Protocol details the preparation of fluorescently labeled target samples and hybridization of these samples to a microarray of Agilent inkjet-deposited cDNAs.  The procedure requires a minimum of 5 mg of purified total RNA as starting material. Includes: First Strand cDNA Synthesis; Second Strand cDNA Synthesis; cDNA Cleanup and Precipitation; In vitro Transcription; Cleanup and Quantification of in vitro Transcribed RNA; Fluorescent Labeling of the Target Samples.

Protocol: Transcript Profiling by Microarray Analysis Protocol.