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Microarrays measure gene expression through complementary hybridization between immobilized probes on glass chips and labeled sample nucleic acids. RNA from cells is reverse transcribed to cDNA, then converted to cRNA and labeled with fluorescent molecules. When the labeled sample hybridizes to matching probes on the chip, fluorescence intensity at each spot indicates expression levels for thousands of genes simultaneously.

Northern blotting uses free-floating probes to detect RNA immobilized on membranes, while microarrays reverse this arrangement. In microarrays, oligonucleotide probes are immobilized on glass slides, and free-floating labeled cDNA or cRNA samples hybridize to them. This allows microarrays to simultaneously evaluate thousands of genes, whereas Northern blots typically assess one or a few genes at a time.

RNA quality is critical because RNases—enzymes that degrade RNA—can destroy samples during isolation and preparation. Workspaces and equipment are treated with RNase-inactivating chemicals to protect RNA integrity. Researchers verify RNA quality and concentration through spectrophotometry before converting it to cDNA, ensuring reliable downstream hybridization and accurate gene expression measurements.

Microarray data undergoes statistical processing including log2 transformation and normalization to account for signal differences between chips. Researchers then cluster genes based on similar expression patterns across conditions. Dendrograms depict these relationships, showing how closely gene expression patterns match. Clustered genes often participate in the same biological pathways, providing insight into gene networks and functional associations.

Hybridization chambers are formed by placing a mixer onto the microarray chip to create isolated compartments for the hybridization mix. These chambers facilitate controlled binding between labeled sample and immobilized probes. Care must be taken to avoid air bubbles during sample loading, as they interfere with binding and produce false negative signals. Chips are then incubated at appropriate temperatures for up to 24 hours.

Researchers use microarrays to compare gene expression between cancerous and normal tissues to identify disease biomarkers. For example, scientists compared endogenous retroviruses (ERVs)—viral sequences in human genomes—between prostate cancer and normal tissues. This identified ERVs upregulated in cancer, which can serve as diagnostic biomarkers. Microarrays enable simultaneous evaluation of thousands of genes to pinpoint expression differences associated with disease.

After hybridization, the dried microarray is scanned to produce a digital image showing fluorescence intensity at each probe location. The scanner is adjusted to prevent signal over-saturation. Data-extraction software then analyzes the image for signal irregularities and processes the data through log2 transformation and normalization. This processed data quantifies fold changes in gene expression between experimental conditions.