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Genomic Core Facility: OverviewBy M.L Sogin and H. G. Morrison
Instrumentation and throughputOur current facility operates an Applied Biosystems 3730XL DNA Analyzer and a LI-COR 4200 IR system that can generate 1100 bp read lengths. Because the LI-COR system is economically inefficient relative to the 3730XL, we reserve its use for special or small-scale projects. There are no other capillary or slab-based sequencing machines within 75 miles of Woods Hole.
Excluding quality control and maintenance runs, we successfully processed ~310,000 reads during 2003 on our existing 3730XL sequencing system. Except for fifteen days of maintenance plus an additional two weeks of scheduled vacations in late December, our 3730XL operated near capacity on a continuous basis, seven days/week. The ability to load a dozen or more 96 or 384-well plates allows the instrument to run unattended for at least 48 hours, or with minimal interactions for longer periods of time. Approximately 50% of our usage in 2003 corresponds to NIH-supported genome projects (Giardia lamblia and the carpenter ant symbiont Blochmannia) while the balance was consumed by our NASA-supported metagenomic studies, an NSF genome project (Nosema locustae) and LEXEN-related cDNA projects.
The remaining machine time (approximately 28,800 reads) was fully utilized by other investigators in the Woods Hole scientific community, including NIEHS-supported work in the laboratories of John Stegeman and Mark Hahn.
Our total usage represented a fifty percent increase over the previous year (2002), which relied upon 3700 technology installed in January 2002. By comparison, the relatively low throughput of five LI-COR systems (purchased before the availability of capillary instruments) constrained our sequencing output to 52,000 reads prior to 2001.