A searchable database of core laboratory facilities. Core Facilities

CPCT Genomics Core (DF/HCC)

Director: Macoska, Jill, Ph.D.

Location: University of Massachusetts Boston, Integrated Sciences Complex, Room 4630, 100 Morrissey Boulevard, Boston, MA 02125

Core Summary:

The Center for Personalized Cancer Therapy (CPCT) Genomics Core was established in 2015 to enable UMass Boston investigators and academic and industry collaborators to carry out basic and translational genomics research. The Core leverages cutting-edge technologies and next-generation sequencing capabilities for research and clinical applications. We help investigators and clinicians analyze samples, identify genetic variants contributing to disease risk, and reveal complex mechanisms involved in human disease.

The Core offers cost-effective massively parallel sequencing with the Illumina HiSeq 2500 (v4, 1TB enabled) and Illumina MiSeq platforms, and next-generation sequencing library preparation from RNA and DNA and nucleic acid quality assessments. Our Nanostring nCounter Analysis System allows highly sensitive, multiplexed gene expression analysis.

The CPCT is a collaborative venture between the University of Massachusetts Boston and the Dana-Farber/Harvard Cancer Center (DF/HCC).

Institutions:
  • Dana-Farber/Harvard Cancer Center
  • University of Massachusetts Boston
Personnel/Contact Information:

Director: Macoska, Jill, Ph.D.
Phone: (617) 287-5783
Email

Member: Avery, Amy
Role: Manager
Phone: (617) 287-6578
Email

Member: Almanza, Diego
Role: Lab Assistant
Email

Member: Abdi, Malyun
Role: Lab Assistant
Email

Member: General Inquiries
Phone: (617) 287-6578
Email

Facilities and Equipment:

Location of Core: University of Massachusetts Boston, Integrated Sciences Complex, Room 4630, 100 Morrissey Boulevard, Boston, MA 02125

Major Equipment:

  • Agilent 2100 Bioanalyzer
  • Agilent 2200 Tapestation
  • Biomek FXp Automated Liquid Handler
  • Covaris S220
  • Illumina cBot
  • Illumina HiSeq 2500 v4; 1 TB enabled
  • Illumina MiSeq
  • Nanodrop Lite
  • Nanostring nCounter Analysis System
  • QuantStudio™ 12K Flex Real-Time PCR System
  • Qubit 2.0 Fluorometer
  • Sage Science Blue Pippin
Services:
  • Agilent 2100 Bioanalyzer Services

    The Agilent 2100 Bioanalyzer is a microfluidics-based platform that provides sizing, quantification and quality control of nucleic acids.

  • Agilent 2200 Tapestation Services

    The Agilent 2200 Tapestation system automates RNA and DNA sample QC. Separation and analysis of nucleic acid is carried out with only 1 ul of material.

  • Illumina HiSeq 2500 Services

    The Illumina HiSeq 2500 System is a powerful high-throughput sequencing system that supports a wide range of applications. Our v4 upgraded Illumina HiSeq 2500 instrument supports massively parallel sequencing using Sequence By Synthesis (SBS) technology that detects single bases as they are incorporated into growing DNA strands. The High Output mode offers up to 8 lanes/run (max 2 x 126 read length), while the Rapid Mode uses a 2-lane flow cell (max 2 x 251 read length). Single or Paired End reads are available.

  • Illumina MiSeq Services

    The Illumina MiSeq is a desktop sequencer which allows for more focused applications such as targeted gene sequencing, metagenomics, small genome sequencing, targeted gene expression, amplicon sequencing, and HLA typing. MiSeq v3 reagents enable up to 15 Gb of output with 25 M sequencing reads and 2 x 300 bp read lengths. Adjustable read lengths, flow cell options, and choice of single or paired-end reads allow unmatched flexibility to meet the needs of a wide range of projects.

  • Library Preparation Services

    Our NGS library prep and sequencing service includes preparation of libraries from DNA and RNA, QC and pooling of samples followed by sequencing on the Illumina HiSeq 2500 v4 instrument or Illumina MiSeq. We offer KAPA library preparations, which provide a robust, streamlined method of sample preparation for Illumina sequencing. The chemistry has been optimized to produce higher yields of adapter-ligated library and lower amplification bias.

    The KAPA Stranded RNA-Seq kit with RiboErase produces high-quality RNA libraries for Illumina platforms. The kit includes KAPA HiFi enzyme for high-efficiency and low-bias library amplification, and includes a streamlined, “with-bead” protocol.

    Library construction is performed on our Beckman Biomek FXp Laboratory Automation Workstation.

  • Nanodrop Lite Services

    The Nanodrop Lite is a UV spectrophotometer designed for quantitation of nucleic acids using microvolumes of sample. Concentration is measured at 260 nm and purity is determined using the 260/280 ratio.

  • Nanostring nCounter Analysis System Services

    The Nanostring nCounter® Analysis System is an automated, multi-application, digital detection and counting system which directly profiles up to 800 unique molecules simultaneously from a single sample in a single reaction using a novel barcoding technology. Each fluorescently labeled barcode is attached to a single target-specific probe corresponding to a gene of interest. The probes form a multiplexed CodeSet. Nanostring also offers Custom CodeSet Design. This is available to assay any target sequences for any organism. All custom CodeSets undergo extensive quality-control testing before they are delivered.

  • QuantStudio™ 12K Flex Real-Time PCR System Services

    The QuantStudio 12K Flex RealTime PCR System workflow includes real-time thermal cycling and fluorescent data collection from TaqMan Assays. The instrument is equipped to process 384 well plates.

  • Qubit Services

    The Qubit 2.0 fluorometer accurately quantifies DNA and RNA. It provides a very sensitive assay as the fluorescent dyes bind only to the target molecule. As little as 1 ul of sample can be used for each measurement.

  • Shearing Services

    The Covaris S220 uses Adaptive Focused Acoustics™ (AFA) to shear DNA for next generation sequencing library applications. The AFA delivers high frequency ultrasonic energy to process samples in a non-contact environment.


Departmental Web Link(s):

Last updated: 2015-11-24T14:39:17.473-06:00