Molecular Biology Core Facility

Gene Expression Analysis

The MBCF offers training and assistance with a wide range of gene expression analysis techniques.  RNA isolation and quality control can be performed by the Core staff or by the individual users. For users interested in the expression of a single gene or a handful of genes, we offer assistance with all aspects of quantitative RT-PCR, from primer and probe design to instrument operation and data analysis.  For a more robust, pathway-focused experiment, we can assist users to find a pre-fabricated RT-PCR array system from a supplier such as SuperArray.  These arrays can also be run and analyzed by the MBCF.  Instruments available for these experiments include a Bio-Rad iQ5 RT-PCR system, an Agilent 2100 Bioanalyzer (for RNA quality control), and a NanoDrop spectrophotometer.

Genome Expression Analysis

For large-scale expressions studies, the MBCF offers whole-genome arrays from Agilent Technologies.  These arrays can be operated as one- or two-color systems and provide very robust and reproducible data for approximately 44,000 transcripts in human, mouse or rat models.  Smaller arrays are available for a growing number of other species.  For downstream analysis of array data, we offer assistance with several platforms, including PathwayStudio (Ariadne Genomics) and GoMiner (NCBI).  The Core also has the capability to print custom arrays for specialized applications.  Instruments available for microarray analyses include an Axon 4000B array scanner, Robbins array hybridization system, and a Virtek (now Bio-Rad) ChipWriter Pro arraying robot.

Proteomic Analysis

The Core is now offering proteomic analyses in an effort to bridge the gap between gene expression and true protein levels.   For identification of proteins, two dimensional gel electrophoresis systems are available.  In collaboration with the Mass Spectrometry and Proteomics Core Facility, spots from these gels or one-dimensional gels can be identified using mass spectrometry for known peptide sequences.  This system also allows us to identify phosphorylation changes in proteins using multiple staining solutions.  Instruments available for proteomics analyses include a Bio-Rad Chemidoc, a Bio-Rad ProteomeWorks Spot Cutter, a Bio-Rad Dodeca 12-gel electrophoresis rig, and a Bio-Rad GS-800 Densitometer

Viral Vector Technology

Viral vector delivery is a relatively new and powerful tool for gene knockdown or expression studies.  This technology allows us to create custom vectors that can be expressed in specific cell types in vivo or in vitro.  Viral vectors can be designed with cell-type specific promoters to deliver small interfering/antisense RNA, reporter genes such as GFP, and exogenous DNA strands for gene therapy.

Basic Molecular Biology

In addition to these specialized techniques, the MBCF also offers assistance and expertise with all aspects of basic molecular biology.  This includes protocol development, experimental assistance and troubleshooting for PCR, gel electrophoresis, western blotting, cloning, restriction digest, nucleic acids and protein purification, genotyping, etc.