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J. Biol. Chem., Vol. 277, Issue 40, 37001-37008, October 4, 2002
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From the Assessment of reproducibility of DNA-microarray
analysis from published data sets is complicated by the use of
different microbial strains, cultivation techniques, and analytical
procedures. Because intra- and interlaboratory reproducibility is
highly relevant for application of DNA-microarray analysis in
functional genomics and metabolic engineering, we designed a set of
experiments to specifically address this issue. Saccharomyces
cerevisiae CEN.PK113-7D was grown under defined conditions in
glucose-limited chemostats, followed by transcriptome analysis with
Affymetrix GeneChip arrays. In each of the laboratories, three
independent replicate cultures were grown aerobically as well as
anaerobically. Although variations introduced by in vitro
handling steps were small and unbiased, greater variation from
replicate cultures underscored that, to obtain reliable information,
experimental replication is essential. Under aerobic conditions, 86%
of the most highly expressed yeast genes showed an average
intralaboratory coefficient of variation of 0.23. This is
significantly lower than previously reported for shake-flask-culture
transcriptome analyses and probably reflects the strict control of
growth conditions in chemostats. Using the triplicate data sets and
appropriate statistical analysis, the change calls from anaerobic
versus aerobic comparisons yielded an over 95% agreement
between the laboratories for transcripts that changed by over 2-fold,
leaving only a small fraction of genes that exhibited laboratory bias.
Reproducibility of Oligonucleotide Microarray Transcriptome
Analyses
AN INTERLABORATORY COMPARISON USING CHEMOSTAT CULTURES OF
SACCHAROMYCES CEREVISIAE*
,§,
,**
Kluyver Laboratory of Biotechnology,
Technical University of Delft, Julianalaan 26, Delft 2628BC, The
Netherlands and the ¶ Center for Process Biotechnology,
BioCentrum-DTU, Bldg. 223, and the Center for Biological
Sequence Analysis, BioCentrum-DTU, Bldg. 208, Technical University of
Denmark, Kongens Lyngby DK-2800, Denmark
*
This work was supported in part by the Delft University of
Technology (Beloning Excellent Onderzoek program).The costs of publication of this
article were defrayed in part by the
payment of page charges. The article
must therefore be hereby marked
"advertisement" in
accordance with 18 U.S.C. Section
1734 solely to indicate this fact.
Copyright © 2002 by The American Society for Biochemistry and Molecular Biology, Inc.
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