Affymetrix GeneChip Instrument System

Affymetrix GeneChip Instrument System  

GeneChip Scanner
GeneChip Hybridization Oven 640
FS450 fluidics stations 


 Genomics Core Facility AS8-1030

When submitting samples for the first time:

Consult with Core staff to discuss experimental design. Please contact or  to arrange a meeting.

All RNA submitted for GeneChip experiments will be assessed for quality using the Agilent Bioanalyzer 2100 and RNA6000 Nanochip, unless a gel image or bioanalyzer trace is submitted with samples.

GeneChip Experiment Options

Whole Transcript GeneChip Arrays  are available from Affymetrix for Human, Mouse, and Rat as well as other model organisms such C. elegans, Drosophila and Zebrafish. The Core uses Affymetrix WT PLUS Reagent Kit for all target preps, except for legacy experiments.

 3’ IVT Expression Arrays are available for legacy experiments as well as for those organisms which are not covered by WT arrays.  GeneChip 3’IVT PLUS Reagent Kit from Affymetrix is used, unless legacy experiments require use of  Ambion WT Expression Kit.

MicroRNA Arrays v4.0 provides 100% mirBase v20 coverage, including 30,424 mature miRNA probe sets from 203 organisms.  Flashtag Biotin HSR RNA Labeling Kits are used to prepare target samples for hybridization to Affymetrix miRNA

                                        Link to Affymetrix Website

Purchase of Arrays

UMass Medical School researchers enjoy a significant discount on Affymetrix GeneChips and reagents. Contact the Genomics Core for a current price list of products. Chips can be purchased directly from Affymetrix online at or by phone (1-888-DNA-CHIP). Discounted prices should appear automatically. For more information, contact our Affymetrix Account Manager,

Access to Data

After scanning and review, pivot files are generated using Expression Console from Affymetrix. Cel files and pivot files will then be transferred by staff into the appropriate lab folder on the Genomics Core R drive: R:\DATA. For security purposes, permission to view generated files is granted only to those authorized by the users.  External researchers will receive data via Dropbox or on a disk.

Data Analysis

For those who plan to do the analysis themselves, data analysis programs are available for use by any UMass researchers:

Genespring GX from Agilent provides powerful statistical tools for data analysis and visualization. This is available on the Genomics Core Workstation in AS8-1030, and can be accessed using your UMass log-on credentials.

Transcriptome Analysis Software. This is available as a free download onto any 64 bit PC, as well as on the Genomics Core Workstation.

Software Downloads and Links

Visit Affymetrix Software Download Center to access:

  • EC (Expression Console) to view cel files, assess quality, and generate pivot files from expression arrays.
  • Transcriptome Analysis Console (TAC) Software from Affymetrix enables identification of differentially expressed genes and exons and visualization of alternative splicing events with an intuitive integrated solution. Using the normalized and summarized data from Expression Console Software, TAC provides for easy interpretation,  differential expression analysis and visualization.
  •  The NetAffx™ Analysis Center enables researchers to correlate their GeneChip® array results with array design and annotation information

Data Analysis Assistance

It is advisable to discuss your experiment design with the Genomics Core staff and your data analyst before beginning the experiment to determine whether you have sufficient controls, required replicates, etc.  These are the current UMass data analysts are available to assist with analysis.
Julie Zhu- PGFE members only

Yvonne Edwards- Molecular Medicine members only

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