Microarray Core Facility
The Lewis-Sigler Institute for Integrative Genomics houses the Microarray Core Facility which is fully equipped for all aspects of microarray production and data acquisition and is operated in conjunction with the Sequencing Core Facility. The staff provide consultation on experimental design, training on use of the equipment, troubleshooting, and assistance with software and data analysis. The Microarray Core Facility works closely with Bioinformatics staff in the Center for Quantitative Biology to provide researchers with computing power and consulting services to analyze sequencing data, including use of the PUMAdb database and analysis system.
Complementary DNA, (cDNA’s) and PCR products are amplified and quality checked using the high throughput liquid handling Beckman Coulter Biomek FX, and MJ Research Tetrad thermocyclers. Spotting of PCR products or long Oligomers is accomplished on in-house Arrayers built according to the Joe DeRisi, Pat Brown design and operated by software written by Joe DeRisi. Hybridization probes are checked prior to labeling using the Agilent Bioanalyzer 2100 and the Nanodrop spectrophotometer. Post labeling efficiency is quantified by Nanodrop prior to application of probes to the array. Post-hybridization image acquisition is accomplished using any of two available scanners, an Axon 4200A Professional Scanner equipped with four laser scanning capability, or an Agilent Microarray scanner , two color, equipped with a 48 slide auto-sampler carousel. Data extraction from the images is accomplished using Axon’s Genepix software, versions 4.0, 5.1, or 6.0, or Agilent’s data feature extraction software v 9.5.
The facility also offers access to an Affymetrix Array station consisting of two fluidics stations handling four chips each, a hybridization oven, and a scanner-3000 complete with the “7G” upgrade. GCOS software is available for data analysis. Two computer workstations are available with Acuity 4.0 Software, and one with Pathway Assist Software.
Complementary to microarray analysis the facility offers access to two ABI 7900 quantitative PCR machines, one equipped with a 96 well block, the other with a 384 well block and robotic plate loader.
The entire lab space is ozone free protecting dye integrity of samples.