19.1.10—Microarrays in genome analysis

A microarray is a chip carrying many gene-specific probes fixed in a grid of spots. Complementary labelled nucleic acids hybridise to the probes, allowing many genes to be detected at the same time; the signal can indicate sequence presence or, when mRNA-derived material is compared, relative gene expression.

1. Choose probes with sequences complementary to the genes or transcripts being investigated and fix the probes at known spots on the chip.
2. Collect the sample material. For a gene-expression comparison, collect mRNA and use reverse transcriptase to make corresponding cDNA; fluorescently label the sample nucleic acids.
3. Denature the labelled material where needed so complementary single strands can pair with the probes.
4. Allow the sample to hybridise with the probes on the chip, then wash away material that has not hybridised.
5. Scan the chip using the supported fluorescence or ultraviolet detection method. A coloured spot indicates hybridisation to the corresponding probe.
6. Compare spot colour or presence with the relevant sample, control and background. Presence can support sequence or transcript detection; for expression studies, relative spot intensity indicates relative mRNA abundance after appropriate comparison and normalisation.
7. State the conclusion with its evidence boundary: a signal reports probe binding under the test conditions, not automatically a complete gene sequence, protein amount or biological function.

Sequence-presence reading — a coloured spot supports that a complementary sequence was detected.
Expression reading — stronger or weaker fluorescence is interpreted comparatively as more or less labelled cDNA from mRNA, provided samples were prepared and normalised comparably.
Controls and background — use matched controls and account for background signal before comparing spots; no probe number, intensity threshold or universal cut-off is assumed.

Microarrays are not a substitute for a full bioinformatics pipeline, and PCR and gel electrophoresis are separate cards. Spot intensity is a relative signal under the stated preparation and normalisation conditions, not an absolute expression value.