The TSRI DNA Array Core Facility was established in 1998 to provide microarray technology to the Scripps research community. Since then the scope has been expanded to include a variety of related services and resources, for example: Sample Quantification, Genotyping, Gene Expression Analysis, and a Data Analysis and Statistics Resource. In addition the DNA Array Core provides custom spotted arrays, image analysis, and general statistics consulting.
The DNA ARRAY Core is an active participant in several research projects at TSRI: The Consortium for Functional Glycomics, General Clinical Research Center (GCRC), The Scripps NeuroAIDS Preclinical Studies (SNAPS) Center, Transplant Genomics Collaborative Group Program Project, and the Vision Research Core Center.
1. The NanoDrop ND-1000 UV-Vis Scanning Spectrophotometer enables accurate quantification of total nucleic acid quantity and quality for 1-2 ul sample volumes. The small volume requirements of this instrument are extremely useful for analysis of small samples obtained from clinical or microdissected specimens.
2. The Agilent 2100 Bioanalyzer uses microfluidics (lab-on-a-chip) technology to quantify DNA, RNA, or proteins in a sample. The key advantage of this instrument is that it allows analysis of total RNA for samples containing as little as 25 picograms. Up to 12 samples can be processed in 30 minutes.
1. Roche Applied Sciences LightTyper detects real time differences in probe fluorescence between perfect match and single base mismatch melting temperatures for SNP genotyping.
2. Genetic Bit Analysis (GBA or minisequencing) is a solid-phase primer extension-based assay for genotyping SNPs.
3. Affymetrix GeneChip Mapping 10K and 100K SNP Mapping Arrays generates over 10,000 or 100,000 human SNP genotypes on the 10K and 100K arrays respectively for association and linkage studies.
Gene Expression Analysis
Affymetrix GeneChip Technology remains the principle technology in the DNA Array Core for high throughput gene expression analysis.
Alternative Technologies: The DNA Array Core offers alternative technologies that may be more appropriate for specific applications. These include: custom spotting on glass slides of nucleic acids, proteins, peptides, carbohydrates or other biological molecules.
Data Analysis and Statistics Resources
The Core offers a statistical resource to the Scripps research community. Statistics consulting, access to computer workstations, general experimental design, summaries of quantification, quality control, and preliminary analysis are routinely provided to customers, with more complex statistical analysis available by request.
In addition, we offer access, training, and assistance in the use of several software packages specifically designed for analysis of microarray data and general statistics. These include both commercial products and publicly available software: for example: GeneSpring (Silicon Genetics); ImaGene (Biodiscovery); StatGraphics (Manugistics), GCOS (Affymetrix), and MS Excel add-ins: for example BRB ArrayTools (NCI), SAM (Stanford University) and a Resampling tool (Resampling Stats).
Current Project Involvement
The Consortium for Functional Glycomics (CFG) is a large research initiative, funded by NIGMS, to understand the role of carbohydrate-protein interactions in cell-cell communication. The Microarray Core (Core E at TSRI) of the CFG has designed a custom Affymetrix GeneChip, GLYCOv2, containing probe sets to monitor the expression of 2,001 human and mouse transcripts of interest to the Consortium. For more information about Core E please see the CFG website [http://web.mit.edu/glycomics/consortium/] or contact the Core Facility at (858) 784-2263.
The Scripps NeuroAIDS Preclinical Studies (SNAPS) Center is an NIMH funded program in Mental Health/AIDS Research (CSPAR) P30 Center Grant to TSRI, supporting biomedical research relevant to neuroAIDS. The objective of the Functional Genomics Core is to facilitate the application of functional genomics to advance our understanding of the structural and functional impact of HIV infection in the CNS. The Core utilizes high-throughput, sensitive state-of-the-art techniques to analyze alterations in gene expression consequent to viral, host response, and therapeutic manipulations, and provides assistance in microarray experimental design and analysis, and biostatistical support. For more information please see the SNAPS website [http://www.scripps.edu/services/snaps/] or contact the Core Facility at (858) 784-2263.
The Transplant Genomics Collaborative Group (TGCG) is a National Institute of Allergy and Infectious Diseases (NIAID) funded multicenter project, the theme of which is to apply developing technologies for gene expression profiling, proteomics, and complex trait genetics to kidney transplantation. Our primary objective is to advance our understanding of both the clinical problems and basic biology of kidney transplantation. The first objective of this project is to integrate data on gene expression profiling with proteomics and complex trait genetics to generate a more comprehensive description of the molecular basis of the clinical response to kidney transplantation. The second is to establish the requisite proof of principle to design a prospective clinical trial to test the hypothesis that PBL profiles can be used to monitor the efficacy of immunosuppression in 'real-time'. For more information on the Genomics for Kidney Transplantation Project check the Salomon laboratory website [http://www.scripps.edu/mem/eht/salomon/ ] or contact the Core Facility at (858) 784-2263.
Vision Research Core Center at TSRI is a National Eye Institute (NEI) funded core that supports shared resources for TSRI and UCSD NEI researchers who have independent programs in vision science. For more information please see the Vision Center website [http://core-eye.scripps.edu/] or contact the Core Facility at (858) 784-2263.
For more information about services offered by the DNA Array Core Facility, please visit the Core Facility website.