Genomics Core
Director: Michael R. Crowley, PhD
Department/Center Association:
Established: November 2001
The Genomics Core has established
three high-priority technological resources: 1) microarray
analyses, 2) high-throughput sequencing, 3) high-throughput genotyping,
including single nucleotide polymorphisms (SNPs) and microsatellite analysis.
Facility Description
The
Genomics Core occupies 250 square feet of research space in room 412 of the
Microarray analyses. The Genomics Core has a GeneMachines Omingrid robotic spotter and TeleChem SMP3 spotting pins for creating custom microarrays. Samples can be spotted from either a 96-well format or rearrayed into the 384-well format using a Beckman Biomek FX liquid handling system. The Genomics Core will be printing the mouse MEEBO and Human HEEBO long oligonucleotide probe sets for expression studies. Hybridized slides can be scanned on an Axon GenePix 4000B dual laser scanner and the accompanying visualization software. The MEEBO and HEEBO slides should be available to the UAB research community by the end of 2006.
High-throughput DNA sequencing. The Core also
offers fee-based fluorescent DNA sequencing services for both UAB and external
clients. It accepts CsCl
purified plasmids, mini-prep plasmids, single stranded DNA, PCR products, and BACs. The Core
processes customer samples according to Applied Biosystems
Big Dye Terminator v3.1 Ready Reaction kit protocol and analyzes reactions on
the 16-channel ABI PRISM 3130 Genetic Analyzer or on the 48-channel 3730
Genetic Analyzer utilizing capillary electrophoresis technology. In addition to standard sequencing analysis, Factura analysis is also available. Turn around time for sequencing is 1-2
business days. Samples are submitted
and data
retrieved through the Core’s secure server. Sequencing results are provided in the .ABI
file format which can be viewed using either the Chromas,
Edit View
programs for the PC or through 4Peaks for the Mac. Information on sample submission, data
retrieval, and fees can be found at www.heflingenetics.uab.edu/sequencing/sequence.shtml.
High-throughput genotyping and SNP analysis. Genotyping and mutation detection: The Genomics Core performs fragment analysis for microsatellite-based genotyping and mutation detection using the DHPLC-based technology of the Transgenomic WAVE nucleic acid fragment analysis system. The system is composed of a solvent degasser, a solvent pump with proportioning valves, a 2 x 96-well plate autosampler with a Peltier chiller, a patented DNASep column, an L7300 column oven, and a UV detector. The WAVE system is controlled through the D-7000 HSM, HSM Administrator, and Navigator software packages. The Navigator software is used to design, run, and view results of projects in a graphical and spreadsheet based format. Mutation detection on the WAVE system uses the Temperature Modulated Heteroduplex Analysis (TMHA) method. Genotyping with the ABI Prism® 3130 and 3730 Genetic Analyzers is accomplished using the GeneScan® Analysis software package.
Single
Nucleotide Polymorphism (SNP) detection: The Genomics Core Facility has partnered with Jeffery C.
Edberg, PhD (Director, GCRC Molecular Genetics Laboratory) to develop high-throughput
SNP genotyping using Pyrosequencing™ technology. Using this technology, many unique samples or
multiple samples of the same SNP sequence can be evaluated simultaneously and
the reactions observed in real time.
Bioinformatics
resources. The Molecular and
Genetic Bioinformatics Facility (MGBF) of the Genomics Core supports the bioinformatic needs of UAB genetic investigators. The MGBF maintains a Sun E450 Solaris server
with over 600 GB of storage to support the various programs and databases available
including the Genetics Computer Group’s (now Accelyrs)
Statistical data management and security will be provided through the UAB Gene Expression Database. It is an on-site, Oracle-based, relational database designed to store raw data, data annotated at both the DNA sequence and experimental treatment levels, as well as results of data analyses. Data import tools are being developed using SQL routines to automatically parse raw data and insert it into the appropriate database tables. Raw data will be annotated with appropriate links to external databases (e.g., the HuGE Index, NCBI, and the Celera Discovery System).
The UAB Microarray Data Analysis Clearinghouse (MDAC) established by Dr. Allison is currently developing a suite of SAS-based routines with a custom-built Graphical-User-Interface for high quality analysis of DNA microarrays. The application is being designed to query the UAB Gene Expression Database directly to obtain raw data (using native SAS SQL) in a format ready for analysis or export to flat file. In addition, the Core also maintains a five seat license for the GeneTraffic software suite available for the analysis of printed microarrays, custom microarrays, and Affimetrix GeneChip data.
Services
All services provided at the
Genomics Core Facility are available to UAB researchers, other academic
researchers, and small businesses and are performed on a sliding-scale
fee-for-service basis. Pricing schedules
are located under the relevant service heading on the website, located at www.heflingenetics.uab.edu.
Contact Information
Core Director: Michael R. Crowley, PhD
Email: mcrowley@uab.edu
Phone: 205-975-2013
Web Site: http://www.heflingenetics.uab.edu/
Approved by: Michael R. Crowley, PhD, Director
Date: June 21, 2006 (Update requested)
Click here to return to the SOM Research Web Site's home page.