MUSC Hollings Cancer Center

Genomics Shared Resource

Scientific Director
Stephen P. Ethier, PhD
Professor, Pathology & Laboratory Medicine

Contact Information
Operations Director

Name: Robert C. Wilson, PhD
Research Associate Professor, Pathology & Laboratory Medicine
Phone: 843-876-2217
E-Mail: wilsorc@musc.edu

Name: Jennifer Schulte
Phone: 843-876-2243
E-Mail: schultej@musc.edu
Location: 433 Bioengineering Building

Description

The Hollings Cancer Center Genomics Core Lab is a shared resource located in the Bioengineering Building room 433. The Genomics Core provides a variety of services including sequencing library preparation and sequencing on Illumina HiSeq2500 and MiSeq platforms. The Core also processes Illumina bead arrays. A complete list of our services can be found below.

The mission of the Hollings Cancer Center Genomics Shared Resource to provide MUSC investigators, including the greater South Carolina area, state-of-the-art high quality, custom genomic services as well as consultation on experimental design and education about genomic analysis.             

Next Generation Sequencing Applications

  • Gene Regulation Analysis (RNA-Seq and miRNA-Seq)
  • Structural Variation Analysis ( DNA-Seq, Exome-Seq and Methyl-Seq)
  • DNA-Protein Interaction Analysis (ChIP-Seq and Methyl-Seq)
  • RNA-Protein Interaction Analysis (RIP-Seq)
  • Targeted Sequencing (Cancer Panels and Custom Panels)
  • Translation Profiling (Ribosome monosome and polysomes)

Mirco-Array Applications

  •  Expression arrays
  • SNP and copy number arrays
  •  Methylation arrays

Equipment

  • Next Generation Sequencing
    The Core has an Illumina HiSeq2500 with the new Version 4 upgrade for faster runs and more output supporting read lengths up to 250 bp (2X125). The HiSeq2500 also has a Rapid mode supporting read lengths up to 300 bp runs (2X150).

    The Core has access to the Illumina MiSeq for sequencing analysis of organisms with small genomes such as Drosophila or bacteria. Other uses for the MiSeq include targeted sequencing or amplicon sequencing. The MiSeq supports read lengths up 600 bp (2X300).
  • Illumina HiScan Applications (Microarray)
    The Core operates an Illumina HiScanSQ that not only does sequencing but scans the large variety of microarrays using Illumina BeadArray technology. Below is a list of some of Illumina arrays that are available.

Quality Control and Processing

The Core uses a Agilent ® 2200 TapeStation which is available for full service or self-service (Tapes are available for purchase) and has access to an Agilent 2100 Bioanalyzer for sample and library QC.

For precise quantitation of RNA and DNA the Core uses a QuBit Fluorometer and other fluorometric methods. The QuBit Fluorometer is available for self-service (the user must provide their own reagents).The Core has access to an Eppendorf realplex2 for qPCR (for Core use only).

A Covaris S220 Focused-Ultrasonicator is available for full service or self-service (tubes are available for purchase).

For automated gel size selection the Core uses a Sage Science Pippin Prep which is available for full service or self-service (gels are available for purchase).

For sonication of large samples (1-15 mls) the Core uses a Diagenode Bioruptor UCD-600 TS which is available for full service or self-service.
 

DATA Analysis

  • Using CASAVA the sequencing data will be generated in the FASTq format for the downstream analysis.
  • Bead array image files will be analyzed by Illumina Genome Studio.  Files will be available for 3rd party software analysis.
  • Investigators may perform their own analysis or elicit the MUSC Bioinformatics Core.

Publication Acknowledgement

If you publish a manuscript including research supported by the Genomics Core Facility, the HCC recommends the following text to be placed in the acknowledgement section: "Supported in part by the Genomics Shared Resource, Hollings Cancer Center, Medical University of South Carolina."

 

 
 
 

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