project

The Clough Lab

Clough Lab Projects

Microarray (Intro)
- Introduction as PowerPoint presentation
  - Nov 2005 (.pdf, 5.1 MB)
  - Nov 2005 (.ppt, 12.8 MB)
- 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 NSF Soybean Functional Genomics Web page (last updated 2001)
  - Dr. Lila Vodkin U of Illinois - Crop Science Dept. Web page (last updated 2001)
  - Iowa State site on soybean ESTs
  - U Minn site on soybean genomics
  - USDA Beltsville Soybean Microarray site

Affymetrix Soybean Gene Chips
- Affymetrix - Soybean Genome Array web site
- Introduction as PowerPoint presentation (Affymetrix)
  - Nov 2005 (.pdf, 0.7 MB)
  - Nov 2005 (.ppt, 2.0 MB)

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)
  - October 29, 2009
    analysis by Marisol Benitez with kind input from Staff of W. M. Keck Center for Comparative and Functional Genomics
    
    .sas version .doc version Demo input file for SAS
    
    Demo experimental design file for SAS
- Affymetrix chips
  - Introduction as PowerPoint presentation (Affymetrix)
    - Nov 2005 (.pdf, 0.7 MB)
    - Nov 2005 (.ppt, 2.0 MB)
    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

This page last updated: January 9, 2007
Designed by: Marisol Benitez and Jason Bant