The COBRE Proteogenomics core
The COBRE Proteogenomics Core is a component of the South Carolina COBRE for Cardiovascular Disease. The mission of this core is to provide COBRE trainees with a resource for expert consultation, technical training/services, and state-of-the-art instrumentation to enable advancement of their research efforts through the application of DNA microarray analysis and protein based ('proteomic') approaches. The DNA microarray analysis component permits investigators to use DNA microarray screening technology to perform comprehensive gene expression profiling through application of both commercial and custom microarray screening and advanced computational/statistical analysis methods. The proteomics component provides investigators with technical assistance and instrumentation resources to use conventional and cutting edge protein biochemistry-based technologies to address questions of protein function.
Proteogenomics Instrumentation:
Affymetrix DNA Microarray System
The facility is equipped with a complete Affymetrix system, comprising a GeneChip® Scanner 3000 7G (with autoloader), hybridization oven and two fluidics workstation.
MJ Research Dyad PCR Machine
The Dyad is a 3-block thermal cycler capable of gradient PCR amplification. The 3 blocks (1 holding 96 samples, 2 holding 48 each) hold 0.2 ml tubes and can be operated independently. The 96-well block has the gradient feature and can create a gradient of temperature differing by approximately 20°C. This feature is particularly useful for optimization of PCR reactions.
Bio-RAD iCycler iQ real-time PCR detection system
The Bio-RAD iCycler is a 96-well capacity thermal cycler and data acquisition system for performing real time quantitative PCR. The iCycler is equipped with a tungsten-halogen lamp and provides for an excitation/emission range of 400-700 nm. PCR reactions are performed in standard 0.2 ml 96-well plates covered with "optically clear" adhesive tape. Up to 4 different fluorophores can be detected (multiplexed) per sample tube. Data is acquired continuously throughout amplification. iCycler iQ software performs automated analysis of product quantities and melting curves.
BioRad BioLogic DuoFlow Chromatography System
The BioLogic DuoFlow Chromatography System is specifically designed for the high-resolution purifications of proteins, peptides and other biomolecules where recovery of biological activity is of primary concern. It also allows higher flow rates up to 20 ml/min and a choice of large size loops of up to 50 ml for scale up purification of proteins from crude extracts. Further, it supports a wide range of column packing materials [Gel filtration (high load Superdex and HiPrep Sephacryl) and ion exchange columns such as mono-S, mono-Q) and large size columns for batch purification. The monitoring unit is capable of UV and temperature compensated conductivity as well as pH monitoring.
BIAcore 3000 System
BIAcore 3000 system is a surface plasmon resonance based system that performs real time biomolecular interaction and kinetic analysis (e.g., receptor-ligand, antibody-antigen, protein-DNA).
Agilent 2100 Bioanalyzer System
The Agilent 2100 Bioanalyzer utilizes microfluidics technology for sizing and quantification of RNA, DNA and proteins. The system is also capable of performing fluorescence cell scanning. For separation of nucleic acids and proteins, samples are loaded into gel-filled chips placed into the Bioanalyzer electrode cartridge and then separated electrophoretically. System software simultaneously collects sample data and automatically calculates sizes and concentrations. The output is a virtual gel and a table of sample data. For detection of nucleic acid the Bioanalyzer is more sensitive than conventional agarose gel electrophoresis, requiring as little as 50 ng of a heterogeneous DNA or RNA sample.
Roche RTS 500
The Roche RTS 500 is a preparative scale cell-free protein purification system. The instrument is designed for protein expression in the scale of 100 to 500 mg in a 1 ml reaction volume from cDNA cloned into a pIVEX vector or another vector, designed for prokaryotic in vitro protein expression and containing a T7 promotor. Proteins in the molecular weight range from 10 to 120 kDa have been successfully synthesized using the RTS 500.
Bio-Rad Protean Isoelectric Focusing System
The BioRad Protean IEF Cell is optimized to use ReadyStrip IPG strips to perform first-dimension isoelectric focusing. The Peltier-cooled platform of the Cell accommodates up to twenty-four 7 cm strips or twelve 11, 17, 18, or 24 cm strips. Combined with second dimension SDS-PAGE the Protean IEF Cell apparatus can be used to quantitatively separate proteins and potentially identify and characterize them.