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Molecular Phenotyping and Genotyping Core (JDC)

Director: Patti, Mary-Elizabeth, M.D.

Location: Joslin Diabetes Center, One Joslin Place, Boston, MA 02215

Summary:

The objective of the Molecular Phenotyping and Genotyping Core is to support investigators in the study of molecular mechanisms of disease by providing equipment, expertise, and services in molecular phenotyping, including nucleic acid sequence analyses, gene expression, and other "-omics" analyses, which would be too specialized or costly for individual laboratories to perform independently. Formerly known as the Advanced Genomics and Genetics Core, the Molecular Phenotyping Core is newly-named in recognition of the expansion of its analytical capacities to reflect not only genetic and genomic analyses but also metabolic phenotyping.

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Instruments

  • ABI GeneAmp 9700 PCR System dual 384-well thermal cycler ( PCR instrument )

    Applied Biosystems 9700 Thermal Cycler with dual 384-well or dual 96-well blocks

  • ABI PRISM 7900HT Fast sequence detection system with automation ( Real-time PCR machine )

    "The 7900HT Fast Real-Time PCR System is the only real-time quantitative PCR system that combines 384-well plate compatibility with fully automated robotic loading—and now also offers optional Fast real-time PCR capability. Acknowledged as the gold standard in real-time PCR, the 7900HT system combined with TaqMan Genomic Assays enables you to achieve unprecedented throughput and flexibility, allowing you to pursue projects beyond the scope of previous real-time instruments."

  • ABI PRISM 7900HT sequence detection system ( Real-time PCR machine )

    "The ABI prism 7900HT Sequence Detection System is a high-throughput real-time PCR system that detects and quantitates nucleic acid sequences. An Automation Accessory combined with 384-well plate capability make the 7900HT system ideally suited to meet the high-throughput requirements of todays drug discovery process. Key applications include gene expression quantitation and the detection of single nucleotide polymorphisms (SNPs) using the fluorogenic 5 nuclease assay."

  • Affymetrix Expression Console ( Genotype analysis platform )

  • Affymetrix GeneChip Fluidics Station 450 ( Fluidics station )

    "The GeneChip® Fluidics Station 450 is used for the wash and stain operation of Affymetrix GeneChip® arrays. The instrument includes design advancements to provide improved ease of use and true walk-away freedom dramatically improving efficiency in your genetic analysis."

  • Affymetrix GeneChip Hybridization Oven 645 ( Hybridization oven )

    "The GeneChip Hybridization Oven 645 provides precise temperature and rotation control to ensure the successful hybridization of as many as 64 GeneChip cartridges at one time.

    An ergonomic front-panel display contains system status indicators and buttons for adjusting the set point temperature and the rotisserie speed. This panel, in addition to a highly visible display and large window, provides immediate feedback of proper operation when using the oven.

    The oven can be configured for 110 or 220V operation."

  • Affymetrix GeneChip Scanner 3000 ( Array scanner )

    "The GeneChip Scanner 3000 incorporates advanced design improvements with space-saving, speed, superior performance, and lower scanner-to-scanner variation to dramatically improve throughput and efficiency in your genetic analysis. This new scanner provides more accurate gridding and more consistent scanner-to-scanner biological performance, improving data integrity and data sharing between researchers."

  • Agilent 2100 Bioanalyzer ( Microfluidics platform )

    "The Agilent 2100 Bioanalyzer is a microfluidics-based platform for sizing, quantification and quality control of DNA, RNA, proteins and cells on a single platform. Results are delivered within 30-40 minutes in automated, high quality digital data.

    The BioAnalyzer can be used for rapidly analyzing RNA, DNA, and proteins. This instrument uses lab-on-a-chip technology to perform automated quality control, quantification, and sizing of samples. Applications include: Microarray sample quality control, PCR optimization, Analysis of protein purifications."

  • Covaris E220 Ultrasonicator ( Sonicator )

    The Adaptive Focused Acoustics (AFA) technology employs a very high frequency ultrasound waves to be focused into a discrete zone in the sample vessel. This efficient delivery requires minimal energy avoiding the adverse effect on the sample. The focused ultrasonicator provides exquisite control and tuning of the power, making the application of the instrument versatile: from gentle, low-power to high-power applications such as chromatin shearing, DNA fragmentation, liposome and nanosuspension formation.

  • MJ Research PTC-200 96-well thermocycler ( Thermal cycler )

    "The MJ Research PTC-200 is a 96 well gradient thermocycler that can be supplied with different alpha blocks such as a 96 well or a dual 48-well block."

