Microarray Shared Research Facility

Overview

he Microarray Shared Research Facility provides crucial research support for investigators interested in using Affymetrix GeneChips, glass slide spotted arrays, or peptide/protein arrays. The facility has a 15K sequence-verified mouse library from NIA, a 40K sequence-verified human library from Research Genetics, and a Tetrad Thermal Cycler for clone amplification. We also have an arrayer and scanner from Affymetrix to spot and analyze the array. As a high throughput and high-quality facility, we equip a fully automatic robot for liquid handling, PCR purification, and re-arraying/cherry-picking and a second high-capacity arrayer from BioRobotics. As we continue to develop the facility, we will include an automatic hybridization/washing station to fulfill our high-throughput demand for spotted array.

The facility has a complete Affymetrix GeneChip system including hybridization oven, automatic fluid station, and high-resolution chip reader. Our shared facility offers full service for RNA validation, target cRNA labeling/preparation, and chip-hybridization/post-processing as well as several control procedures to provide users with consistent and reliable results. We also offer partial service for chip hybridization & post-processing labeled samples. Detailed protocols can be found in the Genechip System > Protocols section of this Web site.

For microarray target labeling procedure, the facility has made available in-house optimized protocols for both spotted arrays, including direct and indirect labeling methods, and Affymetrix GeneChips. For data processing, we have a data analysis workstation with high-speed computers loaded with comprehensive and powerful software packages, which allows users to identify significant changes quickly and to interpret the results comprehensively. We continuously provide an information-rich microarray technology Web site to ensure that the latest technology is available to our users. We also have server licenses for accessing the software remotely.

In addition, the facility has networked nine high-speed NT/2000 workstations, each with 20-60 GB drives. Six stations interface with our GMS fluorescent microarray scanner, GMS arrayer, Qiagen 8000 Liquid-Handeling Robot/UV microplate reader, High speed BioRobotics arrayer, Agilent Bioanalyzer, and Affymetrix fluid station/scanner, respectively. Three of the computers are installed with comprehensive data analysis software packages including Affymetrix Microarray Suite 5.0, MicroDB and Data Mining Tool, Biodiscovery's Imagene & Gene Sight, and Iobion's GeneTraffic software for spotted array.

We are working on setting up a microarray data analysis station with multiple computers and software for our users.

In addition to access to the equipment, the Facility provides consultation and assistance in research efforts. The Facility Director, Dr. Tearina Chu (tearina.chu@mssm.edu), maintains an office in the Facility and is available by appointment for consultation. Dr. Chu and her staff will assist you in the design and execution of your experiments as well as with important data analysis procedures. Use of the Facility is always monitored by the Facility staff.

PLEASE REMEMBER - For funding purposes, it is important to acknowledge the Microarray Shared Research Facility in all publications that include data derived from the facility. Thank you.