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Important Note on Trizol: As of Spring of 2020, the core will no longer process Trizol or Tri-Reagent extract RNA for down stream analysis such as NGS library synthesis, RTqPCR, cDNA reactions, and microarray target synthesis. There will be no exceptions. At this time however, we will be happy to provide QC and/or final SBS sequening on user geneated libraries. Since Phenol can not be cleaned from a Trizol prep, we strongly suggest an alternative RNA extraction.
Shipping
Vermont Integrative Genomics Lab
University of Vermont Cancer Center
Firestone Medical Research Building room 150B
149 Beaumont Ave
Burlington Vermont 05405
[T] 001-802-656-2482
The Vermont Integrative Genomics Resource (VIGR) runs the following instrumentation:
Singular G4 [NEXTGEN SEQUENCER]
Illumina MiSeq [NEXTGEN SEQUENCER]
Illumina MiniSeq [NEXTGEN SEQUENCER]
(3) Oxford Nanopore MinION [NEXTGEN LONG READ SEQUENCER]
(1) Oxford Nanopore GridION [NEXTGEN LONG READ SEQUENCER]
(1) Oxford Nanopore MK1C [NEXTGEN SEQUENCER]
Oxford Nanopore PromethION P2 Solo
10X Chromium Single cell controller [Single Cell GENOMICS]
BioRad QX200 ddPCR [DIGITAL DROPLET PCR]
ABI SeqStudio [SANGER SEQUENCER]
ABI QuantStudio 6 Flex [RTqPCR]
ABI 7500 Fast [RTqPCR]
ThermoFisher SeqStudio [SANGER SEQUENCER]
Agilent Bioanalyzer 2100 [FRAGMENT SIZE ANALYZER]
Innovaprep CP liquid concentrator systems
Qubit 4 Flourometer [DNA QUANTIFICATION]
Nanodrop ND1000 [DNA QUANTIFICATION/QC]
Biorad ChemiDoc XRS+ [GEL DOC/CHEM DOC]
Omni-Prep High Output Bead Mill Homogenizer
Please use the following link to view our website: https://www.med.uvm.edu/vigr/home
Please note any required administrative paperwork by external facility users must be presented and handled prior to sample submission. Please contact Nicole.DeLance@med.uvm.edu to start your paperwork. Post analysis paperwork will not be processed. This allows the core to deny services if paperwork requires added staff time outside of normal activities. Additional administrative processing or paperwork beyond iLabs automatic invoicing will be billed at the standard labor fee set in the "request for services" tab in iLabs as Applied support and automatically added to the ilabs invoice. So please be prepared. The core is very busy.
Please note the core and its staff reserve the right to deny services for any reason as approved by the director(s).
Please contact Amy.Gilman@med.uvm.edu or Nicole.DeLance@med.uvm.edu for card access to FMRB 185A for sample submission and use of VIGR.