  • NanoDrop ND-1000 spectrophotometer ( Spectrophotometer )

  • NanoDrop ND-3300 spectrophotometer ( Spectrophotometer )

  • QuantStudio 6 Flex real-time PCR system ( Digital polymerase chain reaction system )

  • Seahorse XF24 analyzer ( Cell assay platform )

    "The Seahorse XFe24 Analyzer measures OCR and ECAR of live cells in a 24-well plate format. These rates are key indicators of mitochondrial respiration and glycolysis and provide a systems-level view of cellular metabolic function in cultured cells, islets, and ex vivo samples."

  • Seahorse XFe96 analyzer ( Cell assay platform )

    "The Seahorse XFe96 Analyzer measures OCR and ECAR of live cells in a 96-well plate format. These rates are key indicators of mitochondrial respiration and glycolysis and provide a systems-level view of cellular metabolic function in cultured cells and ex-vivo samples."

  • Tecan Freedom EVO Liquid Handler ( Liquid handler )

Services

  • Bioenergetics and molecular phenotyping ( Material analysis service )

    The Core houses an XFe96. This instrument can be used to analyze cultured cells, tissue explants, and whole blood samples though quantification of oxygen consumption and extracellular acidification (a surrogate for glycemic flux and metabolic flexibility).

  • Bioinformatics services ( Analysis service )

    In-house bioinformatics team can provide analysis for microarrays.

  • DNA bioanalyzer services ( Material analysis service )

    We perform analysis of DNA using the DNA High Sensitivity or DNA 1000 assays.

  • DNA purification ( Material processing service )

    Extraction of high quality DNA from human specimens, including blood samples.

  • DNA repository ( Support service )

    The Core repository currently includes about 6,000 DNA samples organized in eight panels, some of which include special forms of diabetes not available in other collections.

  • DNA shearing ( Material processing service )

    The Covaris E220 Ultrasonicator provides high quality shearing of 1 to 96 gDNA samples in a single run.

  • Experimental design services ( Material production service )

    Assistance with sample preparation (RNA isolation), experimental design, and choice of array.

  • Expression analysis ( Material analysis service )

    The Core houses an Affymetrix platform for microarray analysis. Core personnel can provide sample prep from RNA as well as hybridization for multiple species. Additionally, the Core facilitates submission of microarray studies to papers and expression databases such as GEO.

  • Genetic characterization for clinical studies ( Material processing service )

    A next-generation sequencing assay has been developed by the Core to simultaneously screen all known mongenic diabetes genes (e.g. MODY, neonatal diabetes) for mutations and to type all known SNPs associated with T1D, T2D, and complications. This assay will allow the standardized collection of genetic data to study the influence of genetic variation on the response to treatments and exposures in interventional and observational studies at a reasonable price.

  • Next-generation sequencing ( Material modification service )

    The Core offers full service library prep and capture for custom designed or whole exome NGS projects. Sequencing of prepared libraries is completed through collaboration with an external sequencing facility.

  • PCR expression analysis ( Material analysis service )

    The Core houses two ABI 7900's (386 well) and one ABI 7000 (96-well).

  • PCR training service ( Training service )

    Instruction in RT-PCR setup, operation of SDS software, and operation of PCR machines.

  • RNA bioanalyzer services ( Material analysis service )

    We perform analysis of RNA samples using the RNA Nano assay.

  • Seahorse services ( Training service )

    Training on Seahorse instrumentation for new users, with ongoing troubleshooting support.

  • SNP genotyping ( Material modification service )

    The Core provides a single nucleotide polymorphism (SNP) typing service based on the Applied Biosystems TaqMan SNP Genotyping Assays.

Software

  • ABI Primer Express ( Software )

    "The Primer Express® Software v3.0 allows you to design your own primers and probes using TaqMan® and SYBR® Green I dye chemistries for gene quantitation and allelic discrimination (SNP) real-time PCR applications. Developed specifically for use with our 7300, 7500, 7500 Fast, and 7900HT Fast Real-Time PCR Systems, Primer Express® Software provides customized application-specific documents for absolute/relative quantitation and allelic discrimination."

  • Affymetrix Expression Console ( Software )

    "Affymetrix® Expression Console software supports Probe Set summarization and CHP file generation for both 3' Expression (GeneChip® Human Genome U133 Plus 2.0 Array) and Exon Arrays (GeneChip Human Exon 1.0 ST Array)."


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Last updated: 2018-07-05T14:25:25.735-05:00

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