University of Vermont

College of Medicine

Vermont Cancer Center

VCC Massively Parallel Sequencing Facility

Massively Parallel Sequencing Facility

About Us

building of COM

General Information

Rates
Project Description Form
MPS Facility Description
Illumina Flow Cell: The Basics
Frequently Asked Questions

Personnel

Manager:
Tim Hunter
Senior Research Technician:
Scott Tighe

Contact Us

Health Science Research Facility
149 Beaumont Avenue, Room 303
Burlington, VT 05405
Phone (office): (802) 656-2559
Phone (lab): (802) 656-AGTC

The AGTC Massively Parallel Sequencing Facility was initiated by the Vermont Cancer Center and the Lake Champlain Cancer Research Organization, and established in 2011 in collaboration with the College of Medicine and College of Agriculture and Life Sciences to provide genome-scale DNA sequencing. The facility employs the use of massively paralleled sequencing (MPS) technology of the Illumina HiSeq system which is 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 sequence over 350 billion bases of DNA. It can be used for genome wide DNA sequencing, RNA-seq, ChIP-Seq, methylation sequencing, metagenomics, exome sequencing, amplicon sequencing, and microRNA sequencing. All Massively Parallel Sequencing projects are reviewed using an integrated approach to experimental design, workflow, and sample collection in collaboration with the UVM Bioinformatics Core Facilities to ensure high quality, statistically relevant results.

Services Offered

  • Experimental Design Consultation
  • Single End, Paired End, or Mate Paired End Library Construction for the following applications:
    • RNA-seq (prokaryote or eukaryote)
    • Whole Genome DNA Sequencing
    • Methyl-Seq
    • ChIP-Seq
    • Metagenomics
    • Amplicon Sequencing
  • Sequencing by Synthesis
  • Ability to multiplex 16 samples/lane via indexing for prokaryotes and up to 48 fr the standard Illumina TruSeq protocols (multiplex number dependent on coverage/depth required for each sample)

Access Guidelines

  • Step I: Consultation: Consulting on experimental design is mandatory to discuss sample requirements, sequence coverage desired, library construction best approaches, insure appropriate number of replicates for statistical significance, and to draft a project design file in support of downstream bioinformatics analysis.
  • Step II: Quantification and Qualitative assessment of Nucleic Acid: All RNA submitted for sequencing must be tested for integrity and for gDNA contamination (extremely important for prokaryotes). It is highly recommended that all nucleic acids are quantified using a fluorometric approach to insure accuracy.
  • Step III: Submit Nucleic Acid(s) for library construction: This should be done in combination with submitting appropriate order form online. Samples can be dropped off in the -200C Freezer in 303 HSRF that is marked “drop MPS samples here”.
  • Step IV: Data Upload: All data will be transferred to a server at the VACC and stored on the College Of Medicine Shared Drive

Sample Requirements

Application Input concentration required
Whole Genome Sequencing 500 ng
RNA-Seq 1 ug
Methyl-Seq see facility staff
ChIP-Seq >20ng (Purified ChIP DNA)

Citing the VCC-COM Massively Parallel Sequencing Facility

Please remember to cite the VCC-COM Massively Parallel Sequencing Facility 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! Below is an example of how to cite the facility:

  • "The next-generation sequencing was performed in the Advanced Genome Technologies Core Massively Parallel Sequencing Facility and was supported by the Vermont Cancer Center, Lake Champlain Cancer Research Organization, UVM College of Agriculture and Life Sciences, and the UVM College of Medicine."

Links of Interest

Last modified December 16 2013 01:05 PM