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Facilities


The Center for Biomarker Research and Precision Medicine (CBRPM) is housed in McGuire Hall and Annex on the university’s Medical College of Virginia Campus. Our laboratory suite, covering over 2,000 square feet, includes a specialized genomics and epigenomics laboratory, a behavioral laboratory and a pharmacogenomics laboratory as well as a dedicated freezer room for long-term sample storage at -80°C. The laboratories houses several state-of-the-art equipment including a SOLiD 5500xl Wildfire next-generation sequencer, a NextSeq 500 desktop sequencer, advanced robotics for sample preparation and sequencing library construction, a PyroMark Q96MD targeted pyrosequencing platform, and a Muromachi 10kW microwave system for tissue fixation. All laboratory equipment is maintained in a temperature-controlled environment. The main instruments including sequencing platforms and freezers are connected to emergency back-up power, which ensures that data generation and sample storage is uninterrupted and protected. Furthermore, CBRPM is hardwired to VCU’s high performance computing facility and all sequence data is auto exported to this computing facility where we have over 130 TB of dedicated storage space for (sequence) data.

Read more about our Laboratories and Computer Facilities

 


Laboratories

 

Specialized Genomics and Epigenomics Laboratory. This laboratory suite consists of several separate laboratory spaces, each designated for specific aspects of genetic and epigenetic nucleic acid research. Thus, each area 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 the highest possible level.

  1. Sample registration and tracking. All samples that are produced at or arrive at CBRPM are given a unique identifying barcode, which is integrated into the center’s laboratory information management system (LIMS). Using 1D and 2D barcodes this system allows for easy tracking of samples and applications with data stored in a centralized database that is backed-up remotely.
  2. Tissue handling and nucleic acid extraction. This laboratory is set up for extraction of DNA and RNA from mammalian tissue, including extractions from human brain tissues, human whole blood and from dry archived blood spots.  
  3. DNA Fragmentation. This laboratory area is set up for fragmentation of genomic DNA into the required size for the downstream sequencing application. For sequencing of fragment libraries we typically shear the genomic DNA via ultrasonication usin
    g our Covaris™ S2 System (Covaris) with a Compact Chiller (VWR International). For larger fragment sizes we also have a Hydroshear (Genomic Solutions) available.
  4. Pre-PCR work. 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. This platform is frequently used for relatively straight forward pipetting activates such as dilutions and pooling of samples as well as for complex protocols such as library construction for next-generation sequencing.
  5. Nucleic acid quality control. This laboratory space is set up for rigorous quality and quantity control of all major steps of sample preparation and library construction. The instruments used for these procedures are mainly a BioAnalyzer 2100 (Agilent Technologies), a NanoDrop UV spectrometer (NanoDrop) and a Qubit 2.0 Fluorometer (Life Technologies). For traditional quality control the center also has digital gel imaging equipment (BioRad) available.
  6. Next-generation sequencing. This laboratory houses our next-generation (ultra-high throughput) sequencing platforms. CBRPM currently owns a SOLiD™ 5500xl Wildfire Genetic Analyzer (Life Technologies). This is the premier sequencing instrument from Life Technologies, with the highest data generating capability of their line of products. In the fall of 2014 CBRPM installed a NextSeq 500 desktop sequencer (Illumina), which is one of the newest additions to the Illumina line of instruments and currently is the desktop sequencer with the highest output available.
  7. Pyrosequencing. This laboratory is equipped for high-throughput targeted pyrosequencing using a PyroMark Q96MD pyrosequencer (Qiagen).

This laboratory is set up for extraction of DNA and RNA from mammalian tissue, including extractions from human brain tissues, human whole blood and from dry archived blood spots.

In addition to the major equipment described above, our genomics and epigeniomics laboratory suite houses standard equipment such as: a Gold 96-w GeneAmp PCR System 9700 (Applied Biosystems), a four station Eppendorf Mastercycler Pro system, two additional single Eppendorf 96 well Mastercycler Gradient Thermocyclers (Eppendorf), several refrigerators (including flammable materials storage) and -20°C freezers, an automated aliquot system (Genetix), an APX60 precision microbalance (Denver Instruments), a UV Crosslinker CL-1000 (VWR International), 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.

Pharmacogenomics Laboratory. This laboratory area is set up for biomaterial collection and extraction, primarily for studies of central nervous system drugs. For immediate fixation of tissue, the laboratory is equipped with a 10kW microwave tissue fixation system (Muromachi) and liquid N2.

Freezer Room. CBRPM has two Thermo Ultima II -80°C freezers on site in the McGuire facility,  and maintains additional freezer space for collaborative projects in the Virginia Biotechnology Park, adjacent to the MCV Campus. Located in Smith Building two Thermo Scientific High Prerformace -30 freezers that are monitored 24/7 and investigators are automatically alerted of any unusual fluctuations in temperature.


Computing Facilities

 

VCU Center for High Performance Computing

CBRPM is linked through a LAN and is hardwired to VCU’s high performance computing cluster (godel.vcu.edu), which consists of ~1200 Opteron 64 bit and Intel 64 bit cores, each with at least 3 GB RAM/core, and 4.2TB of total RAM. The servers are connected by QDR Infiniband connections. Connected to this cluster CBRPM has 130 TB storage space that is exclusively dedicated for the center’s use.


Updated Aug 2015