The Labelling Reaction

The labelling reaction is described in detail in the GeneChip® Expression Analysis Technical Manual at http://www.affymetrix.com/support/technical/manual/expres-sion_ manual.affx. This section highlights aspects that affect data analysis.

Labelling starts at the polyadenylation site at the 3' end of the transcript. The quality of the RNA and the efficiency of the labelling reaction determine how far the labelling extends toward the 5' end of the transcript. For many genes, the polyadenyla-tion sites are some distance from the coding regions. In such genes a large part, or all, of the probeset is located in the 3' untranslated region (UTR) of the gene. The 3' bias affects array design and data analysis.

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