Service Description

16S/18S/ITS (Internal Transcribed Spacers) are three different types of amplicon-based library preparations that allow for cost-effective, high-throughput analysis of microbial environments within a sample collection. We can extract DNA from your environmental samples or prep the DNA that you provide, depending on your project needs. These amplicon-based library preps are typically sequenced on either the Illumina MiSeq or the NovaSeq 6000. Our expert sequencing specialists can help you delve through any microbial diversity research projects and find the best fit for you.

16S/18S/ITS Workflow


Our 16S prep amplifies the V3-V4 hypervariable regions of the 16S rRNA gene in bacteria. For species- and strain-level detection, we offer full-length 16s rRNA amplicon prep and sequencing on our PacBio Sequel II platform – more information about that service can be found here.


18S and ITS sequencing are both used to identify fungal and other eukaryotic organisms within an environmental sample. Our 18S prep amplifies the V9 region of the 18S rRNA gene. Our ITS prep amplifies both the ITS1 and ITS2 regions. Data from the ITS region is advantageous for fungal phylogenetic analysis because this region has more variation than the ribosomal sequences (18S).

Custom and Index PCR 

Not interested in the microbiome, but still want targeted amplicon sequencing? Please check out the index PCR and custom amplicon sequencing services pages for other possibilities.

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

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.