GeneChips

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. 

Nau ME et al. Technical assessment of the Aflymetrix yeast expression genechip YE6100 platform in a heterologous model of genes that confer resistance to anti-malarial drugs in yeast. J Clin Microbiol 2000 38 1901-1908. 

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... 

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. 

ISHII, M., HASHIMOTO, S.I., TSUTSUMI, S., WADA, Y., MATSUSHIMA, K., KODAMA, T., ABURATANI, H., Direct comparison of genechip and SAGE on the quantitative accuracy in transcript profiling analysis, Genome., 2000, 2, 136-143. 

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... 

Affinity driven molecular transfer (ADMT) system, 78 264-265 Affinity ligands, 6 390 types of, 6 393-394, 396t Affinity method, 10 339 Affinity resins, 20 197 Affinity-selected libraries, 72 515-517 Affymatrix GeneChip HFV PRT, 76 390 Aflatoxins, 72 84... 

Figure 2.3 Affymetrix s GeneChip. (Photo courtesy of Affymetrix, Inc., Santa Clara, CA.)...

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). 

The proteomics field is currently wide open. Only a few protein microarray products have been commercialized. Unlike DNA microarrays that are commonly constructed on essentially two platforms (GeneChip or slide array) employing oligonucleotides or cDNA probes, the protein microarray appears on a variety of platforms and with different types of probes. 

The Affymetrix U95A GeneChip containing 12,500 known human genes was used for this purpose. Two adjacent breast tumors from an 87-year old woman were removed and used in the study along with an additional five breast tumors obtained from different individuals. Thus, seemingly related tumors from one individual could be compared with tumors from different sources to validate the microarray-based prognosis. In addition to validation of the microarray for this purpose, the researchers examined a number of... 

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