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MOLECULAR METHODS (E.G., MICROARRAYS) APPLIED TO PLANT GENOMES FOR ASSESSING GENETIC CHANGE AND ENVIRONMENTAL STRESS
Citation:
WATRUD, L. S. MOLECULAR METHODS (E.G., MICROARRAYS) APPLIED TO PLANT GENOMES FOR ASSESSING GENETIC CHANGE AND ENVIRONMENTAL STRESS. U.S. Environmental Protection Agency, Washington, DC, EPA/600/R-06/151.
Impact/Purpose:
To present a detailed sample standard operating procedure (S.O.P.) for preparing plant nucleic acid samples for microarray analyses
Description:
This is a technical document that presents a detailed sample standard operating procedure (S.O.P.) for preparing plant nucleic acid samples for microarray analyses using commercial ¿chips¿ such as those sold by Affymetrix. It also presents the application of a commercially available software analysis program (GeneSpring) to analyze microarray data. Most simply stated, it provides technical background on a methodology that is becoming broadly used for numerous basic and applied research purposes. The technology provides a potential means to elucidate our understanding at the molecular/genetic levels, of the effects of diverse environmental, chemical and genetic factors on the expression of specific kinds of genes. For example, it may assist our understanding of the potential non-target effects of genetic engineering or of pesticides, by assisting our efforts to identify genes that one might not have expected to be affected by the engineering or by the chemical exposure. The initial and major purpose is for internal use by researchers e.g. at NHEERL-WED who will use it and further modify it for specific experimental methodological plant biotechnology and chemical pesticides risk assessment purposes. However, the document may also be of interest to others inside and outside the Agency who may want to know more about the technical details of carrying out and analyzing the results of microarray experiments. Such technical background information might be useful to regulatory colleagues who may have occasion to review regulatory packages that may contain microarray gene expression data. Externally, the document may be useful to academic collaborators with whom we interact via cooperative agreements, or with other government researchers with whom we interact via inter-agency agreements. Please note that the manner in which it has been presented is as a Standard Operating Procedure (which incidentally has been reviewed and approved by our Quality Assurance Manager). This level of detail is much greater than the way in which it would be presented in the Materials & Methods sections of peer reviewed journal articles in which we use the methods described in the document.