eagle-i Harvard UniversityHarvard University
See it in Search

Advanced Genomics and Genetics Core (JDC)

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

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

Summary:

Genomics Core: High-density oligonucleotide arrays allow quantitative analysis of thousands of transcripts and provide an efficient way to determine the full pattern of alterations in gene expression present in a wide variety of experimental conditions and pathologic states. Affymetrix chips are high-density collections of 25-mer oligonucleotides aligned in arrays on a silicon chip. We also provide RNA quality assessment through Bioanalyzer assays.

PCR Core: The PCR Core is part of the Genomics Core and maintains a suite of real-time PCR instruments.

Metabolic Core: The Genomics Core also houses XFe96 and XF24 Seahorse Analyzers for the real-time measurement of metabolism in live cells.

Affiliations:

People:

Resources:

Instruments

  • 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."

  • 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."

Services

  • Bioanalyzer services ( Material analysis service )

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

  • Bioinformatics services ( Analysis service )

    In-house bioinformatics team can provide analysis for microarrays.

  • Experimental design services ( Material production service )

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

  • Microarray services ( Material production service )

    Supported arrays include Affymetrix 3' expression arrays, transcriptome arrays, gene arrays, exon arrays, and promoter arrays. We perform microarray assays from total RNA, but also perform hybridization of user-prepared cRNA/cDNA samples to experimental arrays. Preliminary analysis of data is done with Affymetrix Expression Console.

  • PCR training service ( Training service )

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

  • Seahorse services ( Training service )

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

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)."


Web Links:

Last updated: 2017-04-27T10:00:04.294-05:00

Copyright © 2016 by the President and Fellows of Harvard College
The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016