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)
  - 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: November 10, 2009
Designed by: Marisol Benitez and Jason Bant