BIO 309 - Genomics, Proteomics and Systems Biology
Dr. Haynes - Fall 2007

Microarray Experiment Source Page

Davidson array logo

Designing your experiment

You will continue to study your favorite disease-linked gene/ protein by tracking the expression of its yeast ortholog under different conditions. We use yeast as a model system for genomics because it is a eukaryote and is thus relevant to human cell biology, is very easy to culture in the lab for large scale RNA purification, is ammenable to site-specific mutagenesis and has very well-studied biochemical pathways. Before you get started, you should do the following...

  1. Identify your favorite human disease gene's yeast ortholog (this was done in Unit 1). Get an overview of your yeast ortholog at the Saccharomyces Genome Database (SGD)*.
  2. Think carefully and consider what microarray expression assays can tell us (the power? the limitations?).
  3. Based on what you know about your favorite gene, think of an interesting research question(s) that can be addressed by tracking gene expression.
  4. Choose at least 3 experiments to use for building informative expression profiles (see Resource Files below). You must have at least 3 points in an expression profile to compute correlation coefficients (for clustering) using Magic Tool. In some experiments, a gene is mutated. You can get information on the genes that are mutated by searching the SGD.
  5. Map out a rough plan. What gene/ genes will you keep track of? What are your controls? What expression profile criteria will you explore?

*You may notice that the SGD has a huge microarray resource called Expression Connection. You will use this later to expand your findings.

 

Resource Files

These data were generated and provided by the lab of Professor Laura Hoopes at Pomona College.

Hybridization 1 - wild type log phase growth vs. stationary phase growth
PO74bottom_635.tiff - Cy3, wild type yeast, stationary phase growth
PO74bottom_532.tiff - Cy5, wild type yeast, log phase growth

Hybridization 2 - wild type stationary phase growth vs. log phase growth
PO968WlogGWstR_635.tiff - Cy3, wild type yeast, log phase growth
PO968WlogGWstR_532.tiff - Cy5, wild type yeast, stationary phase growth

Hybridization 3 - wild type stationary phase growth vs. stationary phase growth
(same vs. same, that's not a typo)
PO75TOP_635.tiff - Cy3, wild type yeast, stationary phase growth
PO75TOP_532.tiff - Cy5, wild type yeast, stationary phase growth

Hybridization 2 - snf1 deletion mutant vs. wild type
PO73Bottom_635.tiff - Cy3, wild type yeast, stationary phase growth
PO73Bottom_532.tiff - Cy5, snf1 deletion mutant yeast, stationary phase growth

Hybridization 3 - asr1 deletion mutant vs. wild type
PO74Top_635.tiff - Cy3, wild type yeast, stationary phase growth
PO74Top_532.tiff - Cy5, asr1 deletion mutant yeast, stationary phase growth

Hybridization 4 - msn2/msn4 deletion mutant stationary phase growth vs. log phase growth
PO968MlogGMstR_635.tiff - Cy3, msn2/msn4 deletion mutant, log phase growth
PO968MlogGMstR_532.tiff - Cy5, msn2/msn4 deletion mutant, stationary phase growth

Hybridization 5 - snf1 deletion mutant stationary phase growth vs. log phase growth
PO968SlogGSstR_635.tiff - Cy3, snf1 deletion mutant yeast, log phase growth
PO968SlogGSstR_532.tiff - Cy5, snf1 deletion mutant yeast, stationary phase growth

Hybridization 6 - msn2/msn4 deletion mutant stationary phase growth vs. wild type log phase growth
PO968WlogGMstR_635.tiff - Cy3, wild type yeast, log phase growth
PO968WlogGMstR_532.tiff - Cy5, msn2/msn4 deletion mutant yeast, stationary phase growth

Gene list file for all experiments: yeast_GCAT_MT.txt

Gene info file for all experiments: yeastinfo.info

 

About the Arrays

The slides (microarrays) used in the experiments above were produced at Washington University, St. Louis. To produce these microarrays, 70-mer oligos from over 6000 yeast ORF's were printed onto epoxy slides.

 

Web Page Links

Microarray technology: