University of Delaware DNA Sequencing & Genotyping Center

 

 

Thank you for visiting the

University of Delaware DNA Sequencing and Genotyping Center

General questions can be sent to DNAsequence@udel.edu

We look forward to working with you on your projects!

 

The DNA Sequencing & Genotyping Center (SGC) supports genomic research through our established expertise with state-of-the-art genomics technologies. The SGC is a part of the Delaware Biotechnology Institute located in the Ammon-Pinizzotto Biopharmaceutical Innovation Center. The Delaware Biotechnology Institute is an interdisciplinary research institution at the University of Delaware.The SGC provides expertise and assistance for experimental design, user training, sample processing, and data analysis. Instrumentation in the SGC supports high-throughput DNA and RNA sequencing, single-molecule DNA and RNA sequencing, qualitative and quantitative analysis of nucleic acids.

If we have contributed data that will be utilized in a publication we kindly request an acknowledgement of the University of Delaware DNA Sequencing and Genotyping Center and the staff that worked with youIf contributions of our staff goes beyond typical fee-for-service please consider co-authorship. Acknowledgement is critical so that UD and various funding organizations can better measure the impact of their support to our center. Consequently, the acknowledgements you provide make it possible for our center to continue to provide access to state-of-the-art equipment and expertise at reasonable rates.

Please note that the server pacifica.dbi.udel.edu is going offline permanently on May 1st, 2022. Pacifica hosts PacBio RSII sequencing data and the old PacBio SMRT Analysis 2.3 portal used to process RSII data.  With the server down, you will lose on-line access to your RSII sequencing data, and the ability to process them with SMRT Analysis software. Please transfer all of your RSII data to your local computer for safekeeping, if you have not done so already.

 

“Patience is not the ability to wait, but the ability to keep a good attitude while waiting”
 
Joyce Meyer

 

 

UD Campus sample drop sites (send a notification email to DNAsequence@Udel.Edu)

DNA Sequencing & Genotyping Center, Ammon-Pinizzotto Biopharmaceutical Innovation Center Suite 146 (Requires check-in if you don't have badge access, there is a sample drop refrigerator in the main lobby)

Brown Laboratory, Room 130 (Main Campus, cold room)

Allen Laboratory, Lobby (South Campus, room temperature)

UD Campus Map and Directions

 

Shipping Address for samples:

 

Ammon-Pinizzotto Biopharmaceutical Innovation Center 

DNA Sequencing & Genotyping Center Suite 146

590 Avenue 1743

Newark, DE   19713

Location and Directions

 

Services:

  • Massively-Parallel DNA Sequencing-By-Synthesis on the Illumina MiSeq, NextSeq 550, NextSeq 2000, or NovaSeq 6000
  • Single-Molecule Real-Time DNA sequencing on the Pacific Biosciences Sequel IIe
  • Sanger DNA Sequencing on the ABI 3500
  • Library preparation for Illumina and Pacific Biosciences systems
  • DNA size selection on the Sage Science Blue Pippin
  • DNA fractionation on the Sage Elf
  • DNA Fragmentation using Diagenode technology
  • Tissue disruption using Covaris technology
  • Nucleic Acid sizing and quality analysis on the AATI Fragment Analyzer
  • Nucleic Acid sizing and quality analysis on the AATI FemtoPulse
  • Nucleic Acid quantification measurements using fluorometry and spectrophotometry

 

 

Equipment and Technologies:

 

  • Illumina NextSeq 550
    • The NextSeq 550 System delivers the power of high-throughput sequencing with the speed, simplicity, and affordability of a benchtop next-generation sequencing (NGS) system. The NextSeq 550 System fits into research laboratories, without need for specialized equipment. Perform many combinations of high- and mid-throughput sequencing applications to advance your studies.

 

  • Illumina MiSeq
    • The MiSeq desktop sequencer allows you to access more focused applications such as targeted gene sequencing, metagenomics, small genome sequencing, targeted gene expression, amplicon sequencing.

