Microarrays affymetrix expression

The commercial success of the spotted microarray, like that of Affymetrix s GeneChip, is content-driven. In order to provide customers with comprehensive gene expression microarray products, manufacturers must obtain gene-specific annotated sequences covering genomes of major interest to the scienhfic community (e.g., genomes of humans, yeasts, and mice). 

Woo Y et al (2004) A comparison of cDNA, oligonucleotide, and Affymetrix GeneChip gene expression microarray platforms. J Biomol Tech 15 276-284. doi 15/4/276 (pii)... 

Vardhanabhuti S et al (2006) A comparison of statistical tests for detecting differential expression using Affymetrix oligonucleotide microarrays. OMICS 10 555-566. doi 10.1089/omi.2006.10.555... 

In this chapter, we describe a method for analyzing S. aureus gene expression during interaction with human PMNs using Affymetrix oligonucleotide microarrays. Except for human PMNs, the methods described herein utilize commercially available reagents and can be reproduced by most standard laboratories. 

There are many protocols and different types of platforms available, e.g. GeneChips from Affymetrix, Illumina Bead Arrays, Arrays from Agilent, Applied Biosystems, GE Healthcare, customized spotted cDNA microarrays etc. the basic procedure for a large-scale measurement of gene expression involves the preparation of total or mRNA from the biological sample(s) under investigation (e.g. candidate tissue) and the hybridization of copied labelled RNA or cDNA to the DNA elements on the array surface (Fig. 1). 

Linton KM, Hey Y, Saunders E, et al. Acquisition of biologically relevant gene expression data by Affymetrix microarray analysis of archival formalin-fixed paraffin-embedded tumours. Br. J. Cancer 2008 98 1398-1402. 

Figure 2.8 Microarray cross-platform showing differentially expressed gene clusters obtained from Amersham, Agilent, and Affymetrix products. (From Barczak, A., etal., Genome Res., 13, 1775-1785, 2003 [Copyright 2003 Cold Spring Harbor Laboratory Press] and Tan, P.K. etal.. Nucleic Acid Res., 31(19), 5676-5684, 2003. With permission.)...

Another important point was made by this study if possible, use reference samples with gene expression levels similar to those expected for the test samples. This should improve quantification at the low end. Moreover, the Tan et al., (2003) and Barczak (2003) studies also demonstrate the need for the standardization of commercial microarray products and reference standards so that both interlaboratory and cross-platform performances can be properly assessed. While commercial microarrays from different vendors all claim substantial gene probe "real estate," the number of probes in common is smaller. This makes it difficult to compare experiments across platforms, especially those from major suppliers such as Affymetrix, Agilent, and Amersham (Figure 2.8). 

FIGURE 23.1 Schematic representation of genome-scale gene expression analysis with DNA microarrays, (a) DNA microarrays produced by probe deposition (b) Oligonucleotide microarrays produced by in situ probe synthesis (Affymetrix technology). 

Figure 1. A diagram of a microarray experiment. The mRNA in a cell is fluorescently labeled and hybridized to the microarray. After the hybridization, the intensity of each probe is captured into an image that is then processed to produce a proxy of the expression level of each gene in the target. In this figure, five microarrays were used to measure the molecular profiles of three healthy cells (Samples 1-3) and two tumor cells (Samples 4 and 5). (Image courtesy of Affymetrix.)...

Figure 2. Distribution of gene expression data from 50 prostatectomy samples measured with the U95Av2 Affymetrix microarray (a) histogram of the expression level of the HSYUBG1 Homo sapiens ubiquitin gene (b) histogram of the same gene expression level after the log-transformation was used.

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