Projects
Microarray (Intro)
Introduction as PowerPoint presentation
CPSC 499 Genomics - Invited class lecture
Use of microarrays to study gene expression
- Part I: Developing arrays (.pdf, 2.9 MB) (.ppt, 20.0 MB)
Part II: Using microarrays to identify differentialy express genes during defense to a bacterial plant pathogen (.pdf, 10.0 MB) (.ppt, 35.9 MB)
Soybean cDNA arrays
Protocols related to cDNA microarrays
Background
- 2000 BMC Genomics article by Vodkin et al. describing soybean cDNA microarray construction
Shoemaker article on soybean EST libraries (abstract)
Clough and Vodkin book chapter on soybean microarrays written for policy maker audience (Clough, S. J. and Vodkin, L. O. 2004. Soybean microarrays: a genomic tool for crop improvement. Pages 267-282 in R. F. Wilson, H. T. Stalker and E. C. Brummer, eds. Legume Crop Genomics. American Oil Chemists Society Press, Champaign, IL)
Dr. Lila Vodkin U of Illinois - Crop Science Dept. Web page
Iowa State site on soybean ESTs
Affymetrix Soybean Gene Chips
Affymetrix - Soybean Genome Array web site
Introduction as PowerPoint presentation (Affymetrix)
Analysis of Microarray Data
- cDNA slides
-
Scanning .ppt (.pdf, 8.9 MB)
Poor Spot Troubleshooting .ppt (.pdf, 1.0 MB)
Image analysis .ppt (.pdf, 10 MB)
Organizing, cleaning, and normalizing (smoothing) cDNA microarray data. (.pdf version) (analysis by Marisol Benitez with kind input from Staff of W. M. Keck Center for Comparative and Functional Genomics)
- Introduction as PowerPoint presentation (Affymetrix)
RMA normalization (.pdf version)
GCRMA normalization (.pdf version)
HR Response
- Gene Expression Profiling of Soybean Response during Compatible and Incompatible Interactions with the Bacterial Pathogen Pseudomonas syringae Poster (.pdf, 2.5 MB)
Nodulation
- Gene Expression Profiling of Soybean Root Response to Nodulation Poster (.gif, 835 k)
Functional Genomics of Root Hair Infection
White Mold (Sclerotinia)
- Genetic Analysis of White Mold Resistance using Microarrays Poster (.pdf, 592 k)
Sudden Death Syndrome (SDS)
Soybean Rust
- Soybean Disease Research Lab
SoyFACE
- SoyFACE Web site
DOE project
Transformation
- Arabidopsis - Floral Dip Protocol
Soybean