 

  • Pacific Biosciences Sequel II Single-Molecule Real-Time Sequencer
    • The Pacific Biosystems  Sequel II is a Single Molecule, Real-Time (SMRT®) DNA Sequencing System that provides the highest consensus accuracy and longest read lengths of any available sequencing technology. SMRT Sequencing is ideal for de novo assembly, full-length transcript analysis, characterization of genomic variation, methylation analysis, microbiology studies, and more.

 

  • ABI Prism 3130XL Genetic Analyzer
    • The Applied Biosystems 3130 XL Genetic Analyzer housed in the center is a state-of-the-art capillary-based instrument capable of moderate- to high-throughput DNA sequencing and fragment analysis (up to 656 samples/day). The 3130XL system is a fully automated, fluorescence-based capillary electrophoresis platform that simultaneously analyzes 16 samples. The system provides automated polymer loading, sample injection, separation and detection, and data analysis. The instrument can run unattended for up to 24 hours.

 

  • ABI 7500 Fast Real-Time PCR System
    • The Applied Biosystems 7500 Fast Real-Time PCR System offers maximum performance in the minimum time. Fully optimized for Fast cycling, the 7500 Fast delivers high-quality results in as little as 30 minutes. Specially designed Fast block ensures thermal uniformity at top speeds. Faster ramp rates enable rapid results without compromising extension times or assay quality. Fast optical plates ensure excellent precision in 10-30 uL reaction volumes. Use TaqMan Fast Universal PCR Master Mix to run multiple Fast assays on one plate. Finish more runs per day with the excellent performance equivalent to that offered by the 7500 System.

 

  • Sage Science BluePippin DNA Size Selection System
    • The Pippin Blue is a preparative electrophoresis platform that separates and extracts DNA fragments. Using pre-cast and disposable gel cassettes, DNA is automatically collected in buffer according to software-input size ranges. DNA fractions (typically adapter-ligate NGS libraries) are removed using standard pipettes. Workflow requires about 1-2 minutes of hands on time per sample, and cassettes are available for extractions between 50 bp and 50 kb. Typical run times (4-5 samples per run) are between 50 and 100 minutes.

 

  • Sage Science Elf DNA and Protein Fractionation System
    • The SageELF is an electrophoresis system that separates DNA or protein samples by size, and then fractionates the whole sample, or section of sample, into 12 fractions. The system is equipped with pulsed-field electrophoresis for resolving large DNA. Fractionation ranges are estimated and adjusted in software, and fractions are collected in buffer. One sample is fractionated on a single precast agarose cassette, and one or two cassettes may be processed at one time.

 

  • Sage Science Pippin Pulse
    • Sage Science‘s Pippin Pulse electrophoresis power supply brings ­field inversion to your lab’s agarose gel apparatus. The system resolves DNA to 100 kb and beyond, economically, and without unwieldy instrumentation and/or chillers. Pulsed-fi­eld protocols are programmed and run from a PC, providing users the flexibility to develop customized protocols to meet specifi­c applications.

 

  • Covaris CryoPrep
    • The Covaris CryoPrep is a microprocessor controlled hammer and anvil mechanism. In practice, it is an electronic solenoid developed to deliver controlled, repeatable mechanical energy (i.e., impact force) to a sample.

 

  • Agilent 5200 Fragment Analyzer Automated Capillary Electrophoresis System
    • The 5200 Fragment Analyzer system is a parallel capillary electrophoresis instrument that improves lab efficiency allowing you to separate 12 samples in parallel in as little as 15 minutes. This system is designed to eliminate laboratory bottlenecks so you can focus on results. The 5200 Fragment Analyzer system performs DNA QC and RNA QC for a broad range of samples including, gDNA, small RNA, cfDNA, large DNA fragments, and total RNA. The diversity of sample types these systems can separate make these instruments ideal for individualized workflows, including NGS library QC and CRISPR workflows.

  • Agilent Femto Pulse Automated Capillary Electrophoresis System
    • The Femto Pulse system provides researchers with a powerful and automated pulsed-field capillary electrophoresis system. Easily achieve 10 times higher sensitivity for smears and up to 100 times for fragments. A meticulously designed optical detection platform and pulsed-field power enable unprecedented sensitivity, detecting nucleic acids into the lower femtogram range. With the ability to separate DNA and RNA samples, the Femto Pulse system is flexible enough to handle any of your workflow scenarios. The ability to separate high molecular weight DNA up to 165 kb and detect nucleic acids down to 50 fg/µL input concentration make the Femto Pulse system ideal for long-read NGS QC, gDNA, small RNA, or cfDNA analysis from low concentration samples.

