Affymetrix

The microarray consists of small DNA fragments, chemically synthesized at specific locations on a coated quartz surface. The number of locations on one array is in the range of millions. DNA is extracted and labeled from experimental samples, and then samples are hybridized on the array. Labels are monitored so that gene- and exon-level expression analysis, novel transcript discovery, genotyping, and resequencing can be carried out. 

The number of sites in the array can be used for combinatorial purposes. Combinatorial experiments can be oriented to a diversity of applications, genomics, proteomics, and biochemical, in general. Molecular inversion and SNP Genotyping are well-proven uses of the technology. 

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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). 

Gene Expression Analysis. Figure 1 Schematic representation of the experimental process of global gene expression analysis using Affymetrix GeneChip arrays. 

Estradiol Medroxyprogesterone acetate Human microvascular endometrial endothelial cells Affymetrix U133A E2 10- M, MDA lO- Mfor 48 h Gene name, fold change 117... 

IVP-Estradiol Human endometrium Affymetrix U133A 17P-Estradiol InM Gene name. Gene symbol. Accession number, fold change in table 119... 

DNA Chips (Affymetrix) High number of SNPs analyzed, but low number of samples High setup cost Low Low Very low... 

The data obtained has been derived from different experimental designs (namely, the number of collected fractions and the hybridization scheme), different microarray platforms (spotted versus Affymetrix arrays), and different data analysis schemes. In this chapter, we discuss various experimental designs for microarray analyses, provide detailed protocols for various experimental steps when using the spotted microarray platform, and discuss aspects of data analysis. 

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. 

Oligonucleotide arrays [6] In-situ on the surface of the matrix 1 cm by 1 cm slide with approximately 40 000 genes Affymetrix s GeneChip can contain up to 400 000 different oligonucleotides and is the densest array Fluorescent tag labeling fluorophore detector is added after hybridization Passive Affymetrix... 

Photolithography Highest Highest as expensive equipments and particular expertise are required Limited to 25-mers or less Photolithography method is protected by patent and currently only Affymetrix has the rights to use this method... 

Some of the gene expression profiling analysis biochips on the market include Affymetrix s standardized GeneChip for a variety of human and yeast genes and HyX Gene Discovery Modules for genes from tissues of the cardiovascular and from tissues that are germ infected. 

The study of osteoclast differentiation is important for understanding potential new treatments for osteoporosis. Such therapies are typically explored in tissue culture models such as the Raw264 mouse monocytic cell line, which is capable of differentiation into functional multinuclear osteoclasts after treatment with the cytokine Rankl. Use of transformed cell lines raises the concern that results may not be extrapolated to normal tissue. To address this question, the transcriptional responses for Rankl treatment of the Raw264 cell line, and of two ex vivo primary cell systems (bone marrow macrophages, and hematopoetic stem cells) were compared using Affymetrix GeneChips [23]. The models proved to... 

Cheadle C, Cho-Chung YS, Becker KG, Vawter MR 2003. Application of z-score transformation to Affymetrix data. Appl Bioinformatics 2 209. 

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