title: Development and validation of a custom microarray for global transcriptome profiling of the fungus Aspergillus nidulans.
abstract: Transcriptome profiling is a powerful tool for identifying gene networks from whole genome expression analysis in many living species. Here is described the first extensively characterized platform using Agilent microarray technology for transcriptome analysis in the filamentous fungus Aspergillus (Emericella) nidulans. We developed and validated a reliable gene expression microarray in 8 × 15 K format, with predictive and experimental data establishing its specificity and sensitivity. Either one or two 60-mer oligonucleotide probes were selected for each of 10,550 nuclear as well as 20 mitochondrial coding sequences. More than 99 % of probes were predicted to hybridize with 100 % identity to their aimed specific A. nidulans target only. Probe sensitivity was supported by a highly narrow distribution of melting temperatures together with thermodynamic features, which strongly favored probe-target perfect match hybridization, in comparison with predicted secondary structures. Array quality was evaluated through transcriptome comparison of two A. nidulans strains, differing by the presence or not of Escherichia coli LacZ transgene. High signal-to-noise ratios were measured, and signal reproducibility was established at intra-probe and inter-probe levels. Reproducibility of microarray performances was assessed by high correlation between two-color dye signals and between technical replicates. Results were confirmed by RT-qPCR analysis on five genes. Though it covers 100 % of the A. nidulans targeted coding sequences, this low density array allows limited experimental costs and simplified data analysis process, making it suitable for studying gene expression in this model organism through large numbers of experimental conditions, in basic, biomedical or industrial microbiology research fields.
authors.affiliation: UMS IPSIT, Plateforme Trans-Prot, Faculté de Pharmacie, Univ. Paris-Sud, Université Paris-Saclay, 5 rue Jean-Baptiste Clément, 92296, Châtenay-Malabry, France. claudine.delomenie@u-psud.fr.
authors.forename: Claudine
authors.identifier: http://orcid.org/0000-0002-6326-966X
authors.initials: C
authors.lastname: Deloménie
authors.affiliation: PharmaBioServices, 1 square du Cèdre, 91370, Verrières-Le-Buisson, France.
authors.forename: Guido
authors.initials: G
authors.lastname: Grentzmann
authors.affiliation: Laboratoire VEAC, Faculté des Sciences, Univ. Paris-Sud, Université Paris-Saclay, Bât. 360, Rue du Doyen André Guinier, 91405, Orsay, France.|Pôle Risques MRSH-CNRS, Université de Caen, Esplanade de la Paix, 14032, Caen, France.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Oestreicher
authors.affiliation: Gene Expression and Therapy Group, Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, 8th Floor, Tower Wing, Guy's Hospital, Great Maze Pond, London, SE1 9RT, UK.|CRIIGEN, 81 rue Monceau, 75008, Paris, France.
authors.forename: Robin
authors.initials: R
authors.lastname: Mesnage
authors.affiliation: Laboratoire VEAC, Faculté des Sciences, Univ. Paris-Sud, Université Paris-Saclay, Bât. 360, Rue du Doyen André Guinier, 91405, Orsay, France.|Pôle Risques MRSH-CNRS, Université de Caen, Esplanade de la Paix, 14032, Caen, France.|CRIIGEN, 81 rue Monceau, 75008, Paris, France.
authors.forename: Christian
authors.initials: C
authors.lastname: Vélot
mesh_terms: D001233:Aspergillus nidulans / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling / Q000379:methods* / Q000592:standards; D023281:Genomics / Q000379:methods / Q000592:standards; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods / Q000592:standards; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D059629:Signal-To-Noise Ratio; D059467:Transcriptome
keywords: Aspergillus nidulans; Microarray; Oligonucleotide probe design; RT-qPCR; Transcriptome analysis