DNA Sequencing
Shared Resource Director: Phillip
SanMiguel
E-mail: pmiguel@purdue.edu
Department: Horticulture and Landscape Architecture
Shared Resource Operator/DNA Sequencing Manager: Doug Murphy
Phone: (765) 496-7368
Building/Room: WSLR, Room S045
Shared Resource Operator/Bioinformatics Specialist: Rick
Westerman
E-mail: westerm@purdue.edu
Phone: (765) 494-0505
Building/Room: WSLR, Room S049
General Information and Services
The objective of the DNA Sequencing Shared Resource
is to provide Purdue Cancer Center researchers the following service:
determination of the sequence of plasmid or PCR product DNA using
a standard vector primer or a custom primer, and web-based delivery
of the sequence, its chromatogram and BLAST searches. Those interested
in utilizing this service should consult its web page: http://www.genomics.purdue.edu/LTL/
An Affymetrix GeneChip Analyzer recently was purchased and DNA Array
Analysis will be an additional service provided by the Shared Resource.
Overview of the DNA Sequencing Shared Resource
The current DNA Sequencing Shared Resource is part of a newly created
campus-wide DNA Analysis Facility that resulted from a reorganization
and consolidation of various DNA analysis services on campus. The
DNA Sequencing Shared Resource is housed in the sub-basement of the
Whistler Building located across the street from the main Cancer Center
building (Hansen).
Description and Management of the Facility
Sequencing is performed on an ABI 3700 sequencer. Plate centrifuges,
a Biomek 2000 laboratory robot, 384-well thermal cyclers and various
multi-channel pipetting devices facilitate this process. Back-end
support for the sequencers is provided by a four-processor Sun Enterprise
450 with four megabytes of RAM and over 400 gigabytes of disk space.
100 megabit/second network connections link the DNA Sequencing Shared
Resource with the Enterprise 450 and the rest of Purdue University.
Richard Westerman, the bioinformatics specialist, maintains various
genetics programs including the GCG and the EMBOSS package and has
written new web-based software customized to the needs of this Shared
Resource.
Samples are submitted, tracked and analyzed via custom web-based software
developed by this Shared Resource. Sample DNA concentrations are validated
using a DNAQUANT fluorimeter. Dye terminator reactions using custom
primers supplied by the investigator or common vector primers stocked
by the Shared Resource can be performed, purified and analyzed in
a single day. The time between sample submission and sequence delivery
is commonly two working days. Sequence quality is monitored and sequence
reads not producing 400 high quality bases are repeated, using a different
chemistry, if necessary.
Users of this shared resource are automatically notified via email
of the availability of their sequence and associated reports. This
email includes a hyper-link to a password-protected user web page.
Graphic displays of the sequence data (chromatograms) are converted
to PDF and JPEG formats using VTRACE and are viewable using Adobe
Acrobat or a browser. BLASTN and BLASTX searches are performed such
that HTML links to GenBank are inserted for each hit. Raw text sequence,
quality-clipped sequence and quality values for each base are included
in the web report.
DNA Sequencing Rates
(Rates for Cancer Center members will be discounted)
1 sample, 2 primers: $25/each
1 sample, 1 primer: $12.50/each
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