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DNA Microarray Core Facility
http://microarray.org/sfgf/jsp/home.jsp
http://genome-www5.stanford.edu
Facility Co-Director: Catherine Ball, PhD; John Coller, PhD, main contact; Mike Fero, PhD; and Gavin Sherlock, PhD
Contact
Catherine Ball, PhD
Co-Director DMCF
Room S201, Grand Building
Stanford, CA 94305
Tel: 650-736-0077
Email: ball@genome.stanford.edu
John Coller, PhD, main contact
Co-Director, DMCF
Room 0120, CCSR Building
Stanford, CA 94305
Tel: 650-736-2434
Email: john.coller@stanford.edu
Mike Fero, PhD
Co-Director, DMCF
Room 4256, CCSR Building
Stanford, CA 94305
Tel:650-736-2431
Email: mike.fero@stanford.edu
Gavin Sherlock, PhD
Co-Director, DMCF
Room S201, Grant Building
Stanford, CA 94305
Tel: 650-498-6012
Email: Sherlock@genome.stanford.edu
Overview
The goal of the DNA Microarray Core Facility (DMCF) is to facilitate the application of cutting-edge microarray technology and analysis techniques by Cancer Center members. Services provided include producing catalog and custom-spotted microarrays, supporting use of multiple formats of Stanford University and commercial microarrays, assisting with experimental design, archiving of array data and providing bioinformatics tools for the annotation, analysis, visualization and publication of microarray data. The DMCF combines the resources of the Stanford Functional Genomics Facility, which develops new technology for genomics, and the Stanford Microarray Database (SMD), which is the largest and mostly widely used public database supporting microarray research. The main objective of the DMCF is to provide Cancer Center members with a complete set of reagents and tools to allow them to carry out high-throughput and high-impact cancer research using microarrays, from assistance with experimental design to publication of the generated data.
Services
Microarray production
The DMCF contains a fully equipped microarray production facility and can produce microarrays based on any type of biological solution compatible with capillary deposition (cDNAs, oligonucleotides, antibodies, proteins, etc.). The primary use is for DNA microarrays. DMCF provides two oligonucleotide-based, full-genome standard production microarrays for researchers, one for human and one mouse. The human gene array contains approximately 43,000 spots, including I.M.A.G.E. consortium clones from the Research Genetics Sequence Verified clone set, the CGAP clone set, positive-control spots and a small number of custom spots as requested. The mouse gene array contains the RIKEN full-length cDNA clones, the NIA 15K clone set, clones from the Brain Molecular Anatomy Project, Research Genetics Verified clones and clones from private libraries. Custom microarrays such as from D. melanogaster, C. elegans, S. pneumoniae and E. coli also are available. These custom arrays range from 1000 spots to 40,000 spots.
Microarray hybridization and scanning
The DMCF provides complete services for carrying out microarray experiments, including experimental design, sample labeling, hybridization, scanning, signal extraction, data analysis and database uploading.
Microarray data management
The DMCF provides researchers with all bioinformatics support necessary for microarray experiments, including data analysis and secure storage. The database and software packages are actively developed to keep abreast of new applications of microarray technology and new data analysis methods. Also supported are “non-expression” applications of microarrays, including array-based comparative genome hybridization (aCGH) and array-based chromatin immunoprecipitation (chip-chIP). All access, including retrieving, annotating, sharing, evaluating, analyzing and publishing DNA microarray data, is web based.
Training
The DMCF provides training and assistance for those researchers who plan to do additional experiments unassisted and for microarray data analysis. Once trained, users have access to equipment and data analysis available in DMCF.
Operation
Microarray production and hybridization experiments are performed in Room 0120, CCSR Building. The microarray data management group is located in the Grant Builing, Room S201. DMCF personnel are present during normal business hours of 8 am to 5 pm for consultation. The data analysis software package is available 24 hours a day via the SMD website. The microarray production facility may run up to 24 hours a day during periods of peak demand.
Procedures
Cancer Center members who want to use DMCF services can create accounts using online registration forms to order microarrays or hybridization services (www.microarray.org) or to use the bioinformatics tools associated with SMD (http://smd.stanford.edu/cgi-bin/tools/display/registration.pl). After accounts are established, researchers simply log into the web sites to request microarray services or to enter, display or analyze microarray data.
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