Vermont Integrative Genomics Resource - VIGR

***NOTICE***

Lab Technician Wanted for the Genomics Core Effective  5/23/2022. Please contact Julie Dragon at Julie.dragon@uvm.edu

 

 

Overview of Services

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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:

Core 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).

Getting Started

  • Login to your iLab account with your approved iLab credentials in the top right corner.
  • Don't have an iLab account? Sign up for one here!

 

Operational Policies

  1. Sample Submission, Storage and Retrieval Policy
  2. Procedure for Qualifying a Grant for the UVMCC subsidy in the DNA Analysis Facility
  3. Policies for accessing Bioinformatics Services

 

 

Location and hours of operation

 Hours

Location

8:30am - 5 pm Mon-Fri.

303 HSRF 

 

Core Contacts:

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

 

7/29/20 Update: Core Access

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 

https://www.uvm.edu/sites/default/files/UVM-CATcard-Service-Center/Undergraduate_Access_Request_Form.pdf

 

5/29/20 Update and Webinar series recordings:

 
Hi folks! VIGR will open June 1. Please honor the new protocols posted on the services page, and on the lab doors.
 
We are continuing the mini-webinars which you can view here:
 
Webinar 6 Digital Droplet PCR: advantages and applications
Webinar 5 Oxford Nanopore Technologies with the GridION MK5: Long Read Sequencing Analysis
Webinar 4 Oxford Nanopore Technologies with the GridION MK5: Long Read Sequencing Applications
Password: 2y+SsI4.
 
Webinar 3 Analysis of Single Cell Data: Assays, Methods, and Requirements with VIGR: https://uvmcom.zoom.us/rec/share/5tN2ArzXzFJJUtb99xqAYq4cOobPT6a80yQfqfZYyx49wE9irZdzpcw_HQyc0DMw
Password: 3K&8*kt&
 
Webinar 2 10x Genomics Chromium Single Cell Sequencing with VIGR: 
[zoom link is coming soon]
 
 
Webinar 1 Nextgen Sequencing with VIGR: Nextgen Sequencing with VIGR
Password: w5=%9&%#
 
 

 

 

  

Location and hours of operation

 Hours

Location

7:30am - 5 pm Mon-Fri.

303 HSRF 

 

Core Contacts:

Dr. Julie Dragon
Director
Director / Bioinformatics 
802-656-7777 
julie.dragon@uvm.edu 

Scott Tighe
Technical Director
scott.tighe@uvm.edu

Dan Vellone
Research Technician
Daniel.vellone@uvm.edu
8026562482
HSRF 303
 
Dr. Kirsten Tracy 
Senior Scientist
kirsten.tracy@med.uvm.edu
 
Kris Finstad
Kristiaan.Finstad@med.uvm.edu
Senior Technician
 

Dr. Ramiro Barrantes
Statistics / Computational Biology
ramiro.barrantes@uvm.edu
Given Courtyard S356

F



Contacts

Name Role Phone Email 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


Search available services: View: by category alphabetically
Bioinformatics Shared Resource (19)
Droplet Digital PCR or RTqPCR (1)
General Genomic Services (15)
Microarray (12)
Nanopore Sequencing (1)
Next Gen Sequencing (13)
Sanger Sequencing (2)