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