DNA Sequencing Facility: Pacific Bioscienses Sequencing

 

The PacBio Sequel 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.  Support for purchasing the PacBio Sequel was provided by a UW2020 grant with matching funds from a number of UW departments. The Sequel has been in operation since April 2017 and 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 DNA Sequencing Facility offers all-inclusive next generation sequencing, DNA extraction and SNP genotyping services on a rolling-submission, fee-for-service basis, with the goal of generating high-quality genomic and transcriptomic data.  We work with our UW system and external collaborators to prepare DNA, RNA, ChIP, GBS, metagenomic, exome, and other sequencing libraries, provide robust sequencing data, and help interpret that data to provide meaningful biological information in a time-sensitive manner.

Getting started

To discuss a project or acquire a quote, please contact our NGS team.  To submit samples, please review our submission guidelines and sequencing policies, fill our our sample submission form, and contact us to set up an account and coordinate sample delivery.

New Services 

Microbial Genome Assembly

Microbial Genome Assembly from HMW DNA, ~5 Mb genomes, rough draft (12 samples): 
    
- Library preparation + sequencing: $140/sample (UW), $180/sample (external)
   
- Library preparation, sequencing + Bioinformatics: $215/sample (UW), $295/sample (external)

Microbial Genome Assembly from HMW DNA, ~5 Mb genomes, polished assembly (12 samples): 
     
- Library preparation + sequencing: $475/sample (UW), $595/sample (external)
   - Library preparation, sequencing + Bioinformatics: $550/sample (UW), $710/sample (external)

Note: We suggest using a DNA extraction method capable of isolating 50kb or higher molecular weight

Pricing

  • Sample Prep: $650 ($935 external) for the first prep and $190 ($240) for each concurrent prep.
  • Primer and Polymerase Binding: $105 ($160) per library pool.
    Once the primer and polymerase are bound, the library pool can be run on the sequencer any time within the next four days and you can run multiple SMRT cells from the bound pool.
  • Sequencing: $1,100 ($1,225) per SMRT cell.
    Runs generate about 5 to 6 Gb of data for shorter fragments, less for longer fragments.

Pricing listed above will be effective starting April 1, 2018.

EXTERNAL RATES: Clients not affiliated with UW Madison or the University of Wisconsin system are charged a 53% surcharge for all labor and incidentals provided; prices are as listed above.  This surcharge is subject to change.

PacBio 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 number of times a library needs to have polymerase and primer bound to it.  Each binding event has a maximum life of four days after which this step needs to be repeated with fresh library before it can be loaded on the sequencer.  Prices are subject to change due to increasing reagent costs.

System Overview

PacBio Sequel:

  • Read Length: 1kb to 3kb (Circular Consensus Sequencing), 1kb to 7kb (multiplexed libraries), 1kb to 80kb (single library, selected for size)

  • Run time:10 hours per SMRTcell, up to seven SMRTcells can be queued at one time

  • Data generation per lane: 200 to 400 thousand fragments sequenced in parallel; 2 to 10 Gbases data output

  • Ideal for: long amplicons, genome assembly, ISO-Seq (full length transcriptome), epigenetic modification discovery, and targeted capture

Scheduling and Sample Submission

Please contact nextgen-seq@biotech.wisc.edu for scheduling information. All projects must be discussed with a project manager prior to submitting samples. No projects will be scheduled until samples and sample submission forms have been dropped off to DNA Sequencing personnel in room 1250 Biotech Center.

Policy Statement

Unless otherwise specified, all data and reagents distributed by the University of Wisconsin Biotechnology Center DNA Sequence 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. 

Acknowledging UWBC and the DNA Sequencing Facility

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 DNA Sequencing Facility for providing Pacific Biosciences library preparation and sequencing  services”.

Bioinformatics

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.  Analysis of PacBio data requires installation of specific software and the data needs to organized in a specific file structure. It is not trivial to install and run.