Sponsored by the U.S. Department of Energy Human Genome Program
Human Genome News, Nov. 1994; 6(4):6
Stanford University DNA Sequence and Technology Center
STANFORD UNIVERSITY DNA SEQUENCE AND TECHNOLOGY CENTER (SUDSTC)
- (NIH, established 1993)
- RONALD W. DAVIS, Director
- David Botstein, Co-Director
- CONTACT: Jackie Couture (415/812-1968, Fax: -1975, couture@genome.stanford.edu); SUDSTC; 855 California Ave.; Palo Alto, CA 94304.
OTHER KEY RESEARCHERS
- Pat Brown
- Mike Cherry
- Fred Dietrich
- Richard Hyman
- Rick Norgren
- Peter Oefner
- Victoria Smith
MAJOR GOALS
- Development of a robust high-throughput sequencing methodology. Center efforts are divided into three parts: (1) automation, (2) sequencing, and (3) investigation of genome-wide approaches to analyzing biological function of uncharacterized DNA sequence.
- Current sequencing efforts focus on sequencing all of chromosome V and half of chromosome IV from Saccharomyces cerevisiae as part of the international effort to sequence the entire yeast genome by 1996.
MAJOR ACCOMPLISHMENTS
- Shotgun sequencing of about 540 kb (>95%) of yeast chromosome V and 300 kb of chromosome IV (average redundancy of 10).
- Efficient DNA sequencing using automation and a 96-well format; two Applied Biosystems Inc. Catalyst robots, one Beckman Biomek 1000 robot with side loader, and five Applied Biosystems Inc. 373 sequencing robots used.
- Development of software (Guile) for extending Biomek 1000 robot.
- Development of the Saccharomyces Genome Database.
- Construction of a prototype robotics system for automatic plaque and colony picking.
- Design and construction of a rapid gel-pouring assembly and construction of a random-access microtiter plate server that can integrate with new instrumentation.
- Completion of an automated multiplex oligonucleotide synthesizer that has produced about 7000 oligonucleotides.
- Development of a new DNA-shearing instrument that yields uniform, cloning-efficient fragments.
- Use of transposon mutagenesis in gene function studies.
AVAILABLE RESOURCES
- Sequence data for most of yeast chromosome V and a large region of chromosome IV [Fred Dietrich (dietrich@genome.stanford.edu)].
- Assistance in database development [Fabien Petel (fabien@genome.stanford.edu) and M. Cherry (cherry@genome.stanford.edu)].
- Yeast Genome Information Server (genome.stanford.edu).
- Saccharomyces Genome Database (415/725-8956, Fax: /723-7016; yeast-curator@genome.stanford.edu).
- Information for Biomek 1000 software (ssmith@genome.stanford.edu), Applied Biosystems Inc. Catalyst software (jdc@genome.stanford.edu), oligonucleotide synthesizer (brennan@genome.stanford.edu), DNA shearing (oefner@genome.stanford.edu), image analysis and robotics (rick@genome.stanford.edu), base-calling software (aberno@genome.stanford.edu), gel slider pouring apparatus (lashkari@genome.stanford.edu), preparation of M13 libraries from poorly growing cosmids and lambda vectors (hyman@genome.stanford.edu).
HGMIS staff
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The electronic form of the newsletter may be cited in the following style:
Human Genome Program, U.S. Department of Energy, Human Genome News (v6n4).
