title: Validation of a novel, fully integrated and flexible microarray benchtop facility for gene expression profiling.
abstract: 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.
authors: febit ag, Käfertaler Strasse 190, 68167 Mannheim, Germany. michael.baum@febit.de
authors: Michael
authors: M
authors: Baum
authors: Simone
authors: S
authors: Bielau
authors: Nicole
authors: N
authors: Rittner
authors: Kathrin
authors: K
authors: Schmid
authors: Kathrin
authors: K
authors: Eggelbusch
authors: Michael
authors: M
authors: Dahms
authors: Andrea
authors: A
authors: Schlauersbach
authors: Harald
authors: H
authors: Tahedl
authors: Markus
authors: M
authors: Beier
authors: Ramon
authors: R
authors: Güimil
authors: Matthias
authors: M
authors: Scheffler
authors: Carsten
authors: C
authors: Hermann
authors: Jörg-Michael
authors: JM
authors: Funk
authors: Anke
authors: A
authors: Wixmerten
authors: Hans
authors: H
authors: Rebscher
authors: Matthias
authors: M
authors: Hönig
authors: Claas
authors: C
authors: Andreae
authors: Daniel
authors: D
authors: Büchner
authors: Erich
authors: E
authors: Moschel
authors: Andreas
authors: A
authors: Glathe
authors: Evelyn
authors: E
authors: Jäger
authors: Marc
authors: M
authors: Thom
authors: Andreas
authors: A
authors: Greil
authors: Felix
authors: F
authors: Bestvater
authors: Frank
authors: F
authors: Obermeier
authors: Josef
authors: J
authors: Burgmaier
authors: Klaus
authors: K
authors: Thome
authors: Sigrid
authors: S
authors: Weichert
authors: Silke
authors: S
authors: Hein
authors: Tim
authors: T
authors: Binnewies
authors: Volker
authors: V
authors: Foitzik
authors: Manfred
authors: M
authors: Müller
authors: Cord Friedrich
authors: CF
authors: Stähler
authors: Peer Friedrich
authors: PF
authors: Stähler
mesh_terms: D001331:Automation / Q000295:instrumentation; D020869:Gene Expression Profiling / Q000295:instrumentation*; D005800:Genes, Fungal / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation*; D012331:RNA, Fungal / Q000032:analysis / Q000235:genetics; D012333:RNA, Messenger / Q000032:analysis / Q000235:genetics; D015203:Reproducibility of Results; D012441:Saccharomyces cerevisiae / Q000235:genetics; D012680:Sensitivity and Specificity
chemical_list: D012331:RNA, Fungal; D012333:RNA, Messenger