During reverse transcription, an amine-modified nucleotide is enzymatically incorporated, followed by chemical coupling with fluorescent succinimidyl esters, a preferred method for labeling cDNA on DNA microarrays. The SuperScriptTM Plus Indirect cDNA Labeling System efficiently generates fluorescently labeled cDNA for gene expression studies on microarrays. It employs aminoallyl- and aminohexyl-modified nucleotides, along with other dNTPs, in a cDNA synthesis reaction using SuperScriptTM III Reverse Transcriptase. After removing unincorporated nucleotides, the amino-modified cDNA is coupled with a monoreactive, NHS-ester fluorescent dye from the kit - Alexa Fluor 555 or Alexa Fluor 647. A final purification step removes unreacted dye, yielding fluorescently labeled cDNA ready for microarray hybridization.