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University of Wisconsin–Madison

Gene Expression Center

The PacBio Sequel II provides long read capability for sequencing large amplicons, whole transcripts, targeted regions of the genome, and whole genomes. It can also provide base modification signatures for epigenetic studies. The facility had a Sequel from April 2017 to January 2020. Then they acquired the Sequel II. The data is proving to be indispensable for accurate phasing of mutations spaced more than 1kb apart and providing genome structure on a larger scale than is currently possible with short read technologies. The Sequel II SMRT cells have 8 million ZMWs! This is 8X the data from the Sequel I.

Getting Started

To discuss a project or obtain a quote please e-mail

Sample Submission

Please contact to arrange all sample submissions.
All sample submissions must included an electronic and hard copy of the Iso-Seq Submission form and an EXCEL sheet with each sample name, concentration and volume.  Samples and sample submission forms may be submitted to the Gene Expression Center in room 3240 Biotech Center. 

Turnaround time for PacBio sequencing is typically 4-6 weeks.

PacBio Iso-Seq RNA Quality Sample Recommendations

Sample issues specific to Iso-Seq typically occur before sample preparation begins.

• RNA samples should be DNAse treated
• A260/A280 should be ≥ 2.0
• Iso-Seq recommended total RNA input 1ug.


Support is available for projects that are run at UWBC facilities, and is provided for a fee by the UWBC Bioinformatics Resource Center. Terminals and software are available in our computer lab for clients of UWBC facilities who are internal to UW-Madison or the University of Wisconsin System who need to perform further analysis but lack the necessary hardware and software.

Acknowledging UWBC and the Gene Expression Center

A visible measure of a core's impact is made through proper acknowledgement of usage in publications. To acknowledge our core, please use the following statement: "The author(s) thank the University of Wisconsin Biotechnology Center Gene Expression Center for providing Iso-Seq RNA library preparation and the DNA Sequencing Facility sequencing services”.

The Sequel System generates long reads that are well-suited for characterizing full-length transcripts produced from high-quality RNA samples. The Iso-Seq RNA Library preparation allows detection of full-length transcripts up to 4 kb (without doing size-selection).

Using the Takara SMARTer PCR cDNA Synthesis kit, RNA is synthesized to cDNA and subsequently amplified to generate double-stranded cDNA, which is used to construct to a SMRTbell library for sequencing.

PacBio recommends performing a no-size selection experiment first to better understand diversity of transcripts in your samples.

Iso-Seq RNA Library Preparation
UW System Rate
Non UW System Rate
Iso-Seq Sample 1
$2,625 $3,885
Each additional sample
$475 $550
All data and services provided by the University of Wisconsin Biotechnology Center Gene Expression Center are intended for research purposes only. Services are not intended nor certified for diagnostic or clinical use.