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The Vermont Integrative Genomics Resource (VIGR) provides servies in four branches of genomics:
Please use the following link to view our website: https://www.med.uvm.edu/uvmcancercenter/core-facilities/genome-technologies
|
Hours |
Location |
|
7:30am - 5 pm Mon-Fri. |
303 HSRF |
Dr. Julie Dragon
Director
Director / Bioinformatics
802-656-7777
julie.dragon@uvm.edu
Jessica Hoffman
Microarray Facility
802-656-2557
jessica.hoffman@uvm.edu
303 HSRF
Scott Tighe
Massively Parallel Sequencing Facility
scott.tighe@uvm.edu
303 HSRF
Dr. Ramiro Barrantes
Statistics / Computational Biology
ramiro.barrantes@uvm.edu
Given Courtyard S356
Dr. Marni Slavik
Biology / Systems Biology
marni.slavik@uvm.edu
303 HSRF
Pheobe Kehoe
DNA Analysis Facility
802-656-2557
pheobe.kehoe@uvm.edu
303 HSRF
| Name | Role | Phone | Location | |
|---|---|---|---|---|
| Jessica Hoffman |
Microarray Facility
|
802-656-2557
|
jessica.hoffman@uvm.edu
|
303 HSRF
|
| Sample Submission and Laboratory Services |
| ► Bioinformatics Shared Resource (19) | |||
| Name | Description | Price | |
|---|---|---|---|
| Amplicon Sequencing | Inquire | ||
| Peak Calling | Inquire | ||
| Data upload | Inquire | ||
| Database mining | Inquire | ||
| Demultiplex | Inquire | ||
| Variant calling | Inquire | ||
| Hi-C | Inquire | ||
| Initial Consultation | Inquire | ||
| Additional Consultation | Inquire | ||
| Letter of support, methods text | Inquire | ||
| Manuscript support | Inquire | ||
| Metagenomics | Inquire | ||
| Methods preparation | Inquire | ||
| Microarray Analysis | Inquire | ||
| Pathway analysis | Inquire | ||
| Preliminary data | Inquire | ||
| RNA-Seq | Inquire | ||
| Troubleshoot Demultiplexing | Inquire | ||
| Workshops or help sessions | Inquire | ||
| ► Droplet Digital PCR or RTqPCR (2) | |||
| Name | Description | Price | |
| [Gene Expression] - PCR Arrays | Inquire | ||
| [Gene Expression] - qPCR-Full Service | Inquire | ||
| ► General Genomic Services (15) | |||
| Name | Description | Price | |
| Applied Support | Inquire | ||
| DNA 1000 Quality Assessment (up to 12 Samples/chip) | Inquire | ||
| High Sensitivity DNA Quality Assessment (up to 11 samples/chip) | Inquire | ||
| human Cell Line Authentication |
Includes gDNA extraction and Genescan Run. |
Inquire | |
| Qubit Quantification | Inquire | ||
| RNA Pico Bioanalyzer Quality Assessment-without Quant |
VCIID
$51.00
each
UVM Internal $60.00 each Vt State Institutions $63.00 each External $81.00 each |
||
| RNA Quality Assessment with Quantification (PICO)-Laser Capture Microdisected Samples Only |
Bioanalyzer analysis of RNA at concentrations below 10 ng/uL -- includes quantification using core-provided standard. Used for samples that cannot be quantified using Qubit, such as FACS Sorted cells and Laser Capture.
