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ESTs, cDNA microarrays, and gene expression profiling: tools for dissecting plant physiology and development
Author(s) -
Alba Rob,
Fei Zhangjun,
Payton Paxton,
Liu Yang,
Moore Shanna L.,
Debbie Paul,
Cohn Jonathan,
D'Ascenzo Mark,
Gordon Jeffrey S.,
Rose Jocelyn K. C.,
Martin Gregory,
Tanksley Steven D.,
Bouzayen Mondher,
Jahn Molly M.,
Giovani Jim
Publication year - 2004
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/j.1365-313x.2004.02178.x
Subject(s) - dna microarray , biology , complementary dna , gene expression profiling , computational biology , transcriptome , microarray , gene expression , functional genomics , genomics , gene , profiling (computer programming) , genetics , genome , computer science , operating system
Summary 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.