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PCPGM Microarray Facility

Director: Morgan, Vance, Ph.D., MBA

Location: Partners HealthCare Center for Personalized Genetic Medicine, 65 Landsdowne Street, Room 350, Cambridge, MA 02139

Core Summary:

The Partners HealthCare Center for Personalized Genetic Medicine Microarray Facility is a full service facility dedicated to providing analysis for DNA or RNA samples.

We provide support for high density microarrays to the Harvard Partners research community, including Harvard medical School, hospitals in the Partners Healthcare network, investigators in the Dana-Farber/Harvard Cancer Center, and the Harvard School of Public Health. Our services are open to both the PHS and non-PHS community.

Institutions:
  • Partners HealthCare Personalized Medicine
Personnel/Contact Information:

Director: Morgan, Vance, Ph.D., MBA
Phone: (617) 768-8518
Email

Member: Brown, Alison
Role: Lab Manager, PCPGM Genotyping Facility
Phone: (617) 768-8470
Email

Facilities and Equipment:

Location of Core: Partners HealthCare Center for Personalized Genetic Medicine, 65 Landsdowne Street, Room 350, Cambridge, MA 02139

Major Equipment:

  • Affymetrix GeneChip Fluidics Station 450
  • Affymetrix GeneChip Hybridization Oven 640
  • Affymetrix GeneChip Scanner 3000 7G with Autoloader
  • Agilent 2100 Bioanalyzer
  • Agilent tape station
  • BeadStudio
  • Beckman Coulter Biomek FXP laboratory automation workstation
  • Gemini XPS Fluorescent Microplate Reader
  • Illumina iScan reader with Autoloader
  • Illumina Tecan EVO 150 Robot Station
  • Thermo Scientific NanoDrop
Services:
  • Affymetrix gene expression

    "Affymetrix arrays are now available in versions using 3’ labeling methods and a newer design for whole transcriptome analysis. Affymetrix single cartridge arrays are used one sample per array. Arrays are manufactured for a wide variety of species. We are able to process cartridge arrays but do not support the plate arrays at this time."

    The lab offers three levels of service:

    * Full Service
    * Hybridize/Scan Only
    * Analysis/Bioinformatics with Full Service

  • Bioanalyzer QC testing

    All RNA must be in aqueous solution (DNase + RNase free water and not in DEPC), in suitable sterile capped tube containers that are clearly labeled with sample IDs (smudge free labels please). RNA submitted to us for Full Service is automatically subject to analysis for QC. Testing for RIN score is done on Agilent Technologies Bioanalyzer 2100 or Tape Station. Optimum specs for your total RNA are a RIN score of > 7.0, and 260/280 = 1.8 - 2.0 and 260/230 1.8 - 2.0 as key markers of RNA purity.

    If you have RNA that you wish only to have tested for RNA quality, we will also perform RNA testing on the Bioanalyzer/Tape Station as a 'stand alone' service.

  • Illumina Gene Expression

    Illumina BeadChip arrays are arranged in array of arrays format providing configurations for six, eight or 12 individual arrays on each BeadChip array. The arrays are separated from one another by a seal so that each array can be hybridized to a different sample; and multiple samples may be interrogated simultaneously. While not limiting, the most efficient use of these arrays is to plan for sample numbers and arrays that allow us to fill the greatest percentage of slots on each single BeadChip array.

    Illumina BeadChip arrays are available for human, mouse and rat samples. According to Illumina WG-6 and HT-12 arrays provide genome-wide transcriptional coverage of well-characterized genes, with a significant portion targeting well-established sequences supported by peer-reviewed literature." Mouse Ref-8 arrays are also available but without the exon based design used for the Mouse WG-6 arrays.

    The lab offers three levels of service:

    * Full Service
    * Hybridize/Scan Only
    * Analysis/Bioinformatics with Full Service

  • NanoDrop RNA testing

    "If you have RNA that you wish only to have tested for RNA concentration, we will also perform RNA testing on the NanoDrop as a 'stand alone' service.

    Samples submitted to us lacking concentration information may be analyzed via the NanoDrop at additional cost to the project."


Departmental Web Link(s):

Last updated: 2011-06-17T17:58:56.209-05:00