Molecular Biology, Genomics & Genetics, DERC - UCSD/UCLA

DERC - UCSD/UCLA Genomics :

Core Description and Goals:

A major goal in efforts to understand the mechanisms by which signal transduction pathways regulate programs of gene expression is to identify their direct target genes in response to regulatory signals The BIOGEM CORE Facility provides services to advance such efforts; conventional microarray analysis and early in 2004 promoter microarray analysis. Conventional microarray analysis will utilize glass slides spotted with PCR products corresponding to specific genes, allowing large-scale assessment of relative levels of gene expression. These arrays are intended to complement the use of commercially available microarrays (e.g., Amersham CodeLink microarrays). For example, microarrays containing a few hundred to a few thousand cDNA targets of particular interest can be printed at relatively low cost, allowing multiple experimental conditions to be examined that would be prohibitively expensive using commercially available arrays.

Services :

Custom Array production:
One of the major functions of the BIOGEM CORE Facility is to "print" cDNA microarrays from various clone and primer sets onto glass slides. BIOGEM offers assistance to investigators wishing to develop custom arrays targeted to a particular developmental stage, a specific cellular process or an organism with minimal genome sequence determined. The expertise available in BIOGEM allows researchers with minimal related experience to take full advantage of the microarray CORE services. As an example, BIOGEM prints a custom microarray of approximately 1000 cDNAs corresponding to genes of interest in metabolism, atherosclerosis and inflammation. Similar custom arrays could be fabricated for other sets of genes of interest, or for other species (e.g., human and rat).

Processing of Commercial Array Slides e.g. Amersham CodeLink™ Bioarrays:
The CodeLink™ system is a complete bioarray solution for high-performance gene expression profiling. CodeLink is an integrated platform that includes catalog and custom gene expression bioarrays, target preparation and bioarray processing reagents, and image analysis and QA/QC software.

The CodeLink™ system is particularly useful when carrying out experiments with very small amounts of RNA. Starting with small quantities total RNA is beneficial for several reasons. First, it results in decreased time, labor and costs associated with not having to purify poly(A)+RNA. Second, many samples (biopsy, for example) do not contain sufficient amounts of total RNA to enable purification of poly(A)+RNA. Such samples could only be processed if the small amount of present total RNA could be used. Third, the less the biological sample is manipulated, the lower the chance that artifacts due to RNA processing will be introduced. Finally, purification of poly(A)+RNA, typically performed on an oligo(dT) column, can bias the sample by enriching for polyadenylated transcripts.

In September 2002 BIOGEM became the official UCSD site for processing of CodeLink™ bioarrays. BIOGEM will provide target labeling, hybridizing and washing of CodeLink™ bioarrays in a service capacity. The investigator will provide RNA and BIOGEM will label the target, perform the hybridization and provide the user with raw and normalized microarray data.

Bioinformatics support.
BIOGEM has numerous public and commercial software tools available for data mining and is connected with numerous bioinformatics experts at UCSD who can provide additional advice.

Personnel training:
The CORE provides training for all DERC investigators engaged, or interested, in array-based research. This training includes assistance in designing and conducting array-based experiments, protocols for labeling fluorescent targets and hybridizing arrays.

Further array resources:
Further array resources are in development including fabricating promotor microarrays. Recent progress in combining the use of chromatin immunoprecipitation (ChIP) assays with DNA microarrays has allowed genome-wide analysis of transcription factor localization to specific promoter sequences in living cells. BIOGEM is currently fabricating murine promoter microarrays to allow genome-wide location analysis of transcription factors such as nuclear hormone receptors and signal-dependent transcription factors. These arrays will be available in early 2004.

People :

Christopher K. Glass, M.D., Ph.D. : Director, Genomics Core, . Phone: 858-534-6011

Gary Hardiman, Ph.D. : Director, Genomics Core, University of California San Diego2234 Bonner Hall9500 Gilman DriveLa Jolla CA 92093-0349 . Phone: 858-822-3792

Jerome I. Rotter, M.D. : Associate Center Director and Co-Director, Human Genetics Core, . Phone: 310-423-6467

Leslie J. Raffel, M.D. : Co-Director, Human Genetics Core, . Phone: 310-423-6451

Cynthia Hernandez : R.N.Genetics Study CoordinatorDivision of Medical Genetics , Cedars-Sinai Medical Center8700 Beverly Blvd. SSB378Los Angeles, California 90048 . Phone: (310) 423-1457