Preparation of the intact rodent organ of Corti for RNAscope and immunolabeling, confocal microscopy, and quantitative analysis

Daniel O.J. Reijntjes, J. Lukas Breitzler, Dora Persic, Sonja J. Pyott*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

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This protocol describes the preparation of the mouse organ of Corti for RNAscope, immunolabeling, confocal microscopy, and quantitative image analysis to examine transcript and protein localization, sensory hair cells, and synapses. This protocol can be applied to mice and other rodents (juvenile and adult) and can be adapted for other techniques, including electrophysiology and RNA sequencing. This protocol features minimal tissue processing to preserve viability for downstream assays, while isolating the organ of Corti is the most challenging step. For additional details on the use and execution of this protocol, please refer to McLean et al. (2009); Schuth et al. (2014); Lingle et al. (2019); Pyott et al. (2020).

Original languageEnglish
Article number100544
Number of pages24
JournalSTAR protocols
Issue number2
Publication statusPublished - 18-Jun-2021


  • Antibody
  • In Situ Hybridization
  • Microscopy
  • Molecular/Chemical Probes
  • Neuroscience

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