scholarly journals Qualitative assessment of gene expression in affymetrix genechip arrays

2007 ◽  
Vol 373 ◽  
pp. 486-496 ◽  
Author(s):  
Radhakrishnan Nagarajan ◽  
Meenakshi Upreti
Keyword(s):  
Gene Expression ◽  
Affymetrix Genechip ◽  
Qualitative Assessment

Custom microarray for glycobiologists: considerations for glycosyltransferase gene expression profiling

2002 ◽  
Vol 69 ◽  
pp. 135-142 ◽  
Author(s):  
Elena M. Comelli ◽  
Margarida Amado ◽  
Steven R. Head ◽  
James C. Paulson
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Affymetrix Genechip ◽  
Microarray Technology ◽  
Gene Arrays ◽  
Glycosyltransferase Gene

The development of microarray technology offers the unprecedented possibility of studying the expression of thousands of genes in one experiment. Its exploitation in the glycobiology field will eventually allow the parallel investigation of the expression of many glycosyltransferases, which will ultimately lead to an understanding of the regulation of glycoconjugate synthesis. While numerous gene arrays are available on the market, e.g. the Affymetrix GeneChip® arrays, glycosyltransferases are not adequately represented, which makes comprehensive surveys of their gene expression difficult. This chapter describes the main issues related to the establishment of a custom glycogenes array.

Abstract 2654: Differential Local versus Systemic Gene Expression Profiling in Acute Coronary Syndromes

Circulation ◽  
2008 ◽  
Vol 118 (suppl_18) ◽  
Author(s):  
Alexander Akhmedov ◽  
Keiko Yonekawa ◽  
Christophe Wyss ◽  
Roberto Corti ◽  
Nils Kucher ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Human Genome ◽  
Expression Profiling ◽  
Acute Coronary Syndromes ◽  
Coronary Occlusion ◽  
Plaque Rupture ◽  
Affymetrix Genechip ◽  
Fluorescent Intensity ◽  
Coronary Syndromes

Introduction: Monocytes and leucocytes (WBC) play a key role in acute coronary syndromes (ACS). We hypothesized that gene expression profiling of WBC from the site of coronary occlusion in direct comparison with peripheral WBC from patients with ACS might reveal genetic patterns involved in plaque rupture. Methods: Thrombi (Thr) were aspirated during primary percutaneous coronary intervention (PCI), snap-frozen, and stored at −80°C. Peripheral blood leukocytes (PBL) from the same patients were extracted and treated accordingly. Total RNA was isolated from thrombi and PBL. The quality and quantity of the isolated RNA was determined using bioanalyzer and nanodrop devices. The cDNA was prepared using a primer mix and reverse transcriptase, followed by fragmentation and biotinilation. Biotin-labeled single-stranded cDNA samples were hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays. An Affymetrix GeneChip Scanner was used to measure the fluorescent intensity emitted by the labelled target. Results: Gene expression profiles of Thr and PBL from 4 patients during PCI were assessed by Affymetrix human genome U133 Plus 2.0 arrays (54′675 probe sets). 653 different genes were locally upregulated in Thr compared to PBL as defined by a more than 8-fold difference in expression and statistical significance (p≤0.01). Genes for proteins of inflammation, thrombosis, endothelial activation, extracellular matrix remodelling, and scavenger receptors were highly upregulated at the site of coronary occlusion (examples see table 1 ). Conclusion: The local gene expression profile in WBC from thrombi differs significantly from the pattern in PBL, reflecting the regulatory and effective role of these cells in plaque rupture and thrombosis. This study identifies the upregulation of genes encoding for a host of established and new pathways involved in inflammation, uptake of oxidized LDL, and coagulation, that might play a crucial role in ACS. Table 1

Transient expression assay for qualitative assessment of gene expression by fowlpox virus

Virus Genes ◽  
1990 ◽  
Vol 3 (3) ◽  
pp. 213-220 ◽  
Author(s):  
Shree Dhawale ◽  
Christopher E. Beisel ◽  
Keyvan Nazerian
Keyword(s):  
Gene Expression ◽  
Transient Expression ◽  
Qualitative Assessment ◽  
Transient Expression Assay ◽  
Fowlpox Virus

The Affymetrix GeneChip® Microarray Platform

2009 ◽  
pp. 251-261 ◽  
Author(s):  
Djork-Arné Clevert ◽  
Axel Rasche
Keyword(s):  
Gene Expression ◽  
Biomedical Research ◽  
New Technology ◽  
Perfect Match ◽  
Microarray Platform ◽  
Affymetrix Genechip ◽  
Background Correction ◽  
Its Analysis ◽  
Basic Understanding

Readers shall find a quick introduction with recommendations into the preprocessing of Affymetrix GeneChip® microarrays. In the rapidly growing field of microarrays, gene expression, especially the Affymetrix GeneChip arrays, is an established technology present on the market for over ten years. Used in biomedical research, the mass of information demands statistics for its analysis. Here we present the particular design of GeneChip arrays, where much research has already been invested and some validation resources for the comparison of the methods are available. For a basic understanding of the preprocessing, we emphasize the steps, namely: background correction, normalization, perfect match correction, summarization, and couple these with alternative probe-gene assignments. Combined with a recommendation of successful methods a first use of the new technology becomes possible.

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