Affymetrix, oligonucleotide arrays

Gerritsen, M.E. et al, Branching out a molecular fingerprint of endothehal differentiation into tube-like structures generated by affymetrix oligonucleotide arrays. Microcirculation, 2003, 10 63-81. 

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... 

Different microarray technological platforms produce data in different formats [19] each have platform-specific errors, which must be processed in slightly different manners. It is beyond the scope of this review to explain these in detail, but we briefly describe the processing of the most commonly used microarray platforms two-channel microarrays and commercial Affymetrix single-channel oligonucleotide arrays. 

For hybridization to Affymetrix oligonucleotide-based microarrays the biotin-labeled cRNA must be first fragmented. Fragmentation shears the cRNA molecules to a size of approximately 100 bases. The smaller size is necessary to facilitate efficient and faithful binding to the complementary oUgonncleotide on the microarray. The protocol described here is for snfficient cRNA to hybridize to one array (15 pg) (see Notes 30 and 32)... 

Mullan etal. (2001) used an oligonucleotide GUO array (Affymetrix) comprising 6800 genes and ESTs to examine expression profiling in BRCAl-induced cell lines in an effort to identify downstream targets. The GUO array contained approximately 1700 cancer-associated genes. 

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