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Microarray Analysis The Basics Thomas Girke December 9 2011 Microarray Analysis Slide 1 42 Technology Challenges Data Analysis Data Depositories R and BioConductor Homework Assignment Microarray Analysis Slide 2 42 Outline Technology Challenges Data Analysis Data Depositories R and BioConductor Homework Assignment Microarray Analysis Technology Slide 3 42 Microarray and Chip Technology Definition Hybridization based technique that allows simultaneous analysis of thousands of samples on a solid substrate Applications Transcriptional Profiling Gene copy number Resequencing Genotyping Single nucleotide polymorphism DNA protein interaction e g ChIP on chip Gene discovery e g Tiling arrays Identification of new cell lines Etc Related technologies Protein arrays Compound arrays Microarray Analysis Technology Slide 4 42 Why Microarrays Simultaneous analysis of thousands of genes Discovery of gene functions Genome wide network analysis Analysis of mutants and transgenics Identification of drug targets Causal understanding of diseases Clinical studies and field trials Microarray Analysis Technology Slide 5 42 Different Types of Microarrays Single channel approaches Affymetrix gene chips Macroarrays Multiple channel approaches Dual color cDNA microarrays Specialty approaches Bead arrays Lynx Illumina PCR based profiling CuraGen Microarray Analysis Technology Slide 6 42 Dual Color Microarrays Microarray Analysis Technology Slide 7 42 Affymetrix DNA Chips Microarray Analysis Technology Slide 8 42 Outline Technology Challenges Data Analysis Data Depositories R and BioConductor Homework Assignment Microarray Analysis Challenges Slide 9 42 Profiling Chips Monitor Differences of mRNA Levels Efficient strategy for down stream follow up experiments important Microarray Analysis Challenges Slide 10 42 Strategies to Validate Array Hits Real time PCR Northern etc Transgenic tests Knockout plants and or activation tagged lines Protein profiling Metabolic profiling Other tests in situ



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