DNA Sequencing

• state-of-the-art capillary-based automated DNA sequencers

• automated sample submission and data retrieval

• primers available for commonly used vectors

• single ($6/rxn) and 96-well ($4/rxn/full-plate) formats

 

DNA SAMPLE SUBMISSION INSTRUCTIONS

• WEB-BASED dnaLIMS for information entry and retrieval

• First-time users must access the site to setup an account

• Samples are brought to MCLM

• Sample Prep Instructions and Available Primers (pdf)

 

Protocols available from the Center for HIV-AIDS Vaccine Immunolgy's (CHAVI) Molecular Biology and Sequencing Core:

• Single Genome Amplification Of HIV-1 Envelope (pdf)

• Whole Genome Amplification of HIV-1 From A Single RNA (pdf)

Available HIV Primers (pdf)

 

Contact:

Maria Salazar

205-934-3972

Email: mgs@uab.edu

 

Microsatellite Analysis

Microsatellite or short tandem repeat (STR) analysis is offered by the CFAR DNA Sequencing Facility using an ABI 3130xl Genetic Analyzer and GeneMapper software. STR analyses are performed by the core primarily for individual identification. Because the number of these STRs varies within a given population, it is possible to identify individuals by analyzing several different STR loci. For instance, the core has used microsatellite analysis effectively to determine if cases of HIV-1 superinfection of the same patient with more than one virus were real or the result of sample contamination.

Investigators interested in using the facility for STR analysis should contact and meet with core personnel to discuss aspects of the protocol, including primer and loci selection.

 

Contact:

Jesus Salazar

205-934-3972

Email: salazarj@uab.edu

 

REAL-TIME PCR

The CFAR DNA Sequencing Facility can provide both qualitative and quantitative polynucleotide analyses using a new ABI 7900HT Fast Real-Time PCR System instrument. Users should contact the core to discuss specific needs and goals. Core personnel will make recommendations concerning the most appropriate assays and suitable chemistries. Users provide microtiter plates containing pre-mixed reagents. Core personnel will perform the run on the 7900HT PCR system using the appropriate program and PCR conditions. At completion of the run, core personnel will provide the user with an analysis report in Excel file format.

 

Examples of applications supported by the ABI 7900HT Fast Real-Time PCR System (96- or 384-well format) include:

• TaqMan assays toward a specific target using comparative (absolute) and/or relative quantitation protocols

• Real-Time PCR SYBRgreen assays

• DNA dissociation curves

• End-point PCR assays for qualitative target sequence detection

• Fast Real-Time PCR assays

• Gene expression and allelic discrimination using commercially available pre-developed assay reagents

• TaqMan Low Density Arrays for quantitative gene expression measurement of 12 to 384 targets in 1 to 8 samples in parallel.

 

Contact:

Jesus Salazar

205-934-3972

Email: salazarj@uab.edu