Lecture11-Functional Genomics I

Lecture11-Functional Genomics I - Lecture 11 - Functional...

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A. mRNA expression pattern (gene-by-gene) Northern blot  qRT-PCR (quantitative Reverse Transcription-PCR) RNA in situ hybridization Transcriptional reporter genes B.   Expression profiling/transcriptome analysis (high throughput) DNA microarrays Oligonucleotide arrays “RNA-Seq” - Next-generation sequencing C. Protein expression pattern Western blot Immunohistochemistry Translational reporter gene  Mass spectrometry   1 Lecture 11 - Functional Genomics Tuesday Oct 25, 2011 Partially covered by Hartwell: p. 306 (hybridization);  pp. 349-351 (high throughput expression); pp. 352-356 (proteomics)
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2 Up to now in this course, you’ve discussed Forward Genetics Mutant phenotype, Genetic analysis, Mapping, Gene cloning, Gene sequence How does the gene sequence explain the phenotype? The amount of genome sequence data is growing enormously What now? What do the sequences mean?  How do they function?  How do you get from the sequence to the phenotype?          This has led to the era of “Functional Genomics”
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What is functional genomics? Research that aims to describe genes at a dynamic functional level (e.g., gene  activity), beyond knowing only the DNA sequence Overall goal is to go from having the DNA sequence to understanding gene  function (ideally for every gene in a genome) 3
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What kinds of information will help to provide an understanding of gene function? 4 What is the encoded protein’s activity? Where and when is the gene expressed? Where and when is the protein expressed? What collection of genes are co-expressed in the genome? What collection of proteins are co-expressed? What is the network of interacting proteins in the cell? What is the mutant phenotype?
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Goals of this lecture 1.Know the types of experimental strategies that scientists can apply  systematically to gain an understanding of any gene’s expression , regardless of  the gene’s specific function.  =“Toolkit” 1.Compare and contrast the methods and their applications  e.g., “high  throughput” vs.“gene-by-gene”, static(snapshot in time) vs. dynamic  (modulations overtime)data, RNA vs. protein.       5
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6 What are the experimental strategies used in functional genomics? Basic approaches that describe/identify:
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Lecture11-Functional Genomics I - Lecture 11 - Functional...

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