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Microarray Technology
• Introduction
– Microarrays are extremely powerful ways to analyze
gene expression.
– Using a microarray, it is possible to examine the
expression level of thousands of genes in one
– Microarrays can be used to compare the expression of
many genes under different conditions (cancer cells
vs. normal cells, skin cells vs. organ cells, rapidly
growing cells vs. quiescent cells, etc.)
• Types of Microarrays
– Microarrays can be classified into two general
• cDNA arrays consist of cDNA copies of mRNA
spotted onto a glass slide.
• oligo arrays consist of strands of oligonucleotides
either spotted onto a glass slide or lithographed
onto a solid surface.
• Oligonucleotide Array
• Microarray experiments
– A typical microarray experiment consists of extracting
RNA from the cells or tissue being examined,
converting the RNA to cDNA, labelling the cDNA with
fluorescent dyes and allowing the labelled cDNA to
hybridize with the material (cDNA or oligonucleotide)
on the microarray slide.
– In some experiments, the control and subject RNAs
are synthesized with different fluorescent dyes and
mixed on the same slide. Other protocols use
separate slides for the subject and control RNAs.
• Microarray experiments
– After hybridization, the slides are scanned using a
laser device to determine the amount of fluorescent
label that is attached to each cDNA on the slide.
– The amount of fluorescence is displayed as a spot on
a matrix corresponding to the original slide.
– The intensity images are colored according to a
standard where a higher level of fluorescent label in
the subject (enhanced gene expression) is colored
red. A lower level (repressed level of gene
expression) is colored green. Equal levels are yellow.
• Microarray experiments
– Follow the link to see a realistic animation of a
cDNA experiment. Microarray animation
– The next step is analyzing the data. See the
Microarray Data Analysis presentation.