Introduction to Affymetrix Microarrays

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Presentation transcript:

Introduction to Affymetrix Microarrays Why use microarrays? Permits expression profiling of thousands of genes in parallel Why use Affymetrix microarrays? Well established platform Arrays for various species Enables combination of different applications Support from the bioinformatic community Well annoted probesets

Introduction to microarrays Steps in analysis

Introduction to microarrays Affymetrix Instrumentation Design Experiment Prepare Sample Wash& Stain Hybridize Scan Hybridization Oven Fluidics Station Scanner Probe Array Data Analysis Software

Introduction to microarrays Chip features

Introduction to microarrays Arrays and Applications

Introduction to microarrays Affymetrix Applications

Introduction to microarrays Development of Affymetrix technology

Introduction to microarrays Bioinformatic flowchart

Computer Lab -in silico microarray study Title: Molecular profiling of tumor progression in NSCLC Geo id: GSE7880 Array: Affymetrix Human HG-Focus Target Array Design: Primary Recurrent stage IIIB or IV Adenocarcinoma (AC) 10 15 Squamous cell carcinoma (SCC) 8 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7880 Lab tasks: Download data set from GEO Add annotations from Affymetrix Perform t-tests to compare expression between groups Answer a set of questions using web resources

Computer Lab Quality Control of data