Affymetrix GeneChips

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

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... 

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)... 

High background Affymetrix GeneChip microRNA array... 

Alternative microarray approaches are available that involve the 3 tailing of the miRNA molecule with poly(A), followed by labeling and hybridization. The NCode miRNA microarray platform (Life Technologies) involves the addition of the poly(A) tail to the miRNA prior to ligation of fluorescent dye molecules and subsequent hybridization to the antisense miRNA probes on the microarray chip. In the case of Affymetrix GeneChip microRNA arrays, the poly(A)-tailed miRNAs are labeled with a biotinylated signal molecule. A limitation of hybridization-based microarrays is that because of the small size of miRNAs, the Tm of the probes has a wide range that may diminish specificity and/or sensitivity for miRNAs with a low GC content (10,56). 

Fig. 2. Computer image of an Affymetrix GeneChip after sample hybridisation...

Boes T, Neuhauser M (2005) Normalization for Affymetrix GeneChips. Methods Inf Med 44 414-417. 

AML profiler Skyline Diagnostics (the Netherlands) Determination of AML subtype Affymetrix GeneChip CE 2011, FDA (premarket approval) Fresh bone marrow... 

Genotyping arrays AmpliChip CYP450 Roche Scientific Drug metabolism Affymetrix GeneChip FDA 2004 Blood... 

The transcriptome is defined as the whole set of transcripts present in a cell in a given developmental stage and under a specific physiological condition. As we have been describing, the transcriptome is composed by mRNAs, rRNAs, tRNAs, and a set of ncRNAs (22,102). Over the past decade, the transcriptome has been analyzed by hybridization-based approaches (microarrays). Typically, the RNA is previously converted into cDNA, fluorescently labeled, and hybridized onto a specific microarray (such as Affymetrix GeneChips). They have been widely used over the past 15 years and have given quite precise information about the way the transcriptome is regulated... 

Affymetrix 418 Array Scanner Laser scanning microscope with two excitation filters can read Affymetrix GeneChips with a sensitivity of less than 1 fluor/pm. www.affymetrix.com... 

As noted in the manufacturer s protocol, correct laboratory set-up has been shown to be critical in the success of the Affymetrix GeneChip Mapping Assay. It is recommended that a single direction of workflow be employed to reduce the risk of contamination, particularly with PCR products. There are three principle areas that should be prepared before commencing the assay. 

Fig. 5.23. The Affymetrix GeneChip consisting of more than 400,000 featnres, with each feature containing miUions of copies of the same oligonucleotide (photo courtesy of...

The patented Affymetrix GeneChip is a very powerful and reliable platform, allowing massively parallel analysis. However, this comes at a cost, that is frequently beyond the budget of most academic research laboratories. Home-made arrays have a much lower density of spots and also tend to be less reliable when compared to the stringent controls applied by Affymetrix. They are, however, much cheaper and can be designed specifically for each particular application. As competing companies try to fill the gap for more affordable array platforms, prices will fall and DNA arrays will find increasing use both in academic and in industrial laboratories. 

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