Hours |
Location |
8:30am - 5 pm Mon-Fri. |
150B FMRB |
Name | Role | Phone | Location | |
---|---|---|---|---|
Dr. Julie Dragon |
Director
|
802-656-7777
|
julie.dragon@uvm.edu
|
149 Beaumont Ave, FMRB 160, Burlington Vermont 05405
|
Scott Tighe |
Technical Director
|
802-656-2482
|
scott.tighe@uvm.edu
|
FMRB 156
|
Kristiaan Finstad |
Senior Technician
|
802-656-2557
|
kristiaan.finstad@med.uvm.edu
|
FMRB 150B
|
Dr. Kirsten Tracy |
Senior Scientist
|
802-656-2557
|
kirsten.tracy@med.uvm.edu
|
FMRB 150B
|
Dr. Ramiro Barrantes |
Statistics/ Computational Biology
|
ramiro.barrantes@uvm.edu
|
FMRB 150B
|
|
Stacia Richard |
Lab Research Technician
|
802-656-2557
|
stacia.richard@uvm.edu
|
FMRB 150B
|
Sample Submission and Laboratory Services |
► Bioinformatics Shared Resource (17) | |||
Name | Description | Price | |
---|---|---|---|
Amplicon Sequencing | Inquire | ||
Peak Calling | Inquire | ||
Data deposition in GEO/SRA | Inquire | ||
Database mining | Inquire | ||
Variant calling | Inquire | ||
Hi-C | Inquire | ||
Custom Consultation | Inquire | ||
Custom bioinformatics project | Inquire | ||
Letter of support, methods text | Inquire | ||
Manuscript support | Inquire | ||
Metagenomics | Inquire | ||
Methods preparation | Inquire | ||
Pathway analysis | Inquire | ||
Preliminary data | Inquire | ||
RNA-Seq | Inquire | ||
Troubleshooting | Inquire | ||
Workshops or help sessions | Inquire | ||
► General Genomic Services (11) | |||
Name | Description | Price | |
Applied Support | Inquire | ||
Bioanalyzer Quality Assessment DNA High Sensitivity (1-11 samples/chip) |
Dilute sample to between 1.5-4.0 ng/ul based on Qubit Submit minimum 2 uL in 0.5mL tubes Place in the DNA HS rack in the sample submission freezer Do not drop off sample stocks
|
Inquire | |
Bioanalyzer Quality Assessment RNA Nano (1-12 samples/chip) |
Dilute sample to between 25-500 ng/ul based on Qubit Minimum 2uL required Trizol or Tri-reagent warning: Keep in mind that RNA extracted by this method will not be eligible for downstream processing by the core due to interferance caused by phenol. It is not possible to clean the sample of phenol once extracted Do not drop off sample stocks |
Inquire | |
Bioanalyzer Quality Assessment RNA Pico (1-11 samples/chip) |
Dilute sample to between 50 pg - 5.0 ng/ul based on Qubit Minimum 2uL required Trizol or Tri-reagent warning: Keep in mind that RNA extracted by this method will not be eligible for downstream processing by the core due to interferance caused by phenol. It is not possible to clean the sample of phenol once extracted Do not drop off sample stocks |
VCIID
$51.00
each
UVM Internal $60.00 each Vt State Institutions $63.00 each External $81.00 each Non-UVM $66.15 each |
|
Human Cell Line Authentication |
Includes gDNA extraction and Genescan Run. |
Inquire | |
Qubit Quantification |
Minimum 2.5 uL required Trizol or Tri-reagent warning: Keep in mind that RNA extracted by this method will not be eligible for downstream processing by the core due to interferance caused by phenol. It is not possible to clean the sample of phenol once extracted. Please put your samples in the designated tubes rack in the sample freezer. The core prefers samples to be dropped off in 0.5ml tubes. Do not drop off sample stocks |
Inquire | |
[Fragment Analysis] - Full 96 well Plate (per plate) | Inquire | ||
[Fragment Analysis] - Per Sample | Inquire | ||
[Image Analysis] - BioRad Image Scan (ChemiDoc) | Inquire | ||
[Nucleic Acid Extraction] - gDNA Extraction (per sample) | Inquire | ||
[Nucleic Acid Extraction] - RNA (per sample) | Inquire | ||
► Nanopore Sequencing (1) | |||
Name | Description | Price | |
Flow Cell - MinION |
Oxford Nanopore Sequencing must be approval by facility staff prior to sample submission. 10.4 Flow cells have general Q-Score average of 14-22 with up to 10gbases. Output depends on sample type and sequence context and speed. Flow cells that are purchased for individual labs are restricted to UVM. No warranty is given beyond active pores count at time of pickup. Store flat at 4-8C. |
UVM Internal
$550.00
each
