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Collaborative Center for Cancer Genomics and Bioinformatics Core

Summary:

The CCGC is being established in Clark Atlanta University as a collaborative effort between the CCRTD and the Ovarian Cancer Institute at Georgia Tech University (OCIGT). The operation will be based on Next-Generation sequencing technology which is the newest molecular genetics technology that allows biomedical scientists to address global genome composition, inter-individual variation, and global gene expression. For both CCRTD and OCIGT, it is essential to acquire this technology to be competitive in the cancer research field. CCRTD will house the “wet” laboratory which will prepare libraries and operate the instrument, while OCIGT will contribute bioinformatics support for processing the data and additional services to complement genomics data. Next-Generation sequencing technology produces massive amounts of sequence data, thus significant computational facilities including hardware, software, and highly qualified personnel are required in order to take advantage of the generated data. In addition, OCIGT will contribute patients sample procurement and complementary technologies including Affymetrix microarray technology and mass-spectroscopy analysis.

Affiliations:

People:

      Member: Zou, Jin, Ph.D.
      Role: Coordinator of CCRTD Core Facilities/Sr. Research Scientist

    Resources:

    Instruments

    • ABI GeneAmp PCR System 9700 ( Thermal cycler )

      "GeneAmp® PCR System 9700 is specifically designed for the amplification of nucleic acids. The GeneAmp® PCR System 9700 consists of a base module and one of many interchangeable sample block modules. The 96-well GeneAmp® PCR System 9700 is designed for use with 0.2 ml reaction tubes or 96-well reaction plates for all of your routine PCR applications."

    • Agilent 2100 Bioanalyzer ( Microfluidics platform )

      microfluidics-based platform for sizing, quantification and quality control of DNA, RNA

    • Applied Biosystems SOLiD 4 System ( DNA sequencer )

      "The SOLiD™ System enables researchers to obtain higher accuracy and sensitivity for variant discovery with less coverage. Read the latest peer-reviewed publications that demonstrate how the SOLiD™ System allows you to see what’s never been seen before."

    • Applied Biosystems SOLiD EZ bead system ( PCR instrument )

      "The new SOLiD™ EZ Bead™ System simplifies next-generation sequencing workflows by providing an automated solution for reproducible templated bead preparation with less than 1 hour of hands-on time. The system is specifically designed with system modularity and quality control check points for greater experimental control. The SOLiD™ EZ Bead™ System streamlines the sequencing workflow through significant time savings and support for up to 96 multiplexed libraries. With automation, minimal costs, and seamless effort, the SOLiD™ EZ Bead™ System dramatically increases sequencing productivity to further accelerate scientific discovery.

      Key product features:

      Streamlined workflow—80% reduction in hands-on time
      Reliable output—increased reproducibility of sequencing results
      Cost efficiency—multiplexed library support for maximized savings of time & resources
      Flexibility—modular to fit individual throughput and lab needs
      Tighter control—quality control checkpoints throughout experimental workflow"

    • Covaris S-series ultrasonicator ( Sonicator )

      DNA/RNA shearing

    • Digilab HydroShear DNA shearing ( DNA shearing instrument )

      "Digilab HydroShear DNA Shearing system is an automated Shearer offering a simple and easy-to-use, reproducible, and controllable method of fragmenting DNA. HydroShear is the best system to generate large DNA fragments needed for long sequencing reads and genomic library construction."

    • Penguin entry level computing cluster ( Computer cluster )

      Computing Cluster

    • SOLiD EZ Bead Emulsifier ( PCR instrument )

    • SOLiD EZ Bead Enricher ( PCR instrument )

    • Thermo Scientific Nanodrop 2000c Spectrophotometer ( Spectrophotometer )

      Measure using either the micro-volume pedestal or cuvette

    Protocols

    Services

    Software

    • 2100 Expert Software ( Software )

      "The 2100 Expert Software for the Agilent 2100 Bioanalyzer provides easy instrument set-up and run control, and offers powerful data evaluation tools for all available assays, automatic and manual integration, smear analysis and many assay-specific tools."


    Web Links:

    Last updated: 2012-09-18T12:59:36.068-05:00

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    The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016