*** KUGR News ***
KUGR Facility Director Scott Ness addresses a national NIH workshop on management of shared facilities.
NCRR Workshop on Efficient Management and Utilization of Core Facilities — July 14 – 15, 2009Dr. Ness begins talking at 2:17:00 on the Day 1 Videocast
KUGR: Facilitating Genomics Research at UNM Health Sciences Center
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 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:
The newest addition to the KUGR facility is a Polonator next-generation sequencing instrument, which will add new services, such as whole genome sequencing, transcriptome sequencing and epigenetics and chromatin immunoprecipitation-sequencing (ChIP-seq) assays. These services should be available by July 2009.
- 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: 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 and for detecting non-coding RNAs.
- Affymetrix SNP Genotyping: By measuring up to 2,000,000 single nucleotide polymorphisms distributed throughout the genome, these arrays are designed for whole genome association studies. The Affymetrix SNP 6.0 arrays can map genetic loci and can detect loss of heterozygosity (LOH) and changes in copy number.
- 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.
- Expert 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.
- Epigenetics Assays: Affymetrix promoter tiling arrays have probes centered 35 nt apart across the promoters of 25,000 genes. These arrays are designed for epigenetics assays such as detecting promoter methylation or for performing chromatin immunoprecipitation (ChIP on chip) assays.
- Whole Genome and Transcriptome Sequencing: In 2009 KUGR will begin offering a new set of advanced services based on the Polonator next-generation genome-sequencing instrument. These will include low cost whole genome sequencing, transcriptome sequencing and chromatin immunoprecipitation (ChIP-seq) assays. Contact us for more information about the availability of these new services.
Please acknowledge the KUGR facility in your publications !
Staff and Contact Information:
The KUGR facility is located in Cancer Research Facility Room 118
Faculty Director:
Scott A. Ness, Ph.D.
Professor, Molecular Genetics and Microbiology
Office: CRF 121; Tel: (505) 272-9883
Technical Director:
Gavin Pickett, Ph.D.
CRF 118
Tel: (505) 272-5564
Senior Technical Staff:
Jamie Padilla
CRF 118
Tel: (505) 272-5564
Important Links:
Affymetrix
Applied Biosystems
Danaher Motion
Polonator