Lab Resources

GeneSpring GX 7.3.1

The latest version of GeneSpring (Agilent Technologies) is installed in a Dell Dimension 4700 desktop computer with an Intel® Pentium®-4 3.20 Ghz processor. Computer specs include: 2.0 GB RAM, 145 GB of memory, 4 USB drive outlets, DVD-RW, DVD-ROM, and a portable USB drive with 80 GHz capacity. This computer is solely used for analysis of microarray gene expression data. Our license is renewed every two years. In addition to GeneSpring, this computer runs CellDesigner 3.0, Macromedia Studio 8, Primer Express™, and Sequence Detection System 2.2.1. The latter two are used for primer design and analysis of real-time RT-PCR data from the 7900HT sequence detector (Applied Biosystems).

Ingenuity Pathway Analysis

This is an essential tool in our genome-wide analyses (microarrays and real-time RT-PCR) of tissue responses to nutrients, physiological state, or disease. It provides the means to model, analyze, and understand the complex biologcial systems under study. Furthermore, it has allowed us to ask more sophisticated questions about the knowledge obtained through gene and metabolic profiling, as well as whole-animal phenotypic observations.

GeneGo - Data Mining for Systems Biology

This is another complementary tool in our genome-wide analyses of tissue responses to nutrients, physiological state, or disease. Similar to IPA, GeneGo's tools and databases help capture and define the underlying biology behind different types of high-throughput experimental data. It provides the means to model, analyze, and understand the complex biologcial systems under our study.

Nanodrop® ND-1000

This is a state-of-the-art spectrophotometer used to quantify RNA, DNA, protein, and Cy3 and Cy5 dye incorporation. Loading volume is typically 2 uL. There is a Dell laser-jet printer attached to this system that enables different types of reports to be created. The laptop that runs the software is a Dell Latitude D510 with an Intel® Celeron® M 1.40 GHz processor. This machine has 504 MB RAM and 55.8 GB memory.

Microarray platforms

Bovine oligonucleotide microarrays and annotation file (collaboration with the Harris Lewin lab), and swine oligonucleotide microarray and annotation file. Both platforms contain over 13,000 oligonucleotides printed in duplicate on glass slides. These microarrays are printed on campus at the Functional Genomics unit of the W. M. Keck Center.

Centrifuges

Eppendorf Vacufuge, Eppendorf 5402 refrigerated microcentrifuge, Eppendorf 5424 microcentrifuge, Beckman Coulter Allegra 6R, and Beckman J2-21M high-speed.

Gel imaging system

Alpha Imager 2000 Documentation and Analysis System with a SONY UP-D895 digital printer.

Thermal cyclers

Three 96-well thermal cyclers, an Eppendorf Master Cycler gradient, a Bio-Rad MyCycler, and an MJ Research PTC-100.

Water system

Milli-Q Synthesis system ensuring high-purity water for molecular biology work.

Tissue and cell culture

MDBK and MacT cells are currently used to support our research. NUAIRE Biological Safety Cabinet and a Forma Scientific carbon dioxide incubator are available for conduct of tissue and cell culture experiments.

Cryo biological storage systems

Two Locator 8 Plus ultra-low storage systems. Combined storage capacity is >8,000 samples.

Microarray miscelaneous

Corning hybridization chambers, stainless-steel slide holders, copling jars, and an UV Stratalinker 1800 (Stratagene) to crosslink oligo probes prior to hybridizing samples to the arrays.

Molecular biology miscelaneous

Various sets of Eppendorf Reference and Research pipettors for dispensing 0.5-10 uL, 10-20 uL, 10-100 uL, 10-200 uL, and 100-1000 uL. Also, Eppendorf Repeater plus pipettors.

Biopsy tools

Mammary biopsy and liver biopsy trocars.

Fatty acid analysis

Gas chromatograph.