Validation of a novel, fully integrated and flexible microarray benchtop facility for gene expression profiling

Here we describe a novel microarray platform that integrates all functions needed to perform any array‐based experiment in a compact instrument on the researcher’s laboratory benchtop. Oligonucle otide probes are synthesized in situ via a light‐ activated process within the channels of a three‐dimen...

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Bibliographic Details
Published in:	Nucleic acids research Vol. 31; no. 23; p. e151
Main Authors:	Baum, Michael, Bielau, Simone, Rittner, Nicole, Schmid, Kathrin, Eggelbusch, Kathrin, Dahms, Michael, Schlauersbach, Andrea, Tahedl, Harald, Beier, Markus, Güimil, Ramon, Scheffler, Matthias, Hermann, Carsten, Funk, Jörg‐Michael, Wixmerten, Anke, Rebscher, Hans, Hönig, Matthias, Andreae, Claas, Büchner, Daniel, Moschel, Erich, Glathe, Andreas, Jäger, Evelyn, Thom, Marc, Greil, Andreas, Bestvater, Felix, Obermeier, Frank, Burgmaier, Josef, Thome, Klaus, Weichert, Sigrid, Hein, Silke, Binnewies, Tim, Foitzik, Volker, Müller, Manfred, Stähler, Cord Friedrich, Stähler, Peer Friedrich
Format:	Journal Article
Language:	English
Published:	England Oxford University Press 01-12-2003 Oxford Publishing Limited (England)
Subjects:	Automation - instrumentation DNA microarrays Gene Expression Profiling - instrumentation Genes, Fungal - genetics NAR Methods Online Oligonucleotide Array Sequence Analysis - instrumentation Reproducibility of Results RNA, Fungal - analysis RNA, Fungal - genetics RNA, Messenger - analysis RNA, Messenger - genetics Saccharomyces cerevisiae - genetics Sensitivity and Specificity
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Summary:	Here we describe a novel microarray platform that integrates all functions needed to perform any array‐based experiment in a compact instrument on the researcher’s laboratory benchtop. Oligonucle otide probes are synthesized in situ via a light‐ activated process within the channels of a three‐dimensional microfluidic reaction carrier. Arrays can be designed and produced within hours according to the user’s requirements. They are processed in a fully automatic workflow. We have characterized this new platform with regard to dynamic range, discrimination power, reproducibility and accuracy of biological results. The instrument detects sample RNAs present at a frequency of 1:100 000. Detection is quantitative over more than two orders of magnitude. Experiments on four identical arrays with 6398 features each revealed a mean coefficient of variation (CV) value of 0.09 for the 6398 unprocessed raw intensities indicating high reproducibility. In a more elaborate experiment targeting 1125 yeast genes from an unbiased selection, a mean CV of 0.11 on the fold change level was found. Analyzing the transcriptional response of yeast to osmotic shock, we found that biological data acquired on our platform are in good agreement with data from Affymetrix GeneChips, quantitative real‐time PCR and—albeit somewhat less clearly—to data from spotted cDNA arrays obtained from the literature.
Bibliography:	istex:0F069AB5A8703BA793503AD8FF5B1BF2A858D74B Received July 6, 2003; Revised September 20, 2003;. Accepted October 9, 2003 ark:/67375/HXZ-6JR0HT88-0 local:gng151 To whom correspondence should be addressed. Tel: +49 621 3804 257; Fax: +49 621 3804 400; Email: michael.baum@febit.de ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Feature-1 content type line 23 ObjectType-Article-1 ObjectType-Feature-2
ISSN:	0305-1048 1362-4962 1362-4962
DOI:	10.1093/nar/gng151