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 nextgen-seq@biotech.wisc.edu if this if your first time using our service.

Concatenation Tool: Illumina Adapter and Region Specific Primer

Custom Amplicon Workflow

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 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.

Submission

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.

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 Pricing

Effective 7/8/24

Service	Details	UW System Rate	External Rate
1x50	15 million reads*	1560	1945
2x75	25 million reads*	1685	2085
2x150	15 million reads*	1985	2465
2x150 Micro	6 million reads*	1030	1360
2x150 Nano	1 million reads*	820	1125
2x250	15 million reads*	2165	2670
2x250 Nano	1 million reads*	1000	1385
2x300	25 million reads*	2770	3390

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

* 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.

NextSeq Pricing

Effective 7/8/24

Service	Details	UW System Rate	External Rate
2x50 P1	100 million reads*	1665	1925
2x300 P1	100 million reads*	3060	3515
2x300 P2	400 million reads*	4720	5350

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

* 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 7/8/24

Service	Details	UW System Rate	External Rate
1.5B 2x50 Full Flowcell	Per Flow Cell (1.5B reads)**	3870	5405
1.5B 2x100 Full Flowcell	Per Flow Cell (1.5B reads)**	4470	6060
1.5B 2x150 Full Flowcell	Per Flow Cell (1.5B reads)**	4710	6335
10B 2x50 Full Flowcell	Per Flow Cell (10B reads)**	10565	12660
10B 2x100 Full Flowcell	Per Flow Cell (10B reads)**	12875	15190
10B 2x150 Shared Lane (10M read increments)	Per 10M reads targeted*	60	66
10B 2x150 Half Lane (450M reads)	Per 450M reads targeted*	895	1160
10B 2x150 10B Full Lane	Per Lane (1.25B reads)**	1790	2320
10B 2x150 10B Full Flowcell	Per Flow Cell (10B reads)**	14320	18055
25B 2x150 Full Flowcell	Per Flow Cell (25B reads)**	22235	26710

* 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.