Equipment

Liquid Handling System: Packard Multiprobe II

The Multiprobe II is a liquid handling system that is used to robotically set up all sequencing reactions in a 96-well format. The robot transfers DNA template, primer, and enzyme mix from individual 1.5 ml flip-top tubes to a specific well for each sequencing reaction. The Multiprobe II uses a Visual Basic interface that allows the setup of custom programs for the different liquid handling needs of the facility. The robot dramatically reduces the possibility of human error and allows the DNA Sequencing Facility to produce DNA sequencing reactions in a standardized and repeatable manner.

Liquid Handling System: Evolution P3 (EP3) Precision

The Evolution P3 (EP3) Precision Pipetting Platform is a flexible automated liquid handler for low-to-high throughput
microplate applications using 96 or 384-channel disposable tip dispense heads. The EP3 can easily be configured to
perform many common lab applications including SNplex PCR OLA transfer, Snplex hybradization, Sequencing Purification Edge Bio Transfer applications.The patented dispense head design is the industry “gold-standard” for pipetting performance which reduce the possibility of human errors and allows the DNA Sequencing Facility to produce DNA sequencing reactions in a standardized and repeatable manner.

Thermal Cycler: MJ Research Tetrad

The MJ Research Tetrad is a high-throughput thermal cycler. The tetrad has four thermal cycling engines.

Centrifuges: Beckman's Allegra 6KR and Savant's DNA Speed Vac

The Allegra 6KR and the DNA Speed Vac are used throughout the ethanol/EDTA precipitation steps, lypholization, and the reconstitution in Hi-Di formamide.

Electrophoresis Systems: ABI's 3730xl, 3730, and 3100 DNA Analyzers

All three of the DNA analyzers are capillary electrophoresis systems. The 3730xl has 96 capillaries, the 3730 has 48 capillaries, and the 3100 DNA Analyzer has 16 capillaries. The ABI 3730xl is used exclusively for DNA sequencing whereas the 3730 is used for fragment analysis and as a backup sequencer for the 3730xl. The ABI 3100 is used exclusively for fragment analysis. The 3730XL sequencer is the latest in capillary-based DNA sequencing technology. As the capillaries are placed into the 96-well reaction plate, a voltage is applied to directly electrophorese the samples through the polymer-filled array. At the end of this array, the laser shines directly into a window in each capillary, fluorescing each base; the wavelengths are captured by a CCD camera. The raw data is then collected, extracted, and analyzed by powerful Applied Biosystems DNA Sequencing Analysis 5.0 software, producing trace files with a quality score for each individual base. These files are then run through a separate Perl script that masks low quality bases in the final text file. Each run on the 3730XL requires 2 hours. The software provides a statistical analysis of sequence quality which we use to monitor performance of the facility.