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MICROARRAY HARDWARE AND SOFTWARE

 

Affymetrix GeneChip system

The GeneChip probe arrays offer high volume and performance by providing high quality probe sequences using factory-manufactured Affymetrix probe array technology. The profiling service allows users to operate Affymetrix GeneChip DNA array equipment, including the Affymetrix hybridization oven, Affymetrix fluidics station, Agilent GeneArray scanner and accessories such as a microcentrifuge and heat block.

 

Microarray Data Mining

Microarray data processing begins with first-tier computations including image acquisition, scaling, normalization, and visualization. Processing proceeds to second-tier computations involving statistical analysis, clustering, and pathway and gene identification. The Microarray Core provides software only for the first-tier analysis because this is intrinsic to the core operating system as purchased. First-tier software includes the Affymetrix Microarray Suite 5.0 (MAS). GeneChip Data Ming Tool and GenePix Pro 3.0, and requires the Core's help with converting and transferring the original microarray data into PC-executable files, such as TIF, Excel, and text files. These services are designed to allow users to perform their downstream data analysis.

 

Equipment and Software

The facility has the following array systems and equipment:

1. Affymetrix GeneChip System (www.affymetrix.com): contains Affymetrix Hybridization Oven 640, Affymetrix Fluidics Station 400, Agilent GeneArray Scanner, Affymetrix computer workstation, Affymetrix Microarray Suite Software 5.0, Affymetrix MicroDB Software, Affymetrix Data Mining Tool Software (DMT) and EASI Expression Analysis Sequence Information Database.

2. A Custom Array System, arrayer: MicroGrid II TAS, Genepix 4000 B Axon Scanner with GenePix Pro 3.0, Biomek FX liquid handling robot, ASP Hybridization System.

Affymetrix GeneChip Expression Analysis Technical Guide

To download a Technical Guide, please visit http://www.affymetrix.com/support/.

 

FEES & HOURS

 

FEES

All users must provide an account to be charged before using the facility. Billing will be generated at the end of each month and processed through the Department of Cell Biology. Users are responsible for properly maintaining the equipment. Damage or problems must be reported promptly to the facility staff.

Full service (chip hybridization, washing, staining and scanning) - $60/chip
Analysis - $40/chip

For more detailed information on fees, please contact facility staff.

 

HOURS

The facility is open Monday-Friday 9 AM-5 PM except on College-designated holidays, and after hours at the discretion of the staff. Scheduling is done by sign-up sheet in 3-day blocks of time. Cancellations must be made at least 1 day in advance.

 

CONTACT

For scientific and technical questions, contact:

Dr. Xian-Cheng Jiang
Department of Cell Biology
Phone: (718)-270-6701 (Office), (718)-270-6720 (lab)
Email: xjiang@downstate.edu

Weimin Liu
Department of Cell Biology
Room BSB 3-116
Phone: (718) 270-1242
Email: wliu@dowstate.edu

For scheduling and billing, contact:

Weimin Liu
Department of Cell Biology
Room BSB 3-116
Phone: (718) 270-1242
Email: wliu@dowstate.edu