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Oregon Clinical & Translational Research Institute Core Laboratory

Director: Woffendin, Clive, Ph.D.

Summary:

The OCTRI Core Laboratory is specifically designed and equipped to perform both basic and specialized research assays and sample processing in support of translational research studies and trials. Laboratory staff have extensive experience in the performance of a wide variety of analytical and genetic based assays and procedures.

Affiliations:

People:

Resources:

Instruments

  • ABI 9800 Fast thermal cycler ( Thermal cycler )

    "The Applied Biosystems 9800 Fast Thermal Cycler is an integral component of the Applied Biosystems 9800 Fast PCR System, which reduces PCR reaction time from 2 hours to as little as 25 minutes."

  • ABI GeneAmp 9700 96-well PCR system ( PCR instrument )

    "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."

  • ABI Prism 3130XL Genetic Analyzer and Sequencer ( DNA sequencer )

    "Applied Biosystems 3130xl Genetic Analyzer is the latest generation of 16-capillary electrophoresis instruments for the medium throughput laboratories."

  • Agilent HPLC fluorescence detector ( High performance liquid chromatography instrument )

  • Beckam Coulter DU 530 UV/Vis spectrophotometer ( UV/vis spectrophotometer )

  • Electrophoresis system for agarose and acrylamide gel(s) ( Agarose gel electrophoresis system )

  • ELISA plate reader ( ELISA microplate reader )

  • Gamma counter ( Gamma counter )

    Lab has two of these instruments.

  • Hewlett Packard 1200 HPLC system ( High performance liquid chromatography instrument )

    Includes fraction collectors and fluorescence detector.

  • MJ Research Tetrad 4 block PCR machine ( PCR instrument )

  • Quantech fluorimeter ( Fluorometer )

    "Photomultiplier tube (PMT) and microprocessor control provide excellent detection sensitivity
    Automatically sets gain (sensitivity) and range—
    eliminates time-consuming manual dial adjustments
    Store up to nine multi-point standard curves in memory
    Linear regression analysis permits direct
    concentration readings
    Operates in English, Spanish, French, and German
    RS-232 provides computer and printer connections
    A retainer clip made of “memory metal” lets you use a variety of tube and cuvette sizes without special adapters"

  • Scintillation counter ( Scintillation counter )

    Used to measure ionizing radiation.

  • Siemens DPC Immulite chemistry analyzer ( Chemistry analyzer )

Protocols

Services

  • Clinical specimen processing ( Material modification service )

    "The OCTRI Core Laboratory staff have extensive experience in a wide range of processing procedures including:

    * Routine serum and plasma separations
    * PBMC purifications via Ficoll or CPT tubes
    * RBC and platelet Isolation procedures
    * Nuclear extract preparations
    * Blood smear preparations
    * Addition of various additives such as antioxidants and protease inhibitors
    * Stabilization of RNA in tissues and blood
    * DNA isolation
    * Guthrie card spotting"

  • Eppstein Bar Virus (EBV) transformation of B-Lymphocyte cells ( Material modification service )

  • Experimental design & consultation ( Support service )

    "Laboratory staff can give advice on many aspects of project development from initial experimental design, sample requirements, assay options and QC parameters through data collection, analysis and data interpretation. When standard types of analyses are not adequate or unavailable, development of new assays and procedures can often be customized to fit the needs of the investigator."

  • Genetic analysis services ( Material analysis service )

    "The OCTRI Core Laboratory can perform a variety of genetic type analyses and procedures including:

    * DNA sequencing, low to medium throughput using our ABI 3130xl Genetic Analyzer
    * Fragment analysis and AFLP analysis (DNA profiler) using GeneMapper software
    * Traditional genotyping and RFLP analysis by electrophoresis (e.g. ApoE genotyping)
    * SNP and STR analysis
    * Cell Immortilization with EBV
    * RNA and DNA isolation"

  • Laboratory assays & analyses service ( Material analysis service )

    "The OCTRI Core Laboratory can complete the following assays and analyses. The Core Laboratory can also conduct new analyses based on a protocol's unique needs. To inquire about an assay that doesn't appear on this list, contact the OCTRI Core Laboratory.

