Microarray TechnologyMicroarray Technology

• IntroductionIntroduction– Microarrays are extremely powerful ways to Microarrays are extremely powerful ways to

analyze gene expression.analyze gene expression.– Using a microarray, it is possible to examine the Using a microarray, it is possible to examine the

expression level of thousands of genes in one expression level of thousands of genes in one experimentexperiment

– Microarrays can be used to compare the Microarrays can be used to compare the expression of many genes under different expression of many genes under different conditions (cancer cells vs. normal cells, skin conditions (cancer cells vs. normal cells, skin cells vs. organ cells, rapidly growing cells vs. cells vs. organ cells, rapidly growing cells vs. quiescent cells, etc.)quiescent cells, etc.)

• Types of MicroarraysTypes of Microarrays– Microarrays can be classified into two Microarrays can be classified into two

general types.general types.•cDNA arrays consist of cDNA copies of mRNA cDNA arrays consist of cDNA copies of mRNA

spotted onto a glass slide.spotted onto a glass slide.

•oligo arrays consist of strands of oligo arrays consist of strands of oligonucleotides either spotted onto a glass oligonucleotides either spotted onto a glass slide or lithographed onto a solid surface.slide or lithographed onto a solid surface.

• Oligonucleotide ArrayOligonucleotide Array

• Microarray experimentsMicroarray experiments– A typical microarray experiment consists of A typical microarray experiment consists of

extracting RNA from the cells or tissue being extracting RNA from the cells or tissue being examined, converting the RNA to cDNA, labelling examined, converting the RNA to cDNA, labelling the cDNA with fluorescent dyes and allowing the the cDNA with fluorescent dyes and allowing the labelled cDNA to hybridize with the material labelled cDNA to hybridize with the material (cDNA or oligonucleotide) on the microarray slide.(cDNA or oligonucleotide) on the microarray slide.

– In some experiments, the control and subject In some experiments, the control and subject RNAs are synthesized with different fluorescent RNAs are synthesized with different fluorescent dyes and mixed on the same slide. Other dyes and mixed on the same slide. Other protocols use separate slides for the subject and protocols use separate slides for the subject and control RNAs.control RNAs.

• Microarray experimentsMicroarray experiments– After hybridization, the slides are scanned using a After hybridization, the slides are scanned using a

laser device to determine the amount of fluorescent laser device to determine the amount of fluorescent label that is attached to each cDNA on the slide.label that is attached to each cDNA on the slide.

– The amount of fluorescence is displayed as a spot The amount of fluorescence is displayed as a spot on a matrix corresponding to the original slide.on a matrix corresponding to the original slide.

– The intensity images are colored according to a The intensity images are colored according to a standard where a higher level of fluorescent label in standard where a higher level of fluorescent label in the subject (enhanced gene expression) is colored the subject (enhanced gene expression) is colored red. A lower level (repressed level of gene red. A lower level (repressed level of gene expression) is colored green. Equal levels are expression) is colored green. Equal levels are yellow.yellow.

• Microarray experimentsMicroarray experiments– Follow the link to see a realistic Follow the link to see a realistic

animation of a cDNA experiment. animation of a cDNA experiment. Microarray animationMicroarray animation

– The next step is analyzing the data. See The next step is analyzing the data. See the Microarray Data Analysis the Microarray Data Analysis presentation. presentation.