|
VCIID
$55.25
each
UVM Internal $65.00 each Vt State Institutions $68.25 each External $87.75 each |
|
| Small Non-Coding RNA Quality assessment (11 samples per chip) | Inquire | ||
| Total RNA Quality Assessment (1-12 samples) | Inquire | ||
| [Fragment Analysis] - Full 96 well Plate (per plate) | Inquire | ||
| [Fragment Analysis] - Genescan Run (per sample) | Inquire | ||
| [Image Analysis] - BioRad Image Scan | Inquire | ||
| [Nucleic Acid Extraction] - gDNA Extraction (per sample) | Inquire | ||
| [Nucleic Acid Extraction] - RNA-Blood (per sample) | Inquire | ||
| [Nucleic Acid Extraction] - RNA-Tissue and Cells (per sample) | Inquire | ||
| ► Microarray (12) | |||
| Name | Description | Price | |
| Bacterial 16S PCR Amplification | Inquire | ||
| cDNA Synthesis and SPIA Amplification | Inquire | ||
| ChIP on Chip including Hyb/scan | Inquire | ||
| GeneChip Hybridization and Scan (USER GENERATED TARGETS) |
Turnaround time: 5-10 business days |
Inquire | |
| Microarray - Applied Support |
Applied Support |
Inquire | |
| miRNA 4.0 array (Affymetrix, 2-pack) |
Affymetrix miRNA 4.0 array (2 pack) |
Inquire | |
| miRNA FlashTag Target Prep with Hyb and Scan (User Purchased Reagents) | Inquire | ||
| miRNA Target Prep including Hyb/Scan |
Turnaround time: 5-10 business days |
Inquire | |
| Phylochip Target Prep including Hyb/Scan |
Turnaround time: 5-10 business days. |
Inquire | |
| SNP / Mapping Target Prep 500K (Nsp or Sty) including Hyb/Scan |
Turnaround time: 5-10 business days |
Inquire | |
| SNP/Mapping 250K (Nsp or Sty) Target Prep (Hyb/Scan with reduced price CORE Arrays) | Inquire | ||
| WT Nugen Pico Ovation Target Prep including Hyb/Scan |
Turnaround time: 5-10 business days |
Inquire | |
| ► Next Gen Sequencing (14) | |||
| Name | Description | Price | |
| 16s microbiome library -V4, Multi-HV, ITS, or combined HV-ITS (Groups of 48) |
Submit DNA at a concentration between 2-20ng/ul Quantify by Qubit and Nanodrop Submit 20ul Three digit sample labels only Minimum 48 samples |
UVM Internal
$39.00
each
Vt State Institutions $40.95 each External $52.65 each |
|
| DNASeq-ChIPSeq library prep (1-9 samples) |
Input: Sample dependent Qubit, Bioanalyzer, and Nanodrop (for quality) data required Submit 10-20ul of sample in a well labelled screw cap tube |
Inquire | |
| Exome/Target Capture/Ampliseq |
By Quote only. |
Inquire | |
| HiSeq Self Generated MPS Libraries Sequencing PE 2x100BP (Paired End) | Inquire | ||
| HiSeq Self Generated MPS Libraries Sequencing SE100BP/SE150 (Single End) |
Samples that are run on a Rapid Run Flow cell can be pushed to SR150, however, produce 10-20% less reads. |
UVM Internal
$1,921.30
each
Vt State Institutions $2,017.37 each External $2,593.76 each |
|
| HiSeq Sequencing PE75BP (Paired End) |
Also used for 10X genomics RNASeq (Paired End 28 x 92) |
Inquire | |
| HiSeq Sequencing-by-Synthesis-100 bp Paired End (200bp) |
UVM Internal
$2,600.00
each
Vt State Institutions $2,730.00 each External $3,510.00 each |
||
| HiSeq Sequencing-by-Synthesis: 100bp Single End |
UVM Internal
$1,750.00
each
Vt State Institutions $1,837.50 each External $2,362.50 each |
||
| HiSeq Sequencing-by-Synthesis: 75 bp Single End |
UVM Internal
$1,380.12
each
Vt State Institutions $1,449.13 each External $1,863.16 each |
||
| NGS Library Quantitation qPCR (KAPA) | Inquire | ||
| NGS Library Quantitation qPCR and Qubit | Inquire | ||
| Oxford Nanopore Sequencing -High Output Nanopore Flow Cell |
Oxford Nanopore Sequencing must be approval by facility staff prior to sample submission. General Q-Score average 10-12 on the MK1B R9.4D Porecell |
UVM Internal
$950.00
each
Vt State Institutions $997.50 each External $1,282.50 each |
|
| Sequencer Prep-Hyb Cocktail Prep for User generated MPS Libraries |
For final assembly of User generated Sequencing libraries. Included is Qubit, HT1 hyb prep, qPCR with KAPA, dilutions and PhiX spike in as needed |
UVM Internal
$171.30
each
Vt State Institutions $179.87 each |
|
| Small RNA Library Prep | Inquire | ||
| ► Sanger Sequencing (2) | |||
| Name | Description | Price | |
| [Sequencing] - Sanger Sequencing 15 samples or less |
Please submit template, primer and water mixed in 0.5 ml tube per sample according to the updated guidlelines. The facility will run the primer extension reaction and complete the sequence run. |
Inquire | |
| [Sequencing] - Sanger Sequencing 16 samples or more |
A minimum of 16 samples is required. Submissions MUST be in a Phenix brand (catalog# MPS-3580) 96 well plate and the user is required to combine the template, primer and water. SAMPLES CAN NOT BE ACCEPTED IN ANY OTHER PLATE. |
Inquire | |
