The Genomics and sequencing core occupies space in a large open laboratory in the Stein Clinical Research Building leased from UCSD by the Veterans Affairs Medical Center. This includes over 150 linear feet of bench space. Bench space incorporates both biosafety level (BL) 2 and BL2+ facilities with two BL2 and one BL2+ safety cabinets dedicated to use by the Genomics and Sequencing (GS) Core. Multiple BL2 and BL2+ facilities are available on a shared use basis as well as an additional 30 linear feet of bench space.
The BL2+ facility available for use by staff at the GS Core is fully equipped, and users follow all UCSD and NIH guidelines for biosafety. These include but are not limited to the wearing of disposable gowns, gloves, goggles, and booties at all times in the BL2+ facility. The practice of double-glove technique is enforced. All Recombinant DNA procedures are performed under BL-2 containment, and work with proviral clones 60% intact is performed in biological safety cabinets. All guidelines for the use of recombinant DNA are followed. All clinical specimens are processed in biosafety cabinets, which minimizes aerosol production. Serological testing for HIV is provided to all laboratory workers on an annual basis, and a baseline serum specimen is obtained and stored at -80°C prior to use of the BL2+ facility.
The Genomics and Sequencing Core offers nucleic acid isolation, quantification and quality control, relative and absolute gene expression quantification, next generation sequencing applications on MiSeq andIon S5/Ion Chef system, sample and library preparation for single cell RNA-Seq using 10X platform (including HIV-infected samples) and bioinformatics support. The Core is equipped with NanoDrop One (ThermoFisher Scientific), Agilent Bioanalyzer 2100, 2 Bio-Rad T100 dedicated thermocyclers, Applied Biosystems 7500 and 7900HT Real-time PCR systems, QUnatStudio Flex 7 system, Bio-Rad QX200 digital PCR instrument, Ion S5/Ion Chef sequencer, Illumina MiSeq desktop sequencer, 10X Genomics Chromium Controller, and PowerEdge T620 Tower Server (Ubuntu Linux). The Core has shared access to Qubit 2.0 fluorometer, Agilent Tape Station 2200 and Veriti thermocyclers.