Affymetrix GeneChip Instrument System

  • GeneChip Scanner 3000, with 7G upgrade
  • GeneChip Hybridization Oven 320
  • two FS450 fluidics stations


Link to Affymetrix Website



Before Submitting Samples

Consultation with Core staff is recommended before submitting samples for the first time. All RNA will be checked on a Bioanalyzer for quality assessment, unless a gel image or bioanalyzer trace is submitted with samples.

Eukaryotic Samples

The Genomics Core uses the Affymetrix 3’ IVT Express Kit to prepare target for hybridization to all classic 3’ arrays such as C. elegans, Drosophila 2.0, Mouse 430 2.0 and Yeast 2.0 Genome Arrays. 

Whole Transcript Arrays, such as the Gene 1.0 ST Arrays and Exon 1.0 ST Arrays are designed for use with Mouse, Rat and Human sense targets. The Core uses the Ambion WT Expression Kit and Affymetrix GeneChip WT Terminal Labeling Kit to prepare cDNA target for ST arrays. 

Tiling array target preparation is performed using the GeneChip WT Double-Stranded cDNA Synthesis Kit, the GeneChip Sample Cleanup Module and the GeneChip WT Double-Stranded DNA Terminal Labeling Kit. Tiling arrays are available for Human, Mouse, Arabadopsis, C. elegans, Drosophila and Yeast samples. 

Prokaryotic Samples 

Target cDNA for all prokaryotic arrays, including E. coli, P. aeruginosa and custom arrays, is prepared using a protocol developed by Affymetrix with recommended components from various vendors to generate sufficient single stranded cDNA for hybridization to the appropriate arrays. 

MicroRNA Samples

Genosphere Flashtag Biotin RNA Labeling Kit is used to prepare target samples for hybridization to Affymetrix miRNA Arrays which includes probe sets from 71 organisms including human, mouse, rat, monkey and rice. An miRNA QC analysis tool is available for free from Affymetrix. 

Quality Control

Before hybridization, all targets are assessed for yield and size distribution on an Agilent Bioanalyzer by Core staff. 

Purchase of Arrays

GeneChips should be purchased directly from Affymetrix by phone (1-888-DNA-CHIP) or online at Discounted prices are available to UMass researchers. 

Access to Data

Once the arrays have been scanned and the data quality reviewed, pivot files are generated using Expression Console from Affymetrix. Cel files and pivot files are then transferred into the appropriate lab folder on the Genomics Core R drive: \\edunivrdir02\genomicscore$\data. For security purposes, permission to view generated files is granted only to those authorized by the user. External researchers will receive data on a CD or DVD.

Data Analysis

Assistance with data analysis is available from a number of sources within the Medical School. It is advisable to discuss your experiment design with the data analyst before beginning the experiment to determine sufficient controls, required replicates, etc. 

Mei Xu in Academic Research Computing
Jeurg Straubhaar, DERC Bioinformaticist
Julie Zhu, PGFE Bioinformaticist (PGFE members only)

Software Downloads 

Visit Affymetrix Software Download Center to download AGCC (Affymetrix GeneChip Command Console) and EC (Expression Console) to view dat and cel files, assess quality, and generate pivot files from expression arrays. For differential expression analysis and visualization, the new Affymetrix® Transcriptome Analysis Console (TAC) Software takes the normalized and summarized data from Expression Console Software to the next level, providing for easy interpretation. Other tools available include Tiling Analysis Software, Sequence Analysis software, and NetAffx. The NetAffx™ Analysis Center enables researchers to correlate their GeneChip® array results with array design and annotation information.