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Lab5-2011 - Lab#5 DNA microarray image and data analysis...

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Lab #5 – DNA microarray image and data analysis Name: Mary Ellen Hoinski Due Feb. 15 or 17 The objective of this lab exercise is to become familiar with microarray images and basic data analysis. Today we are working with a microarray image that was produced by hybridizing two labeled cDNA samples to a B. subtilis DNA microarray. This microarray consists of 65 mer oligonucleotides representing each of the 4,106 protein coding genes in the B. subtilis genome. Strain 1 is a wild-type strain of B. subtilis and Strain 2 is the same strain only it contains a mutation in gene X. We want to determine if the mutation in gene X causes any alterations in the gene expression program of B. subtilis . Because we do not know which gene(s) a mutation in gene X affects it is appropriate to use a DNA microarray containing all the known genes of B. subtilis to investigate changes in gene expression. Strain 1 and strain 2 were grown under indentical conditions in the laboratory. RNA was isolated from each strain, reverse transcribed into cDNA, and labeled with either Cy3 (strain 1) or Cy5 (strain 2). 1. a. Start the GenePix program and open the image file. There are multiple tools on the left side of the screen that allow you to zoom in on the image or select particular portions of the image. There are also multiple tools on the right side of the screen that can be used to open files, flag spots, analyze data, etc. Many of these will be helpful during the lab. Can you determine whether there are any gene expression differences between the two strains simply by looking at the array image? Explain.
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