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Gene expression analysis measures the activity of genes and reveals valuable information about the internal states of living cells. NASA Ames has developed a novel system for conducting quantitative, real-time gene expression analysis that not only significantly improves the sample preparation procedures and provides a quick, cost-effective solution needed in a laboratory, but also minimizes the risk of RNA contamination and degradation. The invention, a novel assay methodology and suite of devices have been developed to isolate nucleic acids from Prokaryotic and Eukaryotic cells and prepare samples for Reverse Transcriptase - quantitative Polymerase Chain Reaction (RT-qPCR) analysis. The invention consists of a method to extract and purify nucleic acids from biospecimen that does not require organics or toxic chemicals, and provides containment for the liquids. The assay employs an aqueous-based non-alcohol method that yields robust RNA quality; and PCR reaction tubes that are pre-loaded with stabilized lyophilized reagents designed to perform RT-qPCR analysis - all in all enabling rapid, cost effective, and portable manual operation in the laboratory or remote field environments. This innovative technology greatly reduces preparation time to less than 10% of the time it would take using standard techniques. This technology could be used with any commercial quantitative Polymerase Chain Reaction (qPCR) machine.