DNA Sequencing and Analysis Core Facility
Director: Beatrice H. Hahn, MD
Department/Center Association: Center for AIDS Research (CFAR) and Comprehensive
Cancer Center (CCC)
Established: 1987
Mission
The DNA Sequencing and Analysis Core provides automated sequencing and computer
analysis services, as well as technical support. The Core operates automated DNA sequencing
instruments with multi-capillary and slab-gel systems and a robotic liquid handler for automation
capabilities. Trained personnel provide critical technical support to facilitate data acquisition
and analysis.
Facility Description
The Core is housed in the McCallum Basic Health Sciences Building. It currently
operates two automated fluorescence-based multicapillary electrophoresis Genetic Analyzers
and one slab-gel electrophoresis system. The laboratories are fully equipped and have access
to shared capital equipment in adjoining common equipment rooms. These facilities include
fume hoods; ultra-, superspeed-, table-top-, and micro-centrifuges; a cold room and warm room;
table top and floor model environmental shakers; incubators; and three GeneAmp
thermocyclers. The labs also include desk space for Core personnel and a conference room
where Core managers can meet with users to discuss individual projects.
All major equipment is housed in the facility located on the 8th floor, room 852 of the
McCallum Basic Health Sciences Building. This equipment includes the following: an ABI
3730xl Genetic Analyzer with a 96 capillary array; an ABI 3130xl Genetic Analyzer with 16
capillary array to provide a high throughput automated fluorescence-based DNA sequencing
using capillary assisted electrophoresis; one ABI 377 sequenator to provide automated
fluorescence-based DNA sequencing using a slab-gel electrophoresis system; a Beckman
Coulter Laboratory Automation Workstation (Biomek NX S8), which provides automated liquid
handling operations for sequencing reaction set-up and clean-up; four GeneAmp PCR Systems
(three 9700, and one 9800) Thermocyclers, which support all cycle sequencing and RT-PCR
reactions that amplify DNA templates through the use of specific primers and Taq polymerase
and cycling temperature steps; a Labnet centrifuge (HERMLE Z300), which supports the
purification step of sequencing reactions that removes unincorporated dye-labeled terminators
from samples that underwent thermocycler-assisted cycle sequencing; two Automated
Environment SpeedVac Systems (Savant models AES1010 and DNA120-115), which dry
cleaned sequencing reactions before they are re-suspended in an appropriate buffer and
electrophoresed in the DNA sequencing instruments; and an ABI 7p00 Sequence Detection
System, which detects and quantifies specific nucleotide sequences by using real-time PCR
signal amplificaton as well as allele discrimination capabilities.
Research Information
The DNA Sequencing and Analysis Core provides the latest automated DNA sequence
analyses using the dye-terminator methodologies with readouts of 700-800 bp (ABI 3130xl DNA
analyzer) and 900-1,000 bp (ABI 3730xl DNA Analyzer). The high accuracy of the base calling
(98.5%) and low ambiguity (<2%) of the service provided by the Core saves time and money for
investigators. Sequencing data are provided as a hard copy printout, on computer diskette, and
by e-mail. Thus, data output can be retrieved using a variety of sequence analysis programs.
Services and Fees
As of July 1, 2004, the fee per sequencing reaction is $8. Core users should provide
DNA templates dissolved in good quality water. For plasmids, 1 ug plasmid DNA in 5 ul of
water (0.2 ug/ul) is optimal for one sequence reaction. PCR products must be gel purified and
dissolved in water. The optimal amount would depend on the length of the PCR product.
Primers must also be dissolved in water at a concentration of 5 picomol/ul and >1 ul per
sequence reaction. For other kinds of templates, please contact the Core. Turnaround time is
two days.
Contact Information
Core Manager: Jesus Salazar-Gonzalez, PhD
Email: salazarj@uab.edu
Core Contact: Maria Salazar
Email: mgs@uab.edu
Phone: 205-934-3972
Core Administrative Contact: Jennifer Wilson
Email: wilsonj@uab.edu
Phone: 205-934-0050
Reaction Submission Form and other important details can be found at:
http://www.main.uab.edu/show.asp?durki=16530
Approved by: Beatrice H. Hahn, MD, Core Director
Date: February 1, 2007
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