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Cyanine dyes are the most commonly used dyes for microarray analysis. They can be used to label total RNA, amplified cRNA, and genomic DNA for gene expression, miRNA, CGH, chIP-on-chip, and methylation array applications.

Alexa dyes are used to label amino-allyl groups incorporated into ss-cDNA's prepared for gene expression arrays. Since there is no amplification for this labeling method it requires a greater amount of starting material--we recommend at least 10ug. We use this method primarily for labeling prokaryotic samples."