DNA Sequencing & Genotyping Center

Bruce Kingham, Director/Associate Scientist
Allen Laboratory, Room 157
Tel: 302-831-0823
Fax: 302-831-8177
Email: brucek@udel.edu


The DNA Sequencing & Genotyping Center provides access to state of the art genomics technologies for university research groups and outside users on a fee-for-service basis.

Bruce Kingham is available for consultation and troubleshooting.

The UD DNA Sequencing & Genotyping Center is equipped with the following instrumentation:

  • Illumina HiSeq 2000 – The HiSeq 2000 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 2000 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.
  • Pacific Biosciences RS Single-Molecule Sequencer – UD is proud to introduce the revolutionary third generation DNA sequencing system: the PacBio RS. Our system incorporates novel, single molecule sequencing techniques and advanced analytics to reveal more biology in real time. We call this SMRT� (Single Molecule Real Time) technology. The PacBio RS conducts, monitors and analyzes biochemical reactions at the individual molecule level, according to your specific protocol and experiment design. Long readlengths, intuitive operation and absolute throughput flexibility combine to deliver the data you need, faster than previously possible.
  • 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
  • Pippin Prep DNA Size Selection System – The Pippin Prep 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 8kb. Typical run times (four samples per run) are between 50 and 100 minutes.
  • 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
  • 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