Quality Control

QUALITY CONTROL AND CUSTOMER PREPARED LIBRARIES

Service Description

We offer quality control services that include initial QC for library development, size selection, and final QC of customer prepared libraries that are ready to go for sequencing. Our scientists have years of experience analyzing libraries and troubleshooting issues. We use state-of-the-art equipment for quantification and sizing of DNA, from initial library input to finished library. Accurate QC ensures high quality libraries are run on the sequencers at the same concentration and helps identify adapter/primer dimers and unintended products that may cause sequencing issues to arise. We also offer automated size selection prior to or after library preparation, which allows for precise, discrete selection of DNA.

QC SERVICE OPTIONS

Quantification

Fluorometric quantification of DNA is performed on two different platforms, depending on the number of samples submitted. All samples and prepared libraries must be quantified before continuing to sample sizing/quality.

Sample Sizing

Following quantification, DNA size, and integrity are evaluated to ensure the best results in customer library generation or sequencing. Evaluation is done via automated electrophoresis on one of the following platforms:

      • Agilent 4200 TapeStation System
      • Agilent Fragment Analyzer
      • Agilen Fempto Pulse System (Ideal for long read platforms)
      • QIAxcel

Each platform offers highly precise, analytical evaluation of various sample types and is capable of high-throughput processing.

Quality

High quality, pure DNA is necessary for samples submitted for Third-Generation Sequencing. In addition to the above metrics, QC of samples intended for Long Read Platforms includes a reading on the NanoDrop 1000. We measure the 260/230 and 260/280 ratios for contaminants, allowing us to provide information on the quality, troubleshoot and suggest possible improvements.

SPRI Purification

Solid Phase Reverse Immobilization (SPRI) purification is an option for customers whose libraries have an adapter/primer dimer and/or small, undesired fragments that may cause sequencing issues to arise. Libraries with ≥ 1% adapter dimer, by molarity, cannot be sequenced on the NovaSeq and libraries with ≥ 5% adapter dimer cannot be sequenced on the MiSeq. SPRI purification is performed using Axygen™ AxyPrep Mag™ PCR Clean-up beads (Corning Inc.). Following SPRI purification, QC is performed again to ensure effective purification. We offer SPRI purification in situations where DNA purity is compromised by organic compounds or other contaminants/inhibitors. Additionally, for labs that do not have the ability to perform this, we offer SPRI purification, as the process is automatable and high-throughput.

Size Selection

We can perform size selection of DNA or prepared libraries on the PippinH and BluePippin (Sage Science). These platforms provide medium-throughput size selection. PippinHT allows for precise size selection of up to 20 ul of sample/prepared Illumina libraries.

Workflow


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

Quality Control and Customer Submitted Guidelines

Contact us at nextgen-seq@biotech.wisc.edu with any questions.

Sample Storage

All input DNA submitted after 9/12/19, along with any intermediate and/or derived products (to include undiluted stock libraries), will be stored for 6 months and then disposed of.

All customer prepared libraries submitted after 4/23/18 will be stored for 6 months and then disposed of.

Customer Prepared Library QC 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.