International Mammalian Genome Society

The 16th International Mouse Genome Conference (2002)


POSTER 58 - ELIMINATING CROSS-HYBRIDISATION: HIGH QUALITY EXPRESSION PROFILING DATA FOR THE MOLECULAR PHENOTYPIC ANALYSIS OF MOUSE MUTANTS

J Beckers
GSF - National Research Center for Environment & Health

Drobyshev A, Machka C, Horsch M, Hrabe de Angelis M, Beckers J
GSF - National Research Centre for Environment & Health

The cDNA-chip technology is a powerful tool for the comprehensive analysis of gene expression at the transcript level. The biological significance of such expression profiling analyses critically depends on the quality and specificity of hybridisation data. Based on experimental data, we describe methods to discriminate between gene specific signals and signals resulting from extensive cross-hybridisation. We identify criteria that can be used for each individual probe on comprehensive DNA-chips to correct expression data to achieve high quality results. For this, we apply in situ fractionation of hybridised targets by means of contiguous washes with increasing stringency. In the course of such washing steps, distinct fractions of hybridised target are washed out at different stringency. The fluorescent intensity data at each step and for each probe of a microarray comprise the fractionation curve. Based on this information, unreliable data can be filtered and gene specific probes relevant for high quality expression data can be identified. In the MouseExpress project we apply this technology for a systematic and comprehensive analysis of expression profiles from a set of organs in a compendium of mouse mutant lines (more than 400 mutant lines) derived from the Munich ENU mutagenesis screen. Such comprehensive transcriptome analyses will lead to the identification of new gene functions and co-regulated synexpression groups of genes, which are the basis for the description of regulatory networks.


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