Lecture 2 - Fertilization

Lecture 2 - Fertilization - Microarrays (gene chips) for...

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Microarrays (gene chips) for assaying global gene expression patterns (some slides courtesy of J. Lieb)
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Spotted Microarrays PCR products (direct from genome, or  from cDNA clones), or oligonucleotides  are spotted by capillary action onto a  glass microscope slide. Up to ~44,000 features per slide  Typically hybridized with 2 differentially  labeled samples simultaneously.
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The Fordham Hall DNA Microarrayer 
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Spotted DNA Microarray 18,000 PCR-amplified cDNA clone inserts Printed on poly-lysine coated 1 X 3 inch glass slide  Each spot corresponds to a different gene circa 1998
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Tumor Pool of Cell Lines A Typical DNA Microarray Experiment Reference or Control Experimental Sample Lower in Tumor Higher in Tumor (tests thousands of genes at a time)
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10_15_DNA.microarrays .jpg Microarray technology
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increased expression decreased expression Use computers to keep track of expression levels of all of the genes in large datasets. Use bioinformatics software to identify genes with interesting expression characteristics.
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these genes have higher expression in normal tissue than breast cancers these genes have lower expression in basal-like breast cancers than in normal tissue or luminal breast cancers Expression profiling: overall patterns of gene expression can be used in diagnosis Each column is from a different tumor. Each row represents one gene. Rows are clustered by similar expression pattern.
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Chu et al., Science 282: 699-705 (1998) Transcription response during yeast sporulation (1116 out of ~5000 genes changed)
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Iyer et al., Science 283: 83-87 (1999) Transcriptional response of human fibroblasts to serum (~6% of genes on microarray changed)
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10_02_cell_sorter.jpg Using a fluorescence- activated cell sorter (FACS) to separate cells
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Birnbaum et al., Nature Methods 2 , 615 - 619 (2005)
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Brady et al., Science 318: 801-806 (2007)
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Lecture 2 - Fertilization - Microarrays (gene chips) for...

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