The Microarray Core Facility at University Of Colorado Health Sciences Center (UCHSC) is an advanced, state-of-the-art Microarray Technology Center providing crucial research support for investigators interested in using Affymetrix GeneChips®, CombiMatrix CustomArray™ Chips or the Nanogen NanoChip®. We also host rtPCR with the Bio-Rad iCycler. Our team is dedicated to providing high-quality microarray laboratory instruction, service, and consultation to the research and clinical community affiliated with UCHSC and other research institutions in the region.

Affymetrix GeneChip® systems utilize proprietary technology which exploits photolithographic fabrication techniques for light-directed chemical synthesis. The process results in extremely high-density arrays of specific oligonucleotide probe sets synthesized directly onto their glass substrate, which is then placed in a plastic cartridge for easy and safe hybridization, staining, washing, and handling. Affymetrix's software performs statistical algorithms of scanned images to analyze the expression data. Further information is available through the Affymetrix and NetAffx™ websites. This platform can analyze all GeneChip® probe arrays for gene expression analysis and DNA SNP analysis. A broad range of whole genome arrays are available in Affymetrix product lines, including but not limited to: the Human, Mouse, Rat, Yeast, C. elegans, Arabidopsis, Drosophila, E. coli and P. aeruginosa genome arrays, human SNP array, rat toxicology and neurobiology arrays. The complete list of arrays is available on the Affymetrix website.

CombiMatrix CustomArray™ uses a specially modified CMOS semiconductor (image) to direct the molecular assembly of a specific sequence of DNA bases in response to a digital command. Each feature on the array (a microelectrode) is digitally addressed to selectively generate acid, by means of an electrochemical reaction which, in turn, controls the detritylation reaction during phosphoramidite synthesis. A software program is used to control the detritylation pattern applied on the chip during synthesis. Oligonucleotide probes for the entire microarray were designed in one step using a web-based probe design algorithm available at no charge to CustomArray™ users. The probe identification system was designed to find specific, compatible probes for hybridization, and used a range of heuristics including: tendency for hairpin formation, base frequency, randomness, and potential to cross-hybridize to multiple targets. Probes were designed to be 35 to 40 bases in length with Tm's falling within a 5ºC window. Probes were randomly distributed across the surface of the array to generate a layout file which was then used to direct the synthesis of oligonucleoties at individual sites on the array.

A typical microarray experiment includes the following procedures:

1. DNA or Total RNA isolation and quality assessment
2. Sample labeling (Generation of biotin-labeled nucleic acid molecules)
3. Chip processing (Hybridization / Washing / Staining / Scanning)
4. Data analysis and interpretation
5. Data validation

We are full service provider and can do all the procedures needed for your microarray experiment, but customers have the choice to perform the tasks (procedures) themselves except the procedure 3. We run hybridization, fluidics and scanning for you. If a customer chooses to do a procedure themselves, it is strongly recommended to do it in the core lab using our standardized protocols and reagents. We can help you design your experiment and provide detailed protocols for both RNA and DNA sample preparations and labeling, RNA and DNA quantification and quality assessment. We also have the capability of providing data analysis and support services for storage of data by commercially available software. An integral part of the core is the formal relationship with the Bioinformatics group to construct and validate expression models using novel algorithms.

The Microarray Core Laboratory is currently located on both the 9th Avenue and Fitzsimons campuses. Customers have the choice to go either location for the services. The facility is equipped with a complete Affymetrix GeneChip® Instrumentation System, including four Model 450 Fluidics Stations, and three model GCS 3000 Gene array scanners. The extra fluidics stations and scanners enable higher throughput, and provide mechanical backup in the case of equipment failure. The core is also equipped with three Dell workstations for running the fluidics and scanners, two hybridization ovens, two Aglient Bioanalyzers, two NanoDrop® ND-1000 UV-Vis Spectrophotometers, one HP UV-Visible ChemStation, and the complete Affymetrix Laboratory Information Management System, which includes a Dell PowerEdge 6300 server, 5-seat license for Expression Data Mining Tool (EDMT), and GeneChip® Operating Software. The Laboratory Information Management System allows us to house and share our data. In addition, the core owns two more Dell server computers, PowerEdge 2600 and PowerEdge 6650, hosting the core lab website and GeneTraffic® software package. More than 2 terabytes of hard drive space and high speed computing power of these computers enable us to handle massive amount of microarray data generated for our customers. 9 more high end workstations are readily available in the core to our customers and core personnel for data analysis and performing managerial tasks. Pictures!

We have several statistical packages, which will be of great importance in analyzing the data. Currently, six distinct bioinformatic packages for gene expression data are available to our customers through our core. These include:

1. Affymetrix GeneChip® Operating Software
2. Affymetrix Expression Data Mining Tool
3. Genespring® by Silicon Genetics
4. Ingenuity pathway analysis software by Ingenuity
5. Partek Genomics Suite
6. GeneTraffic®/ArrayAssist by Iobion™.