Title: Pyrosequencing & Capillary Gel Electrophoresis
Date: Thursday, April 19th, 2012
Time: 12 p.m. - 1 p.m.
Location: Pharmacology Seminar Room, BST Level 8 Room 180
Speaker: Zeeshan Farooq, Specialist, Automated Solutions, QIAGEN
URL: Pyrosequencing & Capillary Gel Electrophoresis
Genomics Core Facility:
|a.||Director - Dr. Dimitri Gnatenko|
| Phone: 631-444-1264|
|b.||Introduction (see details below)|
|1.||Affymetrix Core Facility|
|2.||DNA Sequencing Facility|
|4.||Array-based Comparative Genomic Hybridization (aCGH) service for genome-wide copy number analysis (see details below)|
|6.||Luminex bead assays on the Bio-Plex200|
|7.||QIAxcel System (Formerly known as eGene) automated electrophoresis for standard (unlabeled) DNA|
Introduction to Genomics Core Facility
The facility aims to provide scientists at Stony Brook with the tools required to maximize their research. In the longer term, it is hoped that this facility will pave the way for Stony Brook to become a center of excellence in translational medicine, with particular emphasis on human genetics.
The following represent new methods/tools which are now available in our facility. Fees are being worked out and will be available shortly. We have an open door policy in our facility and welcome both customers for our services and collaborations. We are always interested in new projects!
Due to high demanding for some instruments or staff availability, users wishing to use BioPlex-200 System, Pyrosequencing, QIAxcel (formerly eGene), qPCR are required to make reservations. Please click here to make your reservation.
We use a whole human genome tiling path BAC array for copy number analysis. This array has an effective resolution of 150kb and spans 93% of the human euchromatic genome. In addition to the basic tools/reagents, we have sophisticated bioinformatics tools at our disposal, as well as a large database of copy number variation in normals (currently over 800 individuals). We also offer genome wide copy number analysis using any of the major platforms, including NimbleGen and Agilent oligonucleotide based microarrays.
|Fine tiling NimbleGen oligonucleotide array used to map chromosome 3 breakpoints with enough resolution to generate junction fragments by PCR (Jasmin Roohi, Cristina Montagna, David H. Tegay, Lance E. Palmer, John C. Pomeroy, Susan L. Christian, Norma Nowak and Eli Hatchwell. Disruption of Contactin 4 in 3 Subjects with Autism Spectrum Disorder. Journal of Medical Genetics (Rapid online publication - March 18th 2008).|
QIAxcel System (Formerly known as eGene)
For gel electrophoresis of large numbers of standard DNA samples (e.g., PCR products), impractical using agarose gels, we offer capillary based electrophoresis on the QIAxcel System (formerly eGene system - Qiagen recently acquired eGene). This is a fully automated system for the identification, quantification and sizing of unmodified dsDNA. The system is able to run a 96 well plate in approximately 1.5 hours ( a further 30 minutes is required for analysis).
We accept a minimum of one plate for a run.
See: http://www1.qiagen.com/news/QIAxcel.aspx for further details.
We offer the Bio-Plex 200 system for running assays based on Luminex bead technology, including the complete range of kits available from Millipore, Bio-Rad, Marligen, Panomics and many \others, whether protein or nucleic acid based. Researchers should consult with the facility prior to purchasing a plate. Please enquire for further details.
See: Bio-Rad Bio-Plex page for further details.
Pyrosequencing (PyroMark MD machine)
Pyrosequencing is a highly quantitative sequencing method used in a variety of applications, including analysis of the methylome, detection of rare variants and population analysis.
For more information on Pyrosequencing, please visit http://www.pyrosequencing.com/
We are available to aid in the design of assays and advise on the best tools/methods to use to answer any specific scientific question(s). We strongly advise users to discuss their project goals prior to embarking on the use of any given platform.