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Center for Integrated BioSystems

Courses

Gene Expression & Microarray Analysis

This is an intensive training course covering the main areas of microarray technology. The course focuses on microbial as well as plant gene expression and emphasizes theory, sample preparation, labeling, fluorescent imaging, microarray data analysis, and data mining. Hands-on laboratory sessions cover microarray tools, kits, reagents and services, experimental design, labeling, cDNA synthesis, sample preparation, microarray reaction, microarray detection, data analysis and modeling, Affymetrix demonstration and more.

Day 1

Lecture:
  • Overview of gene expression & microarrays
  • Genome sequencing, oligonucleotide arrays, labeling & sensitivity
  • Spotting media
Laboratory:
  • Printing arrays and quality considerations
  • Pitfalls & troubleshooting of common microarray problems

Day 2

Lecture:
  • Microbial gene expression
  • Eukaryotic gene expression
  • Sample quality before hybridization
Laboratory:
  • AFFYMETRIX ARRAYS: Sample preparation, hybridization, array scanner, image and raw data

Day 3

Lecture:
  • Statistics for microarray analysis
  • Mining of gene expression database
  • Measuring error and data transformation for gene expression
Laboratory:
  • Data analysis and modeling: image and raw data, normalization methods
  • Bioconductor, SAM, ArrayAssist, Pathway Tools, NetAffy

Day 4

Case Studies:
  • Alfalfa, bacterial metabolomics with arrays, yeast & fatty acid production
Adjourn at noon

Instructors:

  • Patti Champine, M.S., Center for Integrated BioSystems, USU
  • Daryll DeWald, Ph.D., Biology, USU
  • Jacob Parnell, PhD., Center for Integrated BioSystems, USU
  • Kamal Rashid, Ph.D., Center for Integrated BioSystems, USU
  • Giovanni Rompato, Ph.D., Center for Integrated BioSystems, USU
  • John Stevens, Ph.D., Mathematics and Statistics, USU