    Laboratory Assays:

    * ACTH
    * Adiponectin
    * Adiponectin (HMW)
    * Aldosterone
    * Anti-factor Xa
    * Apomorphine
    * BSAP
    * CD40 ligand
    * Cortisol
    * Cotinine
    * C-peptide
    * C-reactive protein
    * D-Dimer
    * Estradiol
    * Estrone
    * Ferritin
    * Folate
    * FSH
    * Ghrelin
    * GLP-1
    * Glucose
    * HGH
    * Homocysteine
    * Ibuprofen
    * IGF-1
    * IGFBP-1
    * IGFBP-3
    * IL-1b
    * IL-6
    * IL-8
    * IL-10
    * Insulin
    * Leptin
    * LH
    * Melatonin
    * Metanephrine
    * Myeloperoxidase
    * Normetanephrine
    * Nitrate/nitrite
    * N-teleopeptide
    * Protein S
    * Osteocalcin
    * PAI-1
    * Progesterone
    * Prolactin
    * PSA
    * PTH
    * Pyrilinks-D
    * PYY
    * Salivary cortisol
    * Salivary estradiol
    * Salivary melatonin
    * Salivary progesterone
    * Salivary testosterone
    * Serotonin
    * SHBG
    * 6-Sulfatoxymelatonin
    * TAT
    * tPA
    * T3 & T4 total/free
    * Testosterone
    * TNF-a
    * TSH
    * Vitamin B12
    * Vitamin B6
    * 1,25-Dihydroxyvitamin D
    * 25-Dihydroxyvitamin D

    Carotenoids

    * Lutein
    * b-cryptoxanthin
    * a-carotene
    * b-carotene
    * lycopene
    * Retinol
    * Zeaxanthin"

  • Sample shipping ( Support service )

    "Samples are shipped on a daily basis to other OHSU laboratories and to external testing laboratories, collaborating institutions and sponsor laboratories. Samples can be shipped at ambient temperature, 5C and on dry ice."

  • Sample storage ( Material storage service )

    "High volume storage facilities are available for short and long term storage of clinical samples under various storage conditions.

    * Room temperature
    * 5C walk-in cold room
    * -20C walk-in cold room
    * -80C freezers
    * Liquid nitrogen storage

    All storage facilities have high/low temperature alarms which are also hooked up to OHSU public safety who can contact laboratory staff after hours and on weekends in the event of any equipment malfunction."

Software

  • ABI DNA sequencing analysis software ( Software )

    "This software enables you to basecall, trim, display, edit, and print data from our entire line of capillary DNA sequencing instruments for data analysis and quality control."

  • ABI Prism Genescan and DNA sequencing analysis software ( Software )

    This software performs fragment analysis of data from a gene sequencer.

  • DNASTAR Sequence Alignment Software ( Software )

    This software aligns fragmented DNA sequences from DNA sequencers.

  • GeneMapper ( Software )

    "GeneMapper® Software is a flexible genotyping software package that provides DNA sizing and quality allele calls for all Applied Biosystems electrophoresis-based genotyping systems. This software specializes in multiapplication functionality, including amplified fragment length polymorphism (AFLP®), loss of heterozygosity (LOH), microsatellite, and SNP genotyping analysis. GeneMapper® Software can help users increase data processing efficiency with remote auto-analysis and command line operation, and allows for multiuser, client-server deployment. The software uses Process Quality Values (PQVs) for automated identification that reduces data review time for high throughput genotyping. In addition, the security and audit features help users meet 21 CFR 11 requirements."


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Last updated: 2012-11-01T14:39:21.992-05:00

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