microarray

Microarray is a laboratory tool that enables the simultaneous measurement of the expression levels of thousands of genes or other DNA features. It consists of a solid substrate, typically a glass slide, onto which DNA probes are fixed in a precise grid. Each probe represents a gene or genomic sequence, and the pattern of spots forms a microarray.

In a typical experiment, RNA is extracted from biological samples, converted to labeled cDNA or cRNA, and hybridized to the array. The sample may be labeled with a fluorescent dye (one-color experiments) or with two different dyes in comparative applications (two-color experiments). After washing, the slide is scanned with a fluorescence scanner; the signal intensity at each feature reflects the abundance of the corresponding transcript in the sample.

DNA microarrays are used for gene expression profiling, genotyping, and detection of copy number variations; methylation and other epigenetic assays and, in some cases, protein microarrays (based on immobilized antibodies or other binding reagents) are also described under the broader term. Arrays can be produced by spotting pre-synthesized DNA probes on the surface or by in situ synthesis of oligonucleotides directly on the chip.

Data analysis involves image processing to extract feature intensities, followed by normalization and statistical testing to identify differential signals. Results are often interpreted with clustering, principal component analysis, and pathway analysis, and are commonly deposited in public repositories in accordance with MIAME guidelines.

Limitations of microarrays include cross-hybridization, limited dynamic range, dependence on predefined sequences, and batch effects. Since the rise of high-throughput sequencing, RNA-seq has largely supplanted microarrays for expression profiling, though microarrays remain in use for targeted assays, certain clinical tests, and legacy data.