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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.
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Vermont Integrative Genomics Resource
University of Vermont
Firestone Medical Research Building, Room 150
149 Beaumont Ave., Burlington
Vermont 05405
[T] 001-802-656-2557
The Vermont Integrative Genomics Resource (VIGR) runs the following instrumentation:
Singular G4 [short read, PE, high-volume]]
Illumina MiSeq [short read, mid-volume], MiniSeq [small volume]
Oxford Nanopore PromethION P2 Solo [long reads, high volume], GridION [mid-volume], MinION and MK1C [small volume]
10X Chromium Single cell controller [Single Cell GENOMICS]
BioRad QX200 ddPCR [DIGITAL DROPLET PCR]
ABI QuantStudio 6 Flex [RTqPCR] and 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).
Check out this CBSR instructional and navigation-based video of how to work with the cores using iLab, https://youtu.be/YlKR2pny8Lc
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. |
150 FMRB |
| Name | Role | Phone | Location | |
|---|---|---|---|---|
| Dr. Julie Dragon |
Director
|
802-656-7777
|
julie.dragon@uvm.edu
|
149 Beaumont Ave, FMRB 162, Burlington Vermont 05405
|
| Scott Tighe |
Technical Director
|
802-656-2557
|
scott.tighe@uvm.edu
|
FMRB 156
|
| Dr. Kirsten Tracy |
Senior Scientist
|
802-656-2557
|
kirsten.tracy@med.uvm.edu
|
FMRB 150
|
| Dr. Ramiro Barrantes |
Statistics/ Computational Biology
|
ramiro.barrantes@uvm.edu
|
FMRB 150
|
|
| Stacia Richard |
Lab Research Technician
|
802-656-2557
|
stacia.richard@uvm.edu
|
FMRB 150
|
| 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 | ||
| Epigenomics | 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 interference 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 interference caused by phenol. It is not possible to clean the sample of phenol once extracted Do not drop off sample stocks |
UVM Internal
$73.22
each
Non-UVM $76.88 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 interference caused by phenol. It is not possible to clean the sample of phenol once extracted. Please put your samples in the designated tube racks 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 the time of pickup. Store flat at 4-8C. |
||
| ► Next Gen Sequencing (8) | |||
| Name | Description | Price | |
| 16s microbiome library |
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
$40.95
each
Non-UVM $43.00 each Corporate $65.52 each |
|
| DNASeq-ChIPSeq library prep (1-10 samples) |
DNA Library Preparation-Revvity - ChIPSeq (1-10 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 Output Read length up to Paired End 50 or Single End 100 |
Inquire | |
| G4 F2 Flow Cell, 300 Cycle |
150 Million - 250 Million Reads Output Read length up to Paired End 150 |
Inquire | |
| G4 F3 Flow Cell, 100 Cycle |
300 Million - 450 Million Reads Output Read length up to Paired End 50 or Single End 100 |
Inquire | |
| G4 F3 Flow Cell, 300 Cycle |
300 Million - 450 Million Reads Output Read length up to Paired End 150 |
Inquire | |
| G4 F3 Flow Cell, 50 Cycle |
300 Million - 450 Million Reads Output Read length up to Paired End 25 or Single End 50 Appropriate for NanoString GeoMx NGS Readout |
Inquire | |
| ► Sanger Sequencing (2) | |||
| Name | Description | Price | |
| Bulk Sanger Sequencing - 16+ Samples |
Primer Extension Reaction and Sequencing on SeqStudio (16 Samples or More)
|
Inquire | |
| Sanger Sequencing - 1-15 Samples |
Primer Extension Reaction and Sequencing on SeqStudio (15 Samples or Less)
|
Inquire | |
| ► Training (1) | |||
| Name | Description | Price | |
| Training |
Training for equipment and services |
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 |
||
| 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) |
||
| 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 | |
