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Keck-UNM Genomics Resource
The Keck-UNM Genomics Resource (KUGR) is a shared service facility designed to facilitate the use of microarrays and high-throughput assays of gene expression. The facility receives partial financial support from the UNM School of Medicine, the Cancer Research and Treatment Facility, the New Mexico Center for Environmental Health Sciences (NIEHS Center) and the State of New Mexico, and is available for use by all faculty at UNM and its affiliates.
The KUGR shared resource has a complete Affymetrix system including two automated hybridization/fluidics stations, a high-resolution GeneChip scanner with autoloader and GCOS data server as well as a suite of specialized instruments for the analysis of nucleic acids and the production and analysis of custom spotted microarrays. The KUGR facility offers a range of services including:
- Affymetrix 3'-Expression Arrays: The standard gene expression arrays use up to 22 probe sets per transcript to measure the abundance of the 3'-ends of up to 45,000 well-characterized and less characterized transcripts.
- Affymetrix All-Exon Arrays: New! The most complete gene expression arrays from Affymetrix detect expression of more than 1.4 million well characterized and predicted exons, divided into 250,000 transcript clusters. These arrays are ideal for studying gene expression and alternative RNA splicing.
- Affymetrix SNP Genotyping: New! By measuring up to 500,000 single nucleotide polymorphisms distributed throughout the genome, these arrays can map genetic loci and can detect loss of heterozygosity (LOH) and changes in copy number.
- Affymetrix Targeted Genotyping: New! This approach uses molecular inversion probes to measure 1500 to 20,000 single nucleotide polymorphisms in a highly sensitive, flexible and cost-effective methodology.
- TaqMan SNP Assays: KUGR uses high throughput real time PCR (TaqMan) assays to measure single nucleotide polymorphisms in human samples. This assay is appropriate for measuring a few or a few dozen SNPs per sample.
- Microarray Data Analysis: KUGR facility staff use sophisticated data analysis methods to analyze gene expression and genotyping data and strive to provide our users with publication-quality figures for their manuscripts or grant applications.
- Real Time PCR: The KUGR Facility staff is highly experienced and can perform real-time PCR assays for UNM laboratories. These assays are ideal for quantitative measurements of gene expression and for detection of human SNPs using commercial assays.
- Training Clinics and Workshops: The expert staff trains users to use the resource instruments and to design and implement successful genomics experiments.
- Genomics Software: The KUGR facility coordinates the purchase of genomics software through the UNM School of Medicine Office of Research, which subsidizes the purshase cost through a cost-sharing mechanism.
Please acknowledge the KUGR facility in your publications !
STAFF AND CONTACT INFORMATION
Located in Cancer Research Facility Room 118
Faculty Director:
Scott A. Ness, Ph.D.
Associate Professor, Dept. of Molecular Genetics and Microbiology
Office: CRF 121; Tel: (505) 272-9883; e-mail: ness@unm.edu
Microarray Facility Technical Director:
Gavin Pickett, Ph.D.
Tel: (505) 272-5564
e-mail: ggpickett@salud.unm.edu
Senior Technical Staff:
Beckie Lobb, M.S.
Tel: (505) 272-5564
e-mail: rlobb@salud.unm.edu
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Major Equipment and Resources:
Affymetrix System: A complete suite of instruments including two fluidics/wash stations, a high-resolution scanner with autoloader, a GCOS data server and several workstations for data analysis.
Sample Analysis: An Agilent BioAnalyzer and a Nanodrop spectrophotometer.
PCR & Fluidics: Three Quad-96 MJ Research thermal cyclers and two robots for assay set up.
Data Storage: Dedicated firewall and network subnet, RAID-5 data storage on a dedicated server.
Data Analysis: Affymetrix GCOS, Agilent/Silicon Genetics GeneSpring, Significance Analysis of Microarrays (SAM), statistical package ‘R’.
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Important Links:
Affymetrix
Applied Biosystems
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See the Disclaimer and Copyright Information Page. Copyright 2000. University of New Mexico Health Sciences Center. All rights reserved. Last updated: 6/00.
Questions or comments about this page contact Scott Ness
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