Complete gene expression profiling accessory reagent kits include all components necessary to perform transcript synthesis, fluorescent labeling, and detection and are intended to carry out all processing steps for separately cleared gene expression microarray assays which specify their use. They are designed and optimized for preparation of labeled complementary RNA (cRNA) target using total RNA isolated from specific clinical tissue specimens for hybridization to and measurement of fluorescently-labeled cRNA targets using a specified and cleared microarray instrumentation system. They may also include specified exogenous controls intended to monitor amplification and labeling processes.