A searchable database of core laboratory facilities. Core Facilities
Alert: The Harvard Catalyst website will be unavailable due to system maintenance from Friday (02/24) 10pm to Saturday (02/25) 1pm.

CCIB DNA Core: Sequencing (MGH)

Director: Stange-Thomann, Nicole, Ph.D.

Location: Massachusetts General Hospital, Center for Computational and Integrative Biology, 38 Sidney Street, Suite 100, Cambridge, MA, 02139

Core Summary:

The CCIB DNA Core, founded in 1995, is a well-established major research core laboratory within the Center for Computational and Integrative Biology of Massachusetts General Hospital Boston. The Facility provides a wide range of state-of-the-art services and specialized expertise in genomics, molecular biology, and laboratory automation to the greater Partners research community.

The DNA Sequencing division of the CCIB DNA Core functions both as a small-scale sequencing facility and a high-throughput center for large-scale sequencing projects. It offers solid experience in conventional Sanger DNA sequencing and DNA Fragment Analysis (Microsatellite/MLPA), and reliably provides high-quality services with rapid turnaround time and competitive pricing. In support of the ever-growing research community’s needs, the Sequencing group is now also offering cost-effective high-throughput approaches for specific Next-Generation Sequencing applications such as Complete Plasmid Sequencing and CRISPR Amplicon Sequencing.

Institutions:
  • Massachusetts General Hospital
Personnel/Contact Information:

Director: Stange-Thomann, Nicole, Ph.D.
Phone: (617) 726-0085
Email

PI: Freeman, Mason, M.D.
Role: Faculty Director (Center of Computational and Integrative Biology, Translational Medicine), Professor of Medicine
Phone: (617) 724-7704
Email

Member: Belmonte, Stephen
Role: Manager, DNA Sequencing
Phone: (617) 726-0083
Email

Member: General Inquiries
Phone: (617) 726-5982 / (617) 726-0083
Email

Facilities and Equipment:

Location of Core: Massachusetts General Hospital, Center for Computational and Integrative Biology, 38 Sidney Street, Suite 100, Cambridge, MA, 02139

Major Equipment:

  • ABI 3730xl DNA Analyzers
  • Agilent 2200 TapeStation Nucleic Acid System
  • Biomek FX (dual bridge system)
  • Bio-Rad CFX384 Real-Time System
  • Episonic Multifunctional Bioprocessor 1100
  • Eppendorf Mastercycler pro PCR Systems
  • Illumina MiSeq Desktop Sequencer
  • Tecan Freedom EVO Automated Liquid Handler
Services:
  • Complete Plasmid Sequencing (Next Generation Sequencing)

    The CCIB DNA Core team has developed a low-cost high-throughput approach for complete plasmid sequencing using Next-Generation sequencing technology in combination with automated sequence assembly. This new and unique service offers many advantages over conventional primer walking services, including deep sequencing coverage and highest possible data quality at the lowest cost. Service is available for both individual samples and 96-well plates.

    Service Features include:
    - Complete characterization of unknown plasmids
    - Complete validation of known plasmids
    - No reference sequence required
    - Independent of sequencing primers
    - Cost-effective high-throughput sequencing
    - Multiplexing capability
    - Weekly processing with fast turnaround

  • CRISPR Sequencing (Next Generation Sequencing)

    The Facility has developed a cost-effective, high-throughput strategy for identifying CRISPR/Cas-induced mutations via ultra-deep paired-end sequencing of PCR amplicons. Service is available for both individual samples and 96-well plates.

    Service Features include:
    - Highly sensitive detection levels without bias
    - No need for universal tags on target-specific amplicons
    - No need for time-consuming cloning steps
    - Multiplexing capability
    - Weekly processing with fast turnaround

  • Genotyping DNA Fragment Analysis

    The Facility offers a fast and reliable automated ready-to-run DNA fragment analysis service where fluorescently labeled DNA fragments are electrophoretically separated using the ABI3730xl Genetic Analyzer for accurate sizing, consistency, and minimum run-to-run migration variations. Final data interpretation is available as an add-on service. Quality DNA sizing, allele calling, and relative quantitation is performed using the GeneMapper v4.0 analysis software package. Service is available for both individual samples and 96-well plates.

    Supported DNA Fragment Analysis Applications:
    - Microsatellite Analysis (short tandem repeats (STRs), variable nucleotide tandem repeats (VNTRs))
    - MLPA Analysis (multiplex ligation-dependent probe amplification)

  • Sanger DNA Sequencing

    Sequencing service includes a cycle sequencing reaction using the Applied Biosystems BigDye v3.1 Cycle Sequencing Kit, purification of extension products, and fragment separation and sequence detection via capillary electrophoresis on the 96-well capillary matrix of an ABI3730xl DNA Analyzer.

    Service options include:
    - Individual Tube Sequencing (for purified Plasmids and PCR amplicons)
    - High-Throughput Sequencing (96-well format)
    - Difficult Template Sequencing
    - 96-well PCR Purification


Departmental Web Link(s):

Last updated: 2015-11-19T14:03:46.635-06:00