University of Delaware DNA Sequencing & Genotyping Center

 

Overview of Core

 

About Us:

Thank you for visiting the University of Delaware DNA Sequencing and Genotyping Center.

 

The DNA Sequencing & Genotyping Center (SGC) supports genomic research through our established expertise with state-of-the-art genomics technologies. The Center is located in the Delaware Biotechnology Institute. The Delaware Biotechnology Institute is an interdisciplinary research institution at the University of Delaware. The SGC provides assistance with experimental design, user training, sample and data analysis. Instrumentation in the SGC supports high-throughput DNA sequencing, single-molecule 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 CenterIf 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.

We look forward to working with you on your projects!

 

 

UD Campus sample drop sites (send a notification email to DNAsequence@udel.edu)

Delaware Biotechnology Institute lab 246 (Requires check-in if you don't have access, refrigerator)

Brown Laboratory room 130 (Main Campus, cold room)

Allen Laboratory lobby (South Campus, room temperature)

UD Campus Map and Directions

 

Shipping Address for samples:

UD Sequencing & Genotyping Center

15 Innovation Way

DBI Lab 246

Newark, DE   19711

Location and Directions

 

Services:

  • Sanger DNA Sequencing on the ABI 3130XL
  • Massively-Parallel DNA Sequencing-By-Synthesis on the HiSeq 2500 and MiSeq
  • Single-Molecule Real-Time DNA sequencing on the Pacific Biosciences RSII
  • Library preparation for Illumina and Pacific Biosciences sequencing
  • DNA size selection on the Sage Science Blue Pippin
  • DNA fractionation on the Sage Elf
  • Ultrasonication using Covaris technology
  • DNA Fragmentation using Covaris technology
  • Nucleic Acid sizing and quality analysis on the AATI Fragment Analyzer
  • Nucleic Acid quantification measurements using fluorometry and spectrophotometry

 

 

Equipment and Technologies:

 

  • Illumina HiSeq 2500
    • The HiSeq 2500 sequencing system offers unprecedented output and a breakthrough user experience. Leveraging Illumina's proven and widely-adopted, reversible terminator-based sequencing by synthesis chemistry in combination with innovative engineering, HiSeq 2500 delivers the industry's highest sequencing output and fastest data generation rate. Human interaction design features and the easiest sequencing workflow set a new standard for simplicity and user experience.

 

  • 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 RSII Single-Molecule Real-Time Sequencer
    • The PacBio RS 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, characterization of genetic 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 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 S2 Adaptive Focused Acoustic Disruptor with CryoPrep
    • The Covaris S2 Adaptive Focused Acoustic Disruptor enables improved preparation of small biological samples up to 100ul in volume, larger volumes are accommodated with larger vessels. Its capabilities include DNA and chromatin shearing, tissue disruption and homogenization, and cell lysis among others. The benefits of this method of preparation compared to standard sonication and homogenization techniques are: Isothermal processing which minimizes heat damage. Non-contact, closed vessel processing eliminates cross contamination problems. Precisely controlled energy delivery allows standardized, highly reproducible processing of samples. The 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.

 

  • Advanced Analytical Technologies Fragment Analyzer Automated CE System
    • The Fragment Analyzer™ Automated CE System is a fluorescence-based capillary electrophoresis instrument for both sizing and quantifying nucleic acids (DNA and RNA). By using a sensitive intercalating dye coupled with a powerful LED light source, Fragment Analyzer™ Automated CE System obviates the need for fluorescent labeled primers and can be used to separate dsDNA fragments and RNA (mRNA and total RNA). The Fragment Analyzer™ Automated CE System is the most flexible system on the market today, with the greatest sensitivity, the highest separation resolution over a wide range, the widest dynamic range and the fastest separation times.

 

  • Agilent 2100 Bioanalyzer
    • The Agilent 2100 Bioanalyzer is a microfluidics-based platform for sizing, quantification and quality control of DNA, RNA, proteins and cells on a single platform. Results are delivered within 30-40 minutes in automated, high quality digital data. Two systems and different analysis kits are available.

 

  • 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.

 

  • NanoDrop Technologies ND-1000 UV-Vis Spectrophotometer
    • The NanoDrop® ND-1000 UV-Vis Spectrophotometer enables 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 and 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 Employees

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

 

Summer Thompson - Research Associate, Delaware Biotechnology Institute

Email:  summert@udel.edu

 

Mark Shaw - Laboratory Technician, Delaware Biotechnology Institute

Email:  markshaw@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 - 5:00

Unassisted Use (trained): 24/7

University of Delaware

Delaware Biotechnology Institute

Room 246

15 Innovation Way

Newark, DE  19711

Links and Resources

 

  1. Core Website
  2. How Does DNA Sequencing Work?
  3. Template Submission
  4. DNA Template Concentration
  5. DNA Template Preparation
  6. Interpreting Electropherograms
  7. Software
  8. Links
  9. FAQs
  10. Stock Primers
  11. Fragment Analysis
  12. News

Contacts

Name Role Phone Email Location
Bruce Kingham
Director
 
(302) 831-0823
 
brucek@udel.edu
 
Delaware Biotechnology Institute Room 246
 
Olga Schevchenko
Research Associate
 
(302) 831-0823
 
shevcheo@udel.edu
 
Delaware Biotechnology Institute Room 246
 
Summer Thompson
Research Associate
 
(302) 831-0823
 
summert@udel.edu
 
Delaware Biotechnology Institute Room 246
 

Map


15 Innovation Way Newark, DE 19711


Members at The Delaware Vermont iLab Network (DEVIN)

Delaware State University

Core Name Primary Contact Email Phone Number/Ext
Oscar Imaging Facility Michael Moore mmoore@desu.edu 302-857-7035

Nemours

Core Name Primary Contact Email Phone Number/Ext
Cell Science Core Lisa Glazewski, MS CellScienceCore@Nemours.org (302) 651-6707
HTS and Drug Discovery Sigrid Langhans langhans@nemoursresearch.org (302) 651-6538
Healthcare Delivery Science Jennifer Christofferson jennifer.christofferson@nemours.org 302-298-7876
Histochemistry and Tissue Processing Core Histochemistry and Tissue Processing Core 1600 Rockland Road, Wilmington DE 19803
Translational Neuroimaging Core Shaohui (Shao) Zhang, PhD Shaohui.Zhang@nemours.org 302-651-6869
Biomolecular Core Laboratory Jennifer Holbrook mbcore@nemours.org 302-651-6824 Fax: 302-651-6767

University of Delaware

Core Name Primary Contact Email Phone Number/Ext
Cardiovascular Research Core

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Wendy Nichols BSN RN wnichols@udel.edu (302) 831-3973
University of Delaware DNA Sequencing & Genotyping Center

Bruce Kingham brucek@udel.edu (302) 831-0823
Core Name Primary Contact Email Phone Number/Ext
Bioinformatics Core

Dr. Bryan Ballif bryan.ballif@uvm.edu (802) 656-1389
Proteomics Facility

Dr. Ying Wai Lam Ying-Wai.Lam@uvm.edu (802) 656-4709