Labs and other facilities

The Center is housed in McGuire Hall on the university’s Medical College of Virginia Campus. We have six specialized laboratory suites, covering a total of over 2,000 square feet, in addition to a dedicated freezer room for long-term sample storage at -80°C. The Center owns several state-of-the-art equipment items, e.g. a next generation DNA sequencer (Applied Biosystems SOLiD) plus robotics for sample preparation, exclusively for the use of Center members. To track samples and applications the Center employs an integrated laboratory information management system (LIMS) using 1D and 2D barcode systems (NOVA Biostorage), which allows for easy tracking of all samples with data stored in a centralized database and backed up remotely. Furthermore, the main instruments, including our freezers, computers directly connected to lab equipment, and the sequencers are connected to emergency back-up power to ensure uninterrupted data generation and high quality storage of reagents and samples. All laboratory equipment is maintained in a temperature-controlled environment. The Center is hardwired to VCU’s high performance computing facility where we have over 30 Tb of dedicated storage space for (sequence) data. In addition to the Center’s own labs, some exceptional university shared resources (e.g. high field nuclear magnetic resonance facility) are conveniently located in the same building.

Center Laboratories

Molecular Genetics Laboratory Suite.This laboratory suite consists of four separate laboratory spaces, each designated for specific aspects of genetic and epigenetic nucleic acid research. Thus, the laboratory space and the applied work procedures are carefully optimized to minimize risks of contamination and to maximizing the throughput while keeping the quality of the data at highest possible level.

1. Template handling. This laboratory is dedicated to pre-PCR procedures and houses our primary robotics platform, a Beckman Coulter Biomek® NXP robot, which is equipped with a span-8 head and gripper arm.
2. Library preparation. This room is equipped with a Covaris™ S2 System (Covaris) with a Compact Chiller (VWR International), a Hydroshear (Genomic Solutions) and an EZ-bead automated system for high-through-put preparation of samples for next-generation sequencing.
3. Next Generation Sequencing. This laboratory currently houses a SOLiD™ 5500xl Genetic Analyzer, a next generation (ultra-high throughput) sequencing platform manufactured by Life Technologies / Applied Biosystems (Foster City, CA). This is the premier sequencing instrument from Life Technologies, with the highest data generating capability of their line of products.
4. Pyrosequencing. This laboratory is equipped for high-throughput targeted pyrosequencing using a PyroMark Q96MD pyrosequencer (Qiagen).

In addition to these major equipment items, our genetics laboratories have the following: a BioAnalyzer 2100 (Agilent Technologies, Santa clara, CA), a Gold 96-w GeneAmp PCR System 9700 (Applied Biosystems, Foster City, CA), a 4 station Eppendorf Mastercycler Pro system, plus 2 additional single Eppendorf 96 well Mastercycler Gradient thermocyclers (Eppendorf , Hauppage, NY); we have several refrigerators (including flammable materials storage) and -20°C freezers, an automated aliquot system (Genetix, Boston, MA), an APX60 precision microbalance (Denver Instruments, Bohemia, NY), digital gel imaging equipment and its associated computer (BioRad, Hercules, CA), a NanoDrop UV spectrometer (NanoDrop, Wilmington, DE), a UV Crosslinker CL-1000 (VWR International, Suwanee, GA), Thermo Micromax and Eppendorf microfuges, an Eppendorf 5810R 4x96 well plate centrifuge, a Tuttnauer 2340 bench top autoclave, Milli Q Direct 8 water system (Millipore), vortexes, digitally-controlled water baths and heated blocks, hybridization chambers, pH meter, etc

Behavioral Laboratory. This laboratory is specifically designed for behavioral research. It is equipped with computer-controlled, automated locomotor activity monitoring devices, pre-pulse inhibition devices and conditioning chambers.

Psychopharmacology Laboratory. This laboratory is set up for biomaterial collection and extraction, primarily for metabolomics studies of central nervous system drugs. It is equipped with a 10kW microwave tissue fixation system, centrifuges, fume hood, sample storage facilities and liquid N₂.

Freezer room. The Center has two Thermo Ultima II -80°C freezers on site in the McGuire Annex and maintains additional freezer space for collaborative projects in the Virginia Biotechnology Park, adjacent to the MCV Campus.

Computing Facilities. Our center is linked through a LAN and is hardwired to VCU’s high performance computing cluster (godel.vcu.edu), which consists of 38 servers with Opteron cpus for a total of 548 cores and 1.6 TB of RAM. The servers are connected by QDR Infiniband connections and have a total of 152 TB of storage. Of that total, the Center has 33 TB dedicated exclusively for its own use.

Shared resources

VCU high field nuclear magnetic resonance (NMR) facility. Also located in McGuire Hall, is a Bruker 700MHz NMR spectrometer (Bruker, Billerica, MA). This high-field NMR shared resource for the Health Sciences Campus consists of a 700 MHz Ultrashield+ magnet with a Bruker Avance III NMR with 4 RF channels and a QXI probe (¹H observe, ¹³C, ¹⁵N,³¹P + ²H decouple with a Z-axis pulsed field gradient and automatic tune and match on all channels) with a BCU-05 prechiller. For NMR metabolomics analysis, the Center has user licenses for Advanced Chemistry Development 1D NMR processor (ACD Labs, Totonto, Ontario) and Chenomx NMR Suite (Chenomx, Edmonton, Alberta) with both 600 and 700MHz libraries for compound identification and profiling.

Additional resources such as Affymetrix microarray facilities, real-time PCR instruments and cell laboratories are conveniently located nearby on the university medical campus.