Affymetrix Microarray

Affymetrix Microarray

MBCF offers gene expression profiling, SNP, miRNA, and CNV analysis using array technologies from Affymetrix. We specialize in processing RNA extracted from formalin-fixed parafin embedded tissue.


The core can process almost any of the arrays that are available from Affymetrix.

3′Arrays Whole Transcript Gene Arrays SNP Arrays
Human Genome U133+ 2.0 Human Transcriptome Array (HTA) 2.0 Human Cytoscan HD
Mouse 430 2.0 Human Gene ST 1.0 and 2.0 Human SNP 6.0
Human Primeview Mouse Gene ST 1.0 and 2.0 Mouse Diversity
Mouse Exon 1.0 ST  250K-NSP

Need help choosing an array? This picture might help.



Min. Amount Notes
3′ Arrays
Standard 30-100ng High Quality RNA
Low Input 5-50ng NuGen Ovation v2
Whole Gene Arrays
Standard 50-100ng High Quality RNA
Low Input 1-50ng Nugen Pico WTA
FFPE Whole Transcript
Low input 50-100ng NuGen FFPE WTA
Very low input >20ng AffymetrixSensation
SNP Arrays
750ng min. 10ul at 50ng/ul


Affymetrix Software

Relatively easy to use and free to download. This software is also available on computer workstations in the MBCF Advanced Technologies Core (Jimmy Fund Building).

Other Options

Bioconductor – An open source and open development software project for the analysis and comprehension of genomic data. R programming language.

Broad Institute GenePattern – genomic analysis platform


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DFCI External
 FFPE Whole Transcript NuGEN  Affy NuGEN  Affy
 Human Transcriptome Array v2.0 $530 $580 $765 $810
 Human Exon v1.0 ST $710 $760 $925 $975
 Human Gene ST (1.0 and 2.0) $495 $545 $645 $695


3′Array DFCI External
HG U133 Plus 2.0  $615  $800
Primeview  $355  $460
Mouse 430 2.0  $615  $800
Mouse 430A 2.0  $470  $615
Low Input (<100ng)  +$70  +$85
Whole Transcript Gene Arrays
 Human Transcriptome Array v2.0  $450 $625
 Mouse Exon v1.0 ST  $600  $780
 Human Gene ST (1.0 and 2.0)  $385  $505
 Mouse Gene ST (1.0 and 2.0)  $385  $505
Low Input (<100ng)  +$90  +$115


DNA Arrays  
Human CytoScan HD $620 $810
Genome-Wide Human SNP v6.0 $565 $735
Human Mapping 250K – NSP $360 $470
Mouse Diversity $565 $735