University of Vermont

The University of Vermont Cancer Center

agtc.html

Advanced Genome Technologies Core Facilities

The Advanced Genome Technologies Core is an overarching umbrella encompassing three distinct shared resource facility arms:

  • DNA Analysis: The University of Vermont Cancer Center DNA Analysis Facility provides an array of fast, affordable, user-friendly DNA/RNA analysis services to the members of the University of Vermont Cancer Center, the University of Vermont research community and outside Institutions. Primary services offered for a fee include DNA Sanger sequencing, real-time quantitative PCR, DNA fragment analysis, SNP detection, nucleic acid extraction, image analysis, analytical flow cytometry, and support for absorbance, chemiluminescence, and fluorescence assays.
  • Microarray: The Vermont Genetics Network Microarray Facility utilizes the Affymetrix GeneChip system to support global gene expression profiling using the standard 3’ arrays, miRNA, gene and exon arrays. The facility also provides supports for DNA idenfitification, quantification, and profiling for DNA studies using the DNA mapping (SNP), Promoter, Phylochip, and custom arrays. 
  • Massively Parallel Sequencing Facilities: The University of Vermont Cancer Center/College of Medicine Massively Parallel Sequencing Facility provides genome-scale next generation DNA sequencing.  This facility employs the use of the massively paralleled sequencing (MPS) technology on the Illumina HiSeq 1000 system which is a sequencing by synthesis approach (SBS).  Next generation sequencing (also known as deep sequencing or high throughput sequencing) enables researchers to sequence as much as an entire human or mouse genome with greater than 50 fold coverage. A single run on the Illumina HiSeq 1000 can generate over 350 billion bases of DNA/RNA.

How to Access Services

The Advanced Genome Technologies Core is now using iLab Solutions for all service requests and distribution of data.

To get started, you must register for an account:

  1. Navigate to the core page.
  2. In the upper-right-hand corner of the screen, select sign up.
  3. Complete the registration form on the sign-up page.
  4. Receive a “welcome” email from iLab (typically within one business day) with login credentials
    and basic instructions.

We have developed a number of “How to” Manuals to help with some basic functions:

Common Equipment

The Common Equipment Room is located in HSRF 307 and allows 24/7 access to a variety of user driven equipment for trained investigators. Equipment includes:

  • Imaging equipment including:  Bio-Rad Pharos FX PLUS and Versa Doc 4000 MP
  • Beckman Coulter Analytical Flow Cytometer
  • BioTek Synergy H4 Multi-plate reader
  • NanoDrop Spectrophotometer

Experimental Design Consultations

Design teams for both Microarray and Massively Parallel Sequencing have been assembled that include staff from the respective facilities plus bioinformaticians from the Molecular Bioinformatics Shared Resource and the Vermont Genetics Network Bioinformatics Core.  All design team members maintain dedicated time weekly to provide this support.

Citing the Advanced Genome Technologies Core (DNA Analysis and Massively Parallel Sequencing Core Arms)

Please remember to cite the University of Vermont Cancer Center Advanced Genome Technologies Core in your abstracts and publications. These citations demonstrate to the NCI and other funding organizations (as well as the UVM administration) the importance of this facility to UVM researchers and thereby encourage their continued support. We try to keep a current list of all publications that cite the facility, so please let us know as when your papers are published.

For Cancer Qualifying projects that were completed prior to Nov. 30, 2008:

  • "The automated DNA sequencing (or other molecular analyses, i.e. rtQ-PCR, Molecular Imaging, etc.) was performed in the University of Vermont Cancer Center DNA Analysis Facility and was supported in part by grant P30CA22435 from the NCI. The views expressed are those of the author and do not represent the views of the NCI."

For Cancer Qualifying projects that were completed after Nov. 30, 2008:

  • "The automated DNA sequencing (or other molecular analyses, i.e. rtQPCR, Molecular Imaging, etc.) was performed in the University of Vermont Cancer Center Advanced Genome Technologies Core and was supported by the University of Vermont Cancer Center, Lake Champlain Cancer Research Organization, and the University of Vermont College of Medicine."

For other users, state that DNA sequencing (or other molecular analysis) was performed in the University of Vermont Cancer Center Advanced Genome Technologies Core.

Last modified December 18 2015 12:27 PM