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Genomics

ABI 3130 and ABI 3730

The Applied Biosystems 3130 and 3730 are automated 4 and 48-capillary DNA Analyzers that allow for low and medium-to-high throughput genetic analysis, respectively. Together both DNA Analyzers combine reliability, high data quality, and the production flexibility needed to provide the ideal platforms for rapid, accurate, cost-effective DNA analysis of any size project. The instruments can be used for DNA fragment analysis applications such as microsatellites, AFLP, SNP analysis, mutation detection as well as sequencing. The instruments reliably produces high quality sequencing data with reads up to 1000bp and the ABI 3730 can analyze up to 750 samples in a 24-hr period, allowing for fast turnaround times. We also have tools available to assist with regulatory and compliance requirements.

To analyze data we have ABI software packages loaded at workstations in our facility:

Sequencing Analysis v5.2 – Designed to base-call; assign quality values; trim, display, and edit DNA sequencing data.

Seqscape® v2.5 – Allows the user to perform reference based analysis such as mutation detection and analysis, SNP identification, allele identification, and sequence confirmation.

GeneMapper® v4.0 – Enables automated allele calling and includes tools for SNPlex™ data analysis.

Bio-Rad gel systems
The Bio-Rad Sub-Cell GT and Mini Sub-Cell GT are agarose gel systems that allow analysis of a few to up to 96 nucleic acid samples on a single gel.

Gel Logic 200 Imaging system
The Kodak Gel imaging system features UV and white light illumination capability which allows visualization, imaging and quantitative measurements of nucleic acid and protein in stained gels.

LI-COR 4300
For clients who wish to view their data on true gel images we offer training on the LI-COR 4300. The 4300 is a third generation instrument based on LI-COR's highly sensitivity infrared technology. The instruments can be used for microsatellite, AFLP analysis, reverse genetics and DNA sequencing.

We carry LI-COR software packages for data analysis.

E-seq – Controls electrophoresis, sequences electrophoresis image files, and produces reports for data base submission.

Align-IR – Designed to provide sequencing alignment and assembly functions.

SagaGT – Automates electrophoresis,lane finding, location of standards, calibration of band sizes, and allele scoring.

Sagamx AFLP – Automates electrophoresis through band scoring.

Nanodrop ND-1000
The NanoDrop ND-1000 is a full spectrum (220-750nm) spectrophotometer that can measure 2 ul nucleic acids, protein and cell culture samples with high accuracy and reproducibility. The spectrophotometer utilizes sample surface tension to hold the sample in place eliminating the need for cumbersome cuvettes and allows for easy clean-up.

Pall Life Sciences Multi-Well Plate Manifold
The Pall vacuum manifold can be used with multi-well filter plates for the concentration, fractionation, desalting and buffer exchange of up to 96 samples at a time.

PCR Machines
The genomics facility is equipped with 6 96-well PCR machines. Four GeneAmp PCR system 9700's are specifically designed for amplification of nucleic acids to be analyzed on the ABI DNA Analyzers. A BioRad C1000 thermal cycler has a gradient feature that saves time by optimizing annealing temperatures in a single run.