title: Assessment of a systematic expression profiling approach in ENU-induced mouse mutant lines.
abstract: Comparative genomewide expression profiling is a powerful tool in the effort to annotate the mouse genome with biological function. The systematic analysis of RNA expression data of mouse lines from the Munich ENU mutagenesis screen might support the understanding of the molecular biology of such mutants and provide new insights into mammalian gene function. In a direct comparison of DNA microarray experiments of individual versus pooled RNA samples of organs from ENU-induced mouse mutants, we provide evidence that individual RNA samples may outperform pools in some aspects. Genes with high biological variability in their expression levels (noisy genes) are identified as false positives in pooled samples. Evidence suggests that highly stringent housing conditions and standardized procedures for the isolation of organs significantly reduce biological variability in gene expression profiling experiments. Data on wild-type individuals demonstrate the positive effect of controlling variables such as social status, food intake before organ sampling, and stress with regard to reproducibility of gene expression patterns. Analyses of several organs from various ENU-induced mutant lines in general show low numbers of differentially expressed genes. We demonstrate the feasibility to detect transcriptionally affected organs employing RNA expression profiling as a tool for molecular phenotyping.
authors.affiliation: GSF-National Research Center for Environment and Health, Institute of Experimental Genetics, Ingolstaedter Landstr. 1, Neuherberg, D-85764, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Seltmann
authors.forename: Marion
authors.initials: M
authors.lastname: Horsch
authors.forename: Alexei
authors.initials: A
authors.lastname: Drobyshev
authors.forename: Yali
authors.initials: Y
authors.lastname: Chen
authors.forename: Martin Hrabé
authors.initials: MH
authors.lastname: de Angelis
authors.forename: Johannes
authors.initials: J
authors.lastname: Beckers
mesh_terms: D000818:Animals; D015536:Down-Regulation; D005038:Ethylnitrosourea; D015870:Gene Expression; D020869:Gene Expression Profiling; D014644:Genetic Variation; D007668:Kidney / Q000378:metabolism; D008099:Liver / Q000378:metabolism; D051379:Mice; D008817:Mice, Mutant Strains / Q000235:genetics*; D016296:Mutagenesis; D009153:Mutagens; D020411:Oligonucleotide Array Sequence Analysis; D013154:Spleen / Q000737:chemistry / Q000378:metabolism; D015854:Up-Regulation
chemical_list: D009153:Mutagens; D005038:Ethylnitrosourea