The identification of differential gene expression between two samples can be easily and rapidly done by DNA microarrays. This requires high quality RNA samples, proper labeling and hybridization.
A microarray is a technique used to detect the expression of thousands of genes, at the same time, on microarray slides. These small slides are originally printed with thousands of spots, each with a known DNA sequence. These sequences are probes that help detect gene expression upon hybridization with samples.
During sample preparation, two fluorescent dyes are added, cy3 (green fluorescence) to the ‘to be studied group’ and cy5 (red fluorescence) to the ‘reference group’. Thus; samples that contain DNA sequences complementary to array slide probes hybridize and fluoresce when scanned.
Good quality arrays should produce high signal at relatively low PMT values. Massive or widely spread differential gene expression is probably non significant. Thus; a picture of the array should look more yellow, rather than green or red. Good quality signals should also be in a dynamic range, where the signal histograms fully overlap.
Quality control of RNA samples applied to microarrays is important and can be detected using bioanalyzer 2100. It is worth mentioning that good quality total RNA samples should produce two major peaks corresponding to the 2 major ribosomal RNA species. Severely degraded, low quality RNA will show a broad peak or a series of peaks at low retention times, while the 2 ribosomal RNA peaks will be of very low intensity or not identifiable at all. An RNA Integrity Number (RIN) higher than 9 is preferably used.
Other application of DNA microarray:
Transcriptomes and proteomes.*Gene chips to diagnose several pathogenic and genetic diseases in man.*Species specific probes.*Single nucleotide polymorphism (SNP) analysis.
