Present address: USDA-ARS Cropping Systems Research Laboratory, Lubbock, TX, USA.
ESTs, cDNA microarrays, and gene expression profiling: tools for dissecting plant physiology and development
Article first published online: 16 AUG 2004
The Plant Journal
Volume 39, Issue 5, pages 697–714, September 2004
How to Cite
Alba, R., Fei, Z., Payton, P., Liu, Y., Moore, S. L., Debbie, P., Cohn, J., D'Ascenzo, M., Gordon, J. S., Rose, J. K. C., Martin, G., Tanksley, S. D., Bouzayen, M., Jahn, M. M. and Giovannoni, J. (2004), ESTs, cDNA microarrays, and gene expression profiling: tools for dissecting plant physiology and development. The Plant Journal, 39: 697–714. doi: 10.1111/j.1365-313X.2004.02178.x
- Issue published online: 16 AUG 2004
- Article first published online: 16 AUG 2004
- Received 16 March 2004; revised 23 June 2004; accepted 24 June 2004.
- expressed sequence tags;
- expression profiling;
- digital expression analysis;
Gene expression profiling holds tremendous promise for dissecting the regulatory mechanisms and transcriptional networks that underlie biological processes. Here we provide details of approaches used by others and ourselves for gene expression profiling in plants with emphasis on cDNA microarrays and discussion of both experimental design and downstream analysis. We focus on methods and techniques emphasizing fabrication of cDNA microarrays, fluorescent labeling, cDNA hybridization, experimental design, and data processing. We include specific examples that demonstrate how this technology can be used to further our understanding of plant physiology and development (specifically fruit development and ripening) and for comparative genomics by comparing transcriptome activity in tomato and pepper fruit.