Core D - Proteomics/Genomics
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Director: William H. Robinson (Email: ) John Collier - Director, Stanford Functional Genomics Facility (Tel. 650-736-2434; Email: ) Laboratory Scientists: Elena Seraia (Tel. 650-736-2434; Email: ) - for the Microarray Facility Che-Hong Chen (650-498-7457; Email: ) - in charge of 2D gel analysis Orr Sharpe (650-849-1245); Email: ) - for Mass Spec samples Contact for HTBC: David Solow-Cordero (650-725-6002; Email: ) |
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Functions
- Mass spectrometry peptide analysis and sequencing
- DNA microarray: printing, scanning, and assistance with data analysis
- 2D gel analysis
- High through-put screening
Mass Spectrometry
The DDC Mass Spectrometry component is based upon an Agilent XCT Plus nanospray mass spectrometer with an optional MALDI source. This is an ion trap mass spectrometer with multiple available performance levels and 6 available ionizing sources. It is also equiped with a front-end liquid chromatography unit. This instrument enables identification of polypeptides, including detection of certain postranslational modifications, and peptide sequencing. This Core is located in Building 101 of the Palo Alto VA.
High-Throughput Bioscience
HTBC offers compound screening and assistance in developing high-throughput screens using large commercial compound library (~130,000 compounds) to identify bioactive drugs for the investigator's system of interest; as well as siRNA genomic library (targeting ~21,000 genes). HTBC is administered by James Chen and David Solow-Cordero.
The DDC will cover $500 of usage per investigator, and an additional $1000 should the project continue. A full screen costs between $10,000 to $14,000. The DDC's subsidy can be applied toward the cost of a full screen.
HTBC web site: http://htbc.stanford.edu
2D Gel Analysis
This is provided by Dr. Che-Hong Chen who is an expert in this technique. Dr. Chen works with Ms. Sharpe in cases when spots need to be picked for mass spectrometry identification.
Microarray Component
The DDC provides RBI's with resources in order to facilitate access to, and use of, DNA microarray technology. These resources include:
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Each RBI may purchase up to $1560 per year worth of human or mouse arrays (i.e., ~12 arrays) from Stanford University 's Core facility. Oversight of these purchases is facilitated by Linda Jacob, DDC administrator ( ).
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The Stanford Functional Genomics Facility provides access to Axon microarray scanners for all users. In addition, the DDC has a computer and additional copies of the Axon Scanner GenePix software (with computer enabling devices), to aid with the initial phases of microarray image processing (including "gridding" and "flagging"). This computer is located within the DDC Administrative offices. General protocols for sample RNA preparation, probe labeling, microarray hybridization, and access to the Stanford Microarray Database. The DDC also provides 50% FTE of dedicated technical support that is part of the University Microarray Core. This technical support provides essential expertise at all levels of microarray experiment implementation, and is dedicated to DDC RBIs.
Example of human cDNA microarrays used to define the gene expression profile of gastric cancer. The data presented is the result of hierarchical clustering of 5,200 genes (rows) and 126 tissue samples (columns). Mol Biol Cell . (2003) 14(8):3208-15.
2D Gel Analysis
The major service here is a 2D gel analysis that is provided by Dr. Che-Hong Chen. This facilty further enhances the DDC's support in the field of proteomics, and will be transitioning into our new Proteomics/Genomics Core (Table 3), as an ideal complement to the Mass Spectrometry Facility.
Laser Capture Microdissection
A state-of-the-art Laser Capture Microscope (LCM) is available for DDC member use. This LCM belongs to the Dermatology Department that has graciously agreed to a sharing use arrangement.
