Cochlear whole mount in situ hybridization: identification of longitudinal and radial gradients

The morphology of the organ of Corti has a radial asymmetry and also changes longitudinally from base to apex. Cellular localization of transcripts within the inner ear has relied primarily on the use of sectioned tissue with in situ hybridization. However, radial and longitudinal gradients of expression are not readily recognized using sectioned tissue owing to problems in visualization of signals with varying intensities. Herein, we describe the use of whole mount in situ hybridization for identification of cochlear longitudinal and radial expression gradients in the neurosensory epithelium, hair cells. Not only can these hair cell gradients be shown in adult tissues, but also the developmental up-regulation and down-regulation of genes and their associated spatio-temporal expression patterns can be demonstrated.