Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of mouse mutant for microRNA-96 vs. wildtype mice to identify potential targets

ABSTRACT: The Diminuendo mouse mutant strain displays progressive deafness and carries a mutation in the gene mmu-mir-96, a microRNA. We carried out a microarray analysis using RNA extracted from the organ of Corti from 4-day old mutant (n=6) and wildtype (n=6) mice to compare gene expression of both direct and indirect targets.

ORGANISM(S): Mus musculus

SUBMITTER: Morag Lewis

PROVIDER: E-TABM-489 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

An ENU-induced mutation of miR-96 associated with progressive hearing loss in mice.

Lewis Morag A MA Quint Elizabeth E Glazier Anne M AM Fuchs Helmut H De Angelis Martin Hrabé MH Langford Cordelia C van Dongen Stijn S Abreu-Goodger Cei C Piipari Matias M Redshaw Nick N Dalmay Tamas T Moreno-Pelayo Miguel Angel MA Enright Anton J AJ Steel Karen P KP

Nature genetics 20090412 5

Progressive hearing loss is common in the human population, but little is known about the molecular basis. We report a new N-ethyl-N-nitrosurea (ENU)-induced mouse mutant, diminuendo, with a single base change in the seed region of Mirn96. Heterozygotes show progressive loss of hearing and hair cell anomalies, whereas homozygotes have no cochlear responses. Most microRNAs are believed to downregulate target genes by binding to specific sites on their mRNAs, so mutation of the seed should lead to ...[more]

PMID: 19363478

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Project description:The aim of this study was to characterize the basal expression of OC, MOD and SV of newborn rats (3-5 day old) and its changes by shortâterm cultivation (24 hrs) and mild hypoxia (5 hrs). Three varieties of tissue samples were analyzed (i) Freshly prepared tissue, used as control; (ii) cultures held under normoxic conditions and (iii) cultures exposed during cultivation to 5 h hypoxia. The gene expression was analyzed using the Affymetrix GeneChip RN-U34. The functional specificity of the cochlea regions are well reflected by the gene expression pattern. For example, the basal expression of Organ of Corti is characterized by genes involved in potassium and calcium homeostasis. The MOD is characterized by genes involved in regulation of maturation of neuronal cells. The SV is characterized by genes involved in ion homeostasis and blood flow. Cultivation dramatically changes the gene expression. In contrast, mild hypoxia showed only small changes. The changes are interpreted as stress response. We used this analysis as screening approach to detect significant changes in gene expression and used the RT-PCR analyses of independent sister cultures for confirmation. Correlation analysis showed close relations of the expression levels when aliquots of the biological material were compared. However, comparisons of the expression levels received by microarray and by RT-PCR analysis of independent sister samples resulted in 70-90 % in similar predictions. This data indicate that possible discrepancies has its basis in biological sampling rather than factors of methodical errors on the level of RT-PCR. Experiment Overall Design: Pooled samples of the following cochlea preparations were studied: Experiment Overall Design: (i) Native preparations of Organ of Corti, modiolus and stria vascularis from newborn rats used as controls; (ii) Organotypic cultures of these preparations under normoxic conditions (24 h); (iii) Cultures which were exposed to 5 h hypoxia during cultivation. Samples were collected for total RNA immediately after preparation of the inner ear structures (native samples) or 24 h after onset of cultivation (normoxia, hypoxia).

Dataset Information

Transcription profiling of mouse mutant for microRNA-96 vs. wildtype mice to identify potential targets

Publications

An ENU-induced mutation of miR-96 associated with progressive hearing loss in mice.

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