High throughput gene expression analysis of the inner ear

The mouse auditory and vestibular epithelia consist of a complex array of many different cell types. Over the last decade microarrays were used to characterize gene expression in the inner ear. Studies were performed on wild type mice to identify deafness genes, transcriptional networks activated during development, or identify miRNA with a functional role in the ear. Other studies focused on the molecular response of the inner ear to stimuli ranging from ototoxic medications to hypergravity and caloric restriction. Finally, microarrays were used to identify transcriptional networks activated downstream of deafness genes. As template-free high throughput gene expression profiling methods such as RNA-seq are increasingly popular, we offer a critical review of the data generated over the last decade relating to microarrays for gene expression profiling of the inner ear. Moreover, as most of the published data is available through the gene expression omnibus (GEO), we demonstrate the feasibility of integrating data from independent experiments to reach novel insights.

► Microarrays are commonly used to study gene expression in the mouse inner ear.
► The Gene Expression Omnibus can be accessed to further query submitted datasets.
► The percentage of different cells types varies between the auditory and vestibular epithelia.
► Cell type-specific gene expression analysis is sensitive and specific.