 

  • Qubit Fluorometer
    • The Qubit fluorometer is designed to work seamlessly with the Quant-iT™ assays for DNA, RNA and protein quantitation. It features state-of-the-art optical components, sophisticated data analysis and an intuitive user interface. The result is an easy method to obtain much more accurate and sensitive quantitation than can be obtained with UV absorbance assays, increasing your confidence in taking your sample to downstream applications.

 

  • DeNovix and NanoDrop Technologies ND-1000 UV-Vis Spectrophotometers
    • The DeNovix and NanoDrop® ND-1000 UV-Vis Spectrophotometers enable highly accurate analyses of extremely small samples with high reproducibility. The sample retention system eliminates the need for cuvettes and capillaries. Benefits include full spectrum absorbance (220-750nm) and small sample size (1-2ul).

 

  • MJ Research Tetrad Thermocycler
    • The MJ DNA Engine Tetrad (PTC 225) is a multi-user thermal cycler. The instrument consists of Peltier heated/cooled sample blocks (alphas) that have heated lids. Up to 7 users can run samples simultaneously and the alphas can accommodate 48-96 0.2 ml thin-walled PCR tubes/strips/plates or up to 30 thick-walled 0.5 ml tubes. The MJ Tetrad includes a gradient feature to perform annealing temperature optimization.

 

  • ABI Veriti, ProFlex, GeneAmp PCR System 9700 Thermocycler
    • High-performance thermocyclers offer fidelity, accuracy, NIST traceable calibration, and fast response to temperature changes. Heating and cooling is thermoelectric, a heated lid provides for oil-free operation.

 

  • Eppendorf Centrifuge 5804R
    • The 5804R centrifuge is capable of high-speed centrifugation (up to 20,800 x g) of tubes and plates using interchangeable swing-bucket and high-speed fixed-angle rotors. Internal temperature settings range from –9°C to 40°C.

 

 

Lab Team

Bruce Kingham - Director, UD DNA Sequencing & Genotyping Center; Associate Scientist, Delaware Biotechnology Institute

Email: brucek@udel.edu

 

Olga Shevchenko - Research Associate, Delaware Biotechnology Institute

Email: shevcheo@udel.edu

 

Mark Shaw - Research Associate, Delaware Biotechnology Institute

Email: markshaw@udel.edu

 

Erin Bernberg - Senior Scientist, Delaware Biotechnology Institute

Email: elb@udel.edu

 

 

 

Getting Started

 

  • Sign up for a new account using the link in the upper right hand corner, or click here.

 

  • Login with your approved credentials in the upper right hand corner.

 

 

 

 

Location and hours of operation

 

Hours Location

Monday - Friday

9:00 - 4:00

Unassisted Use (trained): 24/7

University of Delaware

Delaware Biotechnology Institute

Suite 146

590 Avenue 1743

Newark, DE  19713

Contacts

Name Role Phone Email Location
Bruce Kingham
Director
 
(302) 831-0823
 
brucek@udel.edu
 
Ammon-Pinizzotto Biopharmaceutical Innovation Center Suite 146
 
Olga Schevchenko
Research Associate
 
(302) 831-0823
 
shevcheo@udel.edu
 
Ammon-Pinizzotto Biopharmaceutical Innovation Center Suite 146
 
Erin Bernberg
Associate Scientist
 
(302) 831-0823
 
elb@udel.edu
 
Ammon-Pinizzotto Biopharmaceutical Innovation Center Suite 146
 
Mark Shaw
Research Associate
 
(302) 831-0823
 
markshaw@udel.edu
 
Ammon-Pinizzotto Biopharmaceutical Innovation Center Suite 146
 
Alyssa Fedorkowicz
Laboratory Technician
 
(302) 831-0823
 
afedork@udel.edu
 
Ammon-Pinizzotto Biopharmaceutical Innovation Center Suite 146
 

Map


590 Avenue 1743 Newark, DE 19713