Cell (10B reads)**	14784	18224
25B 2x150 Full Flowcell	Per Flow Cell (25B reads)**	22875	27110

* M=million. This is targeted number of reads. Actual read counts may vary ±20% from targeted amounts.
** B=billion. Read specifications based on Illumina PhiX control library. Output may vary based on library type.

* M=million. This is targeted number of reads. Actual read counts may vary ±20% from targeted amounts.

** B=billion. Read specifications based on Illumina PhiX control library. Output may vary based on library type.

Prices are subject to change without notice. Please email nextgen-seq@biotech.wisc.edu to request a quote. In the absence of a valid quote, prices from our current price books will be applied at the time of the service request. Prices may differ from those listed on this page.

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.