High Throughput Genomic Sequencing and Analysis

The University of Utah Genome Depot has participated in a number of large-scale genomic sequencing projects. Our technical capabilities include high throughput sequencing on the ABI 3700 platform using both plasmid and PCR templates. A production sequencing line is capable of processing 4,000 samples a day from DNA purification through base calling analysis. A variety of bioinformatic tools are used to process and analyze the sequence data. Snapshots and descriptions of our automated laboratory devices can be found at our Technology page.

If you have large-scale sequencing needs or a desire to collaborate, please contact us.

Mus musculusRattus norvegicusPyrococcus furiosus

We have generated a global plasmid scaffold as part of the NIH Mouse Genome Sequencing network. A whole genome, medium insert (10 kb), plasmid library was constructed from Mus musculus strain C57BL/6J(female). Paired end sequence reads from this library were generated on ABI3700 sequencing instruments. Paired end reads from ~1.5 million clones, generating approximately 5-fold sequence coverage of the mouse genome, were used in the initial sequencing of the mouse genome (Dec. 5 2002, Nature paper).

Library clones are available through the Utah Genome Depot.

To receive a clone from the UUGC library:

Fill out our Online Mouse Clone Request Form

or Email us: Mouse Contact.

Please include the reference number (GSS, ACC, or UUGC Number).

Related Publications

1.� Initial sequencing and comparative analysis of the mouse genome. The Mouse Genome Consortium, Nature 420, 520-562 (Dec 5, 2002).

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The University of Utah Genome Depot is a member of the Rat Genome Sequencing Consortium. The Consortium is led by the Baylor College of Medicine Human Genome Sequencing Center, and is a collaboration with Celera Genomics, Genome Therapeutics, The Institute for Genome Research, Children’s Hospital Oakland Research Institute, Medical College of Wisconsin, The University of British Columbia. The National Heart, Lung, and Blood Institute (NHLBI) and the National Human Genome Research Institute (NHGRI) funds the National Institutes of Health (NIH) Rat Genome Sequencing network.

We have generated a global plasmid scaffold from a whole genome, medium insert (10kb) library from Rattus norvegicus (female). Paired end sequence reads from this library were generated on ABI3700 sequencing instruments. 1.1 million high-quality paired-end sequences have been deposited at NCBI.

The genome assembly is available for download at http://www.hgsc.bcm.tmc.edu/projects/rat.

Sequence traces are available at NCBI http://www.ncbi.nlm.nih.gov/Traces/trace.cgi.

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We were funded, by the Department of Energy http://www.energy.gov, to sequence the complete genome of Pyrococcus furiosus. The annotated sequence can be accessed at NCBI http://www.ncbi.nlm.nih.gov or on our site at http://www.genome.utah.edu/sequence.html.

Related Publications

1. Robb, FT, Maeder, DL, Brown, JR, DiRuggiero, J, Stump, MD, Yeh, RK, Weiss, RB and Dunn, DM (2001). The Genomic Sequence of the Hyperthermophile, Pyrococcus furiosus: Implications for Physiology and Enzymology. In Methods in Enzymology: Hyperthermophilic Enzymes, Part A Edited by Michael W.W. Adams and Robert M. Kelly Methods Enzymol. 2001; 330:134-57, 500 pp./ISBN: 0121822311.

2. DiRuggiero, J, Dunn, D, Maeder, DL, Holley-Shanks, R, Chatard, J, Horlacher, R, Robb, FT, Boos, W, Weiss, RB (2000) Evidence for recent lateral gene transfer among hyperthermophilic Archaea. Mol. Microbiology 2000 38(4): 684-693.

3. Ma K, Weiss R, Adams MW (2000) Characterization of hydrogenase II from the hyperthermophilic archaeon Pyrococcus furiosus and assessment of its role in sulfur reduction. J Bacteriol 2000 Apr; 182(7): 1864-71.

4. Maeder DL, Weiss RB, Dunn DM, Cherry JL, Gonzalez JM, DiRuggiero J, Robb FT (1999) Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences. Genetics 1999 Aug; 152(4): 1299-305.

5. Roy R, Mukund S, Schut GJ, Dunn DM, Weiss R, Adams MW (1999) Purification and Molecular Characterization of the Tungsten-Containing Formaldehyde Ferredoxin Oxidoreductase from the Hyperthermophilic Archaeon Pyrococcus furiosus: the Third of a Putative Five-Member Tungstoenzyme Family. J Bacteriol 1999 Feb 15; 181(4): 1171-1180.

6. Ghosh M, Grunden AM, Dunn DM, Weiss R, Adams MW (1998) Characterization of native and recombinant forms of an unusual cobalt-dependent proline dipeptidase (prolidase) from the hyperthermophilic archaeon Pyrococcus furiosus. J Bacteriol 1998 Sep; 180(18): 4781-9.

7. Brown JR, Robb FT, Weiss R, Doolittle WF (1997). Evidence for the early divergence of tryptophanyl-and tyrosyl-tRNA synthetases. J Mol Evol 1997 Jul: 45(1): 9-16

8. Riera, J, Robb, RT, Weiss, R, Fontecave. (1997) Ribonucleotide reductase in the archaeon Pyrococcus furiosus: a critical enzyme in the evolution of DNA genomes? Proc. Natl. Acad. Sci. 1997 U.S.A. 94:475-478.