Massively Parallel Sequencing Facility

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 Larner 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 1500 can sequence over 350 billion bases of DNA. 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 for 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 -20C Freezer in 307 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

ApplicationInput concentration required
Whole Genome Sequencing500 ng
RNA-Seq1 ug
Methyl-Seqsee facility staff
ChIP-Seq>20ng (Purified ChIP DNA)

Citing the Vermont Integrative Genomics Resource (DNA Analysis and Massively Parallel Sequencing Core Arms)

Please remember to cite the Vermont Integrative Genomics Resource 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      
    Vermont Integrative Genomics Resource and was supported by the University of Vermont Cancer Center, Lake Champlain Cancer Research Organization, and the University of Vermont Larner College of Medicine."

For other users, state that DNA  sequencing (or other molecular analysis) was performed in the Vermont Integrative Genomics Resource.