The Hollings Cancer Center Genomics Shared Resource offers state-of-the-art next generation sequencing (NGS) including DNA-Seq, RNA-Seq, chromatin immunoprecipitation sequencing (ChIP-Seq), Methyl-Seq, Targeted sequencing utilizing Illumina HiScanSQ and Ion Torrent instrumentation. See below for other types of applications. In addition to NGS, BeadArray analyses for genome-wide association studies (GWAS), RNA expression and other analyses are available.
To request access to this facility, please contact Robert Wilson, Ph.D. at firstname.lastname@example.org or 843-876-2217.
The Genomic Shared Resource is located in Room 433 of the Bioengineering Building.
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).
Next Generation Sequencing
The Shared Resource 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 Shared Resource 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 Shared Resource operates an Illumina HiScanSQ that not only does sequencing but scans the large variety of microarrays using Illumina BeadArray technology.
- Using CASAVA the sequencing data will be generated in the FASTq format for the downstream analysis.
- BeadArray 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.
- Expression arrays.
- SNP and copy number arrays.
- Methylation arrays.
Quality Control & Processing
- The Shared Resource 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 Shared Resource uses a QuBit Fluorometer and other fluorometric methods. The QuBit Fluorometer is available for self-service (the user must provide their own reagents).The Shared Resource has access to an Eppendorf realplex2 for qPCR (for Genomics Shared Resource 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 Shared Resource 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 Shared Resource uses a Diagenode Bioruptor UCD-600 TS which is available for full service or self-service.
If you publish a manuscript including research supported by the Genomics Shared Resource, 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."