Cores and Facilities

Bioinformatics Core | Proteogenomics Facility | Microarray Core | Instrumentation Resource Facility | NMR Facility | Genomics Institute

Bioinformatics Core

The goal of the SC INBRE Bioinformatics Core is to increase the National Institutes of Health research capacity of the state by providing bioinformatics support to faculty, post-doctoral fellows, graduate students, and undergraduate students of the lead and partner institutions.

homayoun valafarDr. Homayoun Valafar
Associate Professor
Department of Computer Science and Engineering
University of South Carolina
(803) 777-2404 | Email

Bioinformatics Pilot Program

 

Proteogenomics Facility at MUSC

Provides genomics services, including Bioanalyzer qualitative analysis of RNA and DNA, Affymetrix DNA microarray-based transcriptome and miRNA expression profiling and SNP analysis, next generation sequencing on the Ion Torrent PGM platform for small scale genomes, targeted/amplicon resequencing and metagenomics. Bioinformatic service is provided for DNA microarray and next generation sequencing analysis. The facility also provides training in bioinformatic analysis, computational workstations (PC and Linux) for investigator use, and proprietary software licenses for Ingenuity Pathway Analysis, Partek Genomics Suite, and GeneAnalytics. Instrumentation available for investigator use includes a Bio-Rad Cfx96 for qPCR, a NanoDrop One for small volume spectrophotometric analysis, a Qubit fluorometer and a Luminometer.

jeremy barthDr. Jeremy Barth
Research Associate Professor
Department of Regenerative Medicine and Cell Biology
Medical University of South Carolina
(843) 792-9984 | Email

Visit the Proteogenomics Facility website


Microarray Core Facility at USC

The Microarray Core Facility is a state-of-the-art facility that conducts gene expression profiling, using the Agilent and Affymetrix platforms, to monitor the levels of expression of all genes in the genome. Using our technology, a single experiment allows researchers to determine specific alterations in gene expression in various disease states, or progression, following exposure to drugs or chemicals. The Microarray Core Facility also prepares samples for clients wanting to determine gene expression using RNA-Seq.

kim creekDr. Kim Creek
Professor and Department Chair
Department of Drug Discovery and Biomedical Sciences
University of South Carolina College of Pharmacy
(803) 777-0952 | Email

Visit the Microarray Core Facility website


Instrumentation Resource Facility at the USC School of Medicine

The Instumentation Resource Facility (IRF) is an integral component of the research and teaching mission of the University of South Carolina School of Medicine (USC SOM). Located within the facility are several major pieces of state-of-the-art biomedical research equipment that provide techniques ranging from whole animal through single cell imaging to analysis at the molecular level. The IRF also houses a full range of ancillary equipment that is available for sample preparation. In addition to serving as a resource for acquisition of primary data, the IRF also has the capacity for image enhancement and related data analysis.

The mission of the IRF is to provide state-of-the-art biomedical research instrumentation for use in the USC SOM and USC main campus research environments. As time and resources permit, outside use of the facility is also permitted and encouraged. Technical assistance and training are available in most areas of research sponsored in the IRF.

bob priceDr. Bob Price
Research Professor
Department of Cell Biology and Anatomy
University of South Carolina School of Medicine
(803) 216-3824 | Email

Visit the Instrumentation Resource Facility website


Claflin University Nuclear Magnetic Resonance (NMR) Facility

Claflin's NMR facility, in addition to its 700 MHz NMR, also has an automated nuclear magnetic resonance (NMR) sample changer to do NMR-based metabolomics research. The field of metabolomics focuses on changes to the small molecules that make up metabolism upon some stressful event or condition. NMR serves as an excellent detector of these small compounds; and statistical analysis is applied to many NMR sample replicates to increase the robustness of the metabolomics technique. Claflin University has the third highest field NMR laboratory in the state of South Carolina, just behind the Medical University of South Carolina (MUSC) and the Hollings Marine Laboratory (HML). Although a predominately undergraduate university and HBCU (Historically Black Colleges and Universities). 

rajaDr. Muthukrishna Raja
Professor, Chemistry
Chemistry Molecular Science Research Center
Claflin University
(803) 535-5673 | Email

 

Clemson University Genomics Institute (CUGI)

Also affiliated with SC INBRE is Clemson University Genomics Institute (CUGI): CUGI is a research/service engine tailored to design experiments built around functional hypotheses. CUGI has a breadth of experience in complex prokaryotic and eukaryotic genomics, transcriptomics, and bioinformatics and offers a comprehensive package of services from the extraction of nucleic acid to the collection of proper biological measurements with complex data analysis and interpretation through second-generation DNA/RNA sequencing and custom bioinformatics. Specifically, CUGI offers genomic library construction, transcriptome profiling (RNAseq) and statistical analysis, positional cloning and targeted sequencing, denovo genome sequencing and reference-based resequencing, GWAS experiments with complex variant analysis, methyl-seq, small RNA seq, genomic database construction, and custom bioinformatics. These tools are focused on the discovery and functional analysis of important genes, networks, and genomic regions from plants, animals, fungi, microbes, and humans and consist of extant and emerging technologies.

saskiDr. Christopher A. Saski
Director, CUGI
Research Faculty
Department of Genomics and Biochemistry
(864) 656-0973 | Email

Visit the Clemson University Genomics Institute website

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SC INBRE is funded by grant P20GM103499 from the National Institute of General Medical Sciences, National Institutes of Health

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