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DNA Microarrays Purpose • Measure the activity of thousands of genes at the same time • Have a plate that has the genes on it • You then add your sample to see if it hybridizes with any of the genes • Other techniques that we have studied only allows you to study one or a few genes are the same time Genes are differentially regulated • All somatic cells in an organism contain the same genes • Different genes are expressed in different tissues under different conditions • Different tissues have different functions because different genes are expressed • In some tissues, different genes may be expressed at different times in development High vs. low expression of genes • It is not always best to have high expression of genes – What would be an example in cancer? – What genes would you not want to be expressed? – What genes would you want to be expressed? DNA chip = microarray = gene chip = genome chip • Have a slide – Imprinted with a pattern of spots – Each spot has many copies of a specific sequence representing a gene Quick overview of procedure • Have two different groups – look at genes that are up or down regulated or absent • Isolate mRNA • make cDNAs • Tag the DNA with dyes so they can be detected • Add the labeled DNA to the slides • Analyze if hybridization took place – computer analysis Mock DNA microarray experiment • Use a DNA microarray to study expression of 6 different genes • Normal lung cells vs. cancerous lung cells • 4 different types of genes: – Some genes transcribed less in cancer than in normal cells – Some genes transcribed more in cancer than in normal cells – Some genes transcribed at the same level – Some genes are not expressed at all in normal or cancerous lung cells Compare data • Control vs. patient • Indication of who might have genes involved in cancer – What are the genes that cause cancer Colors • If you had red, green and yellow, which color would be the mix of the other two colors? • If you had pink, purple and blue, which color would be the mix of the other two colors? Color interpretation • You do not always get genes that are highly expressed or highly repressed, there may be intermediary colors • For example, dark red may indicate a gene that is highly expressed but if it is a light red, it might be only slightly expressed We will use the color scheme below to quantitate our results from our microarray experiment Ratio = gene expression in cancer cells/gene expression in normal cells Which range of numbers indicate expression in cancer cells but not in normal Cells? Which range of numbers indicate expression in normal cells but not in cancer Cells? Which range of numbers indicate expression in both normal cells and cancer cells? Are there numbers where there is expression in neither normal nor cancer cells?
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