DNA microarray technology has given rise to the study of functional genomics (Brown and Botstein 1999; Lockhart and Winzeler 2000). The entire set of genes of an organism can be microarryed on an area as small as a fingernail and the expression levels of thousands of genes are simultaneously studied in a single experiment.

  illumina® Sentrix Beadchip

   Total RNA or poly(A) mRNA can be used as a template for microarray analysis. An array generally requires 2~200µg of total RNA or 0.2~2µg of poly(A) mRNA as a starting material.

   These values are adjusted depending on the number of elements, area of hybridization, method of labeling, etc.

   Fluorescently labeled samples are hybridized onto the target DNA or oligonucleotide fixed on the slide.
   In one-color hybridization, sample is labeled with Cy3 fluorescent dye.

  illumina® Hybridization Chamber

   Hybridized slides are scanned with a confocal laser scanner, such as Beadstation-500 - beadarray reader (illumina®), GenePix 4000A scanner (Axon instruments, Union city, CA), ScanArray (GSI lumonics, Farmington Hills, MI), Agilent Scanner (Agilent, Palo Alto, CA), etc.

  illumina® Beadstation-500, Beadarray reader

   Data analysis is done with several statistical adjustments, such as total intensity normalization, regression normalization, normalization using ratio statistics.

   DNA microarray experiments generate unprecedented quantities of genome-wide data which can greatly overwhelm biologists. To extract useful information from expression profiles, computational tools that cluster and display data can be used.

 Related resources

- GEO B cell data

- DNA Chips and Microarray Analysis

- Current issues for DNA microarrays

- AfCS Procedure Protocol PP00000019

- AfCS Procedure Protocol PP00000174

- AfCS Procedure Protocol PP00000179

- AfCS Procedure Protocol PP00000184