Vt State Institutions $555.00 each External $1,110.90 each |
|
► Next Gen Sequencing (8) | |||
Name | Description | Price | |
16s microbiome library |
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 Non-UVM $43.00 each Corporate $65.52 each |
|
DNASeq-ChIPSeq library prep (1-19 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 | |
G4 - Illumina to Singular Conversion |
Please provide at least 3uL of library at a 1ng/uL concentration. |
Inquire | |
G4 F2 Flow Cell, 100 Cycle |
150 Million - 250 Million Reads Ouput Read length up to Paired End 50 or Single End 100 |
Inquire | |
G4 F2 Flow Cell, 300 Cycle |
150 Million - 250 Million Reads Ouput Read length up to Paired End 150 |
Inquire | |
G4 F3 Flow Cell, 100 Cycle |
300 Million - 450 Million Reads Ouput Read length up to Paired End 50 or Single End 100 |
Inquire | |
G4 F3 Flow Cell, 300 Cycle |
300 Million - 450 Million Reads Ouput Read length up to Paired End 150 |
Inquire | |
G4 F3 Flow Cell, 50 Cycle |
300 Million - 450 Million Reads Ouput Read length up to Paired End 25 or Single End 50 Appropriate for nanostring GeoMx NGS Readout |
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 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 for this request Submissions MUST be in a Phenix brand (catalog# MPS-3580) 96 well plate. User is required to combine the template, primer and water. SAMPLES CAN NOT BE ACCEPTED IN ANY OTHER PLATE |
Inquire | |
► VIGR Retired Services (10) | |||
Name | Description | Price | |
Bioanalyzer Quality Assessment DNA 1000 (1-12 samples/chip) |
NOT for NGS libraries. Please select DNA High Sensitivity instead Dilute sample to between 0.2-40 ng/ul based on Qubit Do not drop off sample stocks |
Inquire | |
Bioanalyzer Quality Assessment with Quantification RNA Pico - Laser Capture Microdisected Samples Only (1-12 samples/chip) |
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. Minimum 2uL required Trizol or Tri-reagent warning: Keep in mind that RNA extracted by this method will not be eligible for downstream processing by the core due to interferance caused by phenol. It is not possible to clean the sample of phenol once extracted Do not drop off sample stocks |
VCIID
$55.25
each
UVM Internal $65.00 each Vt State Institutions $68.25 each External $87.75 each Non-UVM $71.66 each Corporate $109.20 each |
|
Bioanalyzer Quality Assessment Small Non-Coding RNA (1-11 samples/chip) |
Dilute sample to between 1.5-90.0 ng/ul based on Qubit Minimum 2uL required Trizol or Tri-reagent warning: Keep in mind that RNA extracted by this method will not be eligible for downstream processing by the core due to interferance caused by phenol. It is not possible to clean the sample of phenol once extracted Do not drop off sample stocks |
Inquire | |
Exome/Target Capture/Ampliseq |
By Quote only. |
Inquire | |
G4 F2 Flow Cell, 200 Cycle |
150 Million - 250 Million Reads Ouput Read length up to Paired End 100 or Single End 150 |
Inquire | |
G4 F3 Flow Cell, 200 Cycle |
300 Million - 450 Million Reads Ouput Read length up to Paired End 100 or Single End 150 |
Inquire | |
NGS Library Quantitation qPCR (KAPA) | Inquire | ||
Sequencer Run Only-user supplied reagents and libraries (Nanopore excluded) |
Assembly of User generated sequencing libraries. Included is Qubit, HT1 hyb prep, Agilent BA2100, PhiX spike in. Data Transfer. User supplied flow cell and SBS reagents. Sequencing run is NOT guaranteed, reagent performance is not guaranteed. No data support. Prior arrangement is required. TAT determined on case by case basis. (Oxford Nanopore excluded) |
UVM Internal
$171.30
each
Vt State Institutions $179.87 each Non-UVM $188.86 each Corporate $287.78 each |
|
Small RNA Library Prep |
Absolutely no Trizol, Tri-reagent, or Phenol-based RNA accepted |
Inquire | |
[Gene Expression] - PCR Arrays |
Trizol-TriReagent RNA is not accepted by the core. No exceptions. Trizol or Tri-reagent warning: Keep in mind that RNA extracted by this method will not be eligible for downstream processing by the core due to interferance caused by phenol. It is not possible to clean the sample of phenol once extracted |
Inquire |