In response to the growing demand to learn how to extract maximum information from the tremendous amount of data generated in a micorarray experiment. This workshop was designed to pick up where Bio-Trac® “DNA Microarrays: Fabrication and Applications” left off. Beginning with a hybridized array, this four-day course spends extensive time on optimizing the scanning process and acquiring an informative scan. This data will then be analyzed using GeneSpring software to generate clustering associations. Finally, using microarray and protein interaction data, pathways defining gene interactions will be assessed using Pathway Studio software.
Microarray Scanning and Acquisition of a Good Image; Analysis of Microarray Data by GeneSpring; Managing Microarray Data; Pathway Analysis; TM4: Open-source Software for Advanced Microarray Data Analysis (with a Concentration in TIGR MIDAS and TIGR MeV) Normalize and filter Expression Files. Methods for Clustering Expression Data and Classifying Experimental Samples. Laboratories will Include Scanning a Microarray and Computer-based Experiments Involving Analysis and Manipulation of the Data Using Such Programs as QuantArray, GeneSpring and Pathway Studio.
Global transcription patterns as well as nucleotide polymorphisms can now be readily evaluated using DNA microarrays. This functional genomics technology offers a powerful, non biased approach to the analysis of molecular mechanisms associated with any type of physiological change in a cell. Moreover, DNA microarrays have become a prominent technological tool for genotype characterization. This lecture and laboratory course will show how DNA microarrays can be used for different applications in the biomedical sciences and will introduce hands-on training to a complex yet exciting technology.
Overview of DNA microarrays; Transcriptional analysis from single genes to whole genomes; Types and applications of microarrays; Use of microarrays for genotyping; comparative genome hybridization providing a molecular karyotype of the genome; Fabrication of DNA microarrays; microarray data analysis; Concepts of microarray bioinformatics; Dove-tailing expression data to genome sequences and other types of functional genomics; genotyping and resequencing using genechip technology; high throughput profiling platforms: development of tools for diagnosis and management of disease; introduction of new technologies – microfluidics-generated microarrays with in situ synthesized probes, Illumina bead technology.
Isolation of total RNA; purification and quantitation of mRNA; fluorescent labeling of cDNA; Hybridization of cDNA to DNA arrays; Scanning and data collection; Analysis and display of data using clustering programs; Validation of microarray expression analysis by real-time and conventional RT-PCR.