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Comparison of sampling techniques for parallel analysis of transcript and metabolite levels in Saccharomyces cerevisiae
Author(s) -
Margarida Martins Ana,
Sha Wei,
Evans Clive,
MartinoCatt Susan,
Mendes Pedro,
Shulaev Vladimir
Publication year - 2007
Publication title -
yeast
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.923
H-Index - 102
eISSN - 1097-0061
pISSN - 0749-503X
DOI - 10.1002/yea.1442
Subject(s) - biology , saccharomyces cerevisiae , metabolite , sampling (signal processing) , computational biology , genetics , yeast , biochemistry , computer science , filter (signal processing) , computer vision
Mathematical modelling of cellular processes is crucial for the understanding of the cell or organism as a whole. Genome‐wide observations, at the levels of the transcriptome, proteome and metabolome, provide a high coverage of the molecular constituents of the system in study. Time‐course experiments are important for gaining insight into a system's dynamics and are needed for mathematical modelling. In time‐course experiments it is crucial to use efficient and fast sampling techniques. We evaluated several techniques to sample and process yeast cultures for parallel analysis of the transcriptome and metabolome. The evaluation was made by measuring the quality of the RNA obtained with UV‐spectroscopy, capillary electrophoresis and microarray hybridization. The protocol developed involves rapid collection by spraying the sample into −40 °C tricine‐buffered methanol (as previously described for yeast metabolome analysis), followed by the separation of cells from the culture medium in low‐temperature rapid centrifugation. Removal of the residual methanol is carried out by freeze‐drying the pellet at −35 °C. RNA and metabolites can then be extracted from the same freeze‐dried sample obtained with this procedure. Copyright © 2007 John Wiley & Sons, Ltd.