Reference : Design and evaluation of Actichip, a thematic microarray for the study of the actin c...
Scientific journals : Article
Life sciences : Biochemistry, biophysics & molecular biology
http://hdl.handle.net/10993/6273
Design and evaluation of Actichip, a thematic microarray for the study of the actin cytoskeleton
English
Muller, J. [Laboratoire de Biologie Moléculaire, d'Analyse Génique et de Modélisation, Centre de Recherche Public-Santé, 84 rue Val Fleuri, L-1526 Luxembourg, Luxembourg, Laboratoire de Bioinformatique et Génomique Intégratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université Louis Pasteur, F-67400 Illkirch, F-67000 Strasbourg, France, Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany]
Mehlen, A. [Laboratoire de Biologie Moléculaire, d'Analyse Génique et de Modélisation, Centre de Recherche Public-Santé, 84 rue Val Fleuri, L-1526 Luxembourg, Luxembourg]
Vetter, G. [Laboratoire de Biologie Moléculaire, d'Analyse Génique et de Modélisation, Centre de Recherche Public-Santé, 84 rue Val Fleuri, L-1526 Luxembourg, Luxembourg, Cytoskeleton and cell plasticity laboratory, Life Sciences RU, University of Luxembourg, 162a Avenue de la faïencerie, L-1511 Luxembourg, Luxembourg]
Yatskou, M. [Laboratoire de Biologie Moléculaire, d'Analyse Génique et de Modélisation, Centre de Recherche Public-Santé, 84 rue Val Fleuri, L-1526 Luxembourg, Luxembourg]
Muller, A. [Laboratoire de Biologie Moléculaire, d'Analyse Génique et de Modélisation, Centre de Recherche Public-Santé, 84 rue Val Fleuri, L-1526 Luxembourg, Luxembourg]
Chalmel, F. [Laboratoire de Bioinformatique et Génomique Intégratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université Louis Pasteur, F-67400 Illkirch, F-67000 Strasbourg, France, GERHM-Inserm U625, Université Rennes I, Avenue du General Leclerc, F-35042 Rennes cedex, France]
Poch, O. [Laboratoire de Bioinformatique et Génomique Intégratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université Louis Pasteur, F-67400 Illkirch, F-67000 Strasbourg, France]
Friederich, Evelyne mailto [University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Life Science Research Unit >]
Vallar, L. [Laboratoire de Biologie Moléculaire, d'Analyse Génique et de Modélisation, Centre de Recherche Public-Santé, 84 rue Val Fleuri, L-1526 Luxembourg, Luxembourg]
2007
BMC Genomics
BioMed Central
8
Yes (verified by ORBilu)
International
1471-2164
[en] RNA ; Actinome ; DNA microarray ; GenBank ; RefSeq ; RNA extraction ; UniGene ; DNA microarray ; Actins ; Breast Neoplasms ; Cell Line, Tumor ; Cluster Analysis ; Computational Biology ; Cytoskeleton ; Data Interpretation, Statistical ; Databases, Nucleic Acid ; DNA, Complementary ; Equipment Design ; Gene Expression ; Humans ; Microarray Analysis ; Nucleic Acid Hybridization ; Oligonucleotide Array Sequence Analysis ; Oligonucleotide Probes ; Polymerase Chain Reaction ; Reproducibility of Results ; RNA ; Sensitivity and Specificity ; Software
[en] Background: The actin cytoskeleton plays a crucial role in supporting and regulating numerous cellular processes. Mutations or alterations in the expression levels affecting the actin cytoskeleton system or related regulatory mechanisms are often associated with complex diseases such as cancer. Understanding how qualitative or quantitative changes in expression of the set of actin cytoskeleton genes are integrated to control actin dynamics and organisation is currently a challenge and should provide insights in identifying potential targets for drug discovery. Here we report the development of a dedicated microarray, the Actichip, containing 60-mer oligonucleotide probes for 327 genes selected for transcriptome analysis of the human actin cytoskeleton. Results: Genomic data and sequence analysis features were retrieved from GenBank and stored in an integrative database called Actinome. From these data, probes were designed using a home-made program (CADO4MI) allowing sequence refinement and improved probe specificity by combining the complementary information recovered from the UniGene and RefSeq databases. Actichip performance was analysed by hybridisation with RNAs extracted from epithelial MCF-7 cells and human skeletal muscle. Using thoroughly standardised procedures, we obtained microarray images with excellent quality resulting in high data reproducibility. Actichip displayed a large dynamic range extending over three logs with a limit of sensitivity between one and ten copies of transcript per cell. The array allowed accurate detection of small changes in gene expression and reliable classification of samples based on the expression profiles of tissue-specific genes. When compared to two other oligonucleotide microarray platforms, Actichip showed similar sensitivity and concordant expression ratios. Moreover, Actichip was able to discriminate the highly similar actin isoforms whereas the two other platforms did not. Conclusion: Our data demonstrate that Actichip is a powerful alternative to commercial high density microarrays for cytoskeleton gene profiling in normal or pathological samples. Actichip is available upon request. © 2007 Muller et al; licensee BioMed Central Ltd.
http://hdl.handle.net/10993/6273
10.1186/1471-2164-8-294

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