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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
Health Science Research Facility room 303
149 Beaumont Ave
Burlington Vermont 05405
[T] 001-802-656-2482
The Vermont Integrative Genomics Resource (VIGR) runs the following instrumentation:
Ilumina HiSeq 1500/2500 [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]
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]
ABI 3130XL [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 Outpu Bead Mill Homogenizer
Affymetrix Microarray System
Please use the following link to view our website: https://www.med.uvm.edu/uvmcancercenter/core-facilities/genome-technologies
Please note any required administrative paperwork by external facility users must be presented and handled prior to sample submission. 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).
|
Hours |
Location |
|
8:30am - 5 pm Mon-Fri. |
303 HSRF |
Dr. Julie Dragon
Director
Director / Bioinformatics
802-656-7777
julie.dragon@uvm.edu
Scott Tighe
Technical Director
scott.tighe@uvm.edu
303 HSRF
Dan Vellone
802-656-2482
Daniel.vellone@uvm.edu
303 HSRF
Dr. Ramiro Barrantes
Statistics / Computational Biology
ramiro.barrantes@uvm.edu
Given Courtyard S356
Please follow this link to the form you will need to get Request_For_Keys_Revised_Sept2020.pdf (uvm.edu) to the HSRF building and HSRF 303.
*Note* You will need to put the date of your VOSHA CoVid19 training on this form in the table and you will need your PeopleSoft (not Net) ID, and the signature of your department chair or college dean.
If you only need access to HSRF 303, digitally fill out the form and email to Julie.Dragon@med.uvm.edu
If you are requesting access to HSRF as well as access to HSRF 303, follow these steps:
1) Digitally complete the form
2) Obtain appropriate signatures from your department
3) Once signed off by your department, email the form to Julie Dragon (Julie.Dragon@med.uvm.edu), NOT directly to CatCard or the Lock Shop
Please send this form to Julie Dragon (julie.dragon@med.uvm.edu), NOT directly to CatCard or the Lock Shop.
To get Undergraduates card swipe access, follow the same procedure but use this form
|
Hours |
Location |
|
7:30am - 5 pm Mon-Fri. |
303 HSRF |
Dr. Julie Dragon
Director
Director / Bioinformatics
802-656-7777
julie.dragon@uvm.edu
Scott Tighe
Technical Director
scott.tighe@uvm.edu
Dr. Ramiro Barrantes
Statistics / Computational Biology
ramiro.barrantes@uvm.edu
Given Courtyard S356
F
| Name | Role | Phone | Location | |
|---|---|---|---|---|
| Dr. Julie Dragon |
Director
|
802-656-7777
|
julie.dragon@uvm.edu
|
95 Carrigan Dr., HSRF 306, Burlington Vermont 05405
|
| Scott Tighe |
Technical Director
|
802-656-2482
|
scott.tighe@uvm.edu
|
HSRF 303
|
| 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 (1) | |||
| Name | Description | Price | |
| [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 | |
| ► General Genomic Services (15) | |||
| Name | Description | Price | |
| DNA Quality Assessment-High Sensitivity (up to 11 samples/chip) |
Dilute sample to between 1.5-4.0 ng/ul based on Qubit 11 samples per run submit apx 2 uL in 0.5mL tubes Place in the DNA HS rack in the sample submission freezer turnaround is between 4 to 48hrs. Usually less than a day |
Inquire | |
| Applied Support | Inquire | ||
| DNA 1000 Quality Assessment (up to 12 Samples/chip) |
NOT for NGS libraries. Please select DNA High Sensitivity instead |
Inquire | |
| 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 |
Inquire | |
| RNA Pico Bioanalyzer Quality Assessment-without Quant |
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 |
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. 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
|
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) |
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 |
Inquire | |
| Total RNA Quality Assessment (1-12 samples) |
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 |
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 |
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 | |
| 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 |
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 | |
| 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 | |
| ► Nanopore Sequencing (1) | |||
| Name | Description | Price | |
| Oxford Nanopore Sequencing -High Output Nanopore Flow Cell 9.4 |
Oxford Nanopore Sequencing must be approval by facility staff prior to sample submission. General Q-Score average 10-14 on the MK1B R9.4D Porecell. Up to 18 gBases |
UVM Internal
$550.00
each
Vt State Institutions $555.00 each External $1,282.50 each |
|
| ► Next Gen Sequencing (13) | |||
| 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 Single End 150 bp (Cost Per Lane) |
Samples that are run on a Rapid Run Flow cell can be pushed to SR150, however, produce 10-20% less reads. |
UVM Internal
$1,800.16
each
Vt State Institutions $1,890.17 each External $2,593.76 each |
|
| HiSeq Sequencing by Synthesis-Paired End 2x85BP (Cost per Lane) |
Also used for 10X genomics RNASeq (Paired End 28 x 92) |
Inquire | |
| HiSeq Sequencing Paired End 2x80BP (Cost per Lane) |
Also used for 10X genomics RNASeq (Paired End 28 x 92) |
Inquire | |
| HiSeq Sequencing-by-Synthesis-150 bp Paired End (Onboard Clustering- 2 Lanes) |
Single Pool split between two lanes. Rapid Onboard clustering. Price for total of two lanes of sequencing |
UVM Internal
$4,466.40
each
|
|
| HiSeq Sequencing-by-Synthesis: 150bp Single End (Per Lane) |
UVM Internal
$1,800.16
each
Vt State Institutions $1,890.17 each External $2,362.50 each |
||
| HiSeq Sequencing-by-Synthesis: 50 / 75 bp Single End (Per Lane) | Inquire | ||
| NGS Library Quantitation qPCR (KAPA) | Inquire | ||
| NGS Library Quantitation qPCR and Qubit | 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 |
|
| Small RNA Library Prep |
Absolutely no Trizol, Tri-reagent, or Phenol-based RNA accepted |
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 | |
