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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 $63.25 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 (16) | |||
| Name | Description | Price | |
| 16s V4 or ITS microbiome amplicon library (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 Subsidy Rate
$39.00
each
UVM Internal $39.00 each Vt State Institutions $39.00 each External $39.00 each |
|
| ChIP-Seq DNA Library Preparation |
Have you included an "Input" and "IgG control"? |
Inquire | |
| DNA Library Preparation-Nextgen Sequencing | Inquire | ||
| Exome Capture |
By Quote only. |
Inquire | |
| HiSeq Self Generated MPS Libraries Sequencing PE 2x100BP (Paired End) | Inquire | ||
| HiSeq Self Generated MPS Libraries Sequencing PE75BP (Paired End) | Inquire | ||
| HiSeq Self Generated MPS Libraries Sequencing SE100BP (Single End) | Inquire | ||
| HiSeq Sequencing-by-Synthesis-100 bp Paired End (200bp) | Inquire | ||
| HiSeq Sequencing-by-Synthesis: 100bp Single End | Inquire | ||
| HiSeq Sequencing-by-Synthesis: 75 bp Single End | Inquire | ||
| NGS Library Quantitation qPCR (KAPA) | Inquire | ||
| NGS Library Quantitation qPCR and Qubit | Inquire | ||
| Oxford Nanopore Sequencing Library and Sequencng |
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
External $1,425.00 each Vt State Institutions $950.00 each |
|
| RNASeq Library Preparation |
****All samples must be run on the Bioanalyzer and quantified using the Qubit spectrofluorometer**** Input requirement in 0.5ml tubes: Total RNA:-0.5-20ng for Takara Total RNASeq Method (10ul) mRNA: 500-1000 ng for TruSeq mRNASeq (20ul at 50ng/ul) Small RNA: 20-100ng mRNA (10 ul total per reaction)-5-20ng/ul total RNA
RIN 4+
|
Inquire | |
| 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
External $317.10 each |
|
| Small RNA Library Prep | Inquire | ||
| ► Sanger Sequencing (3) | |||
| Name | Description | Price | |
| [Sequencing] - Bulk Sequence (min. 48 samples) |
A minimum of 48 samples is required for Bulk Sequence Requests. 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. IF ANY OTHER PLATE IS USED, SAMPLES WILL AUTOMATICALLY BE CHARGED AT NON BULK RATE WITHOUT NOTIFICATION. |
Inquire | |
| [Sequencing] - Cycle Sequence Rxn and Sequence Run |
For this request, please submit template and primer and the facility will set up the cycle sequence reaction and complete the sequence run. |
Inquire | |
| [Sequencing] - Sequence Run Only |
User must complete Cycle Sequencing Reaction and clean the Cycle Sequence products before bringing to the facility. |
Inquire | |
