The transcriptional landscape of the murine middle ear epithelium in vitro

Middle ear epithelium (MEE) is an extended part of the respiratory mucosa and mucociliary differentiation of MEE is crucial for the maintenance of homeostasis and sterility of the middle ear cavity. Previously we developed an in vitro model of murine MEE using air-liquid interface (ALI) culture that replicates aspects of the in vivo middle ear. Defects in MEE function can lead to the development of otitis media (OM). Decoding differential gene expression (DGE) across the MEE during mucociliary differentiation is valuable in understanding the mechanism underpinning the development of OM. We used ClariomTM S Mouse assay to understand the global gene expression at different time points of murine MEE differentiation at ALI culture and to identify sets of genes up-regulated and down-regulated during this process. Murine MEE cells were isolated from 5-6 middle ears of adult C57/BL6 mice and cultured at the ALI for up to seven days. Total RNA was extracted from freshly isolated MEE cells, and at cells at day 0 (grown at submerged culture and collected prior to ALI culture) and at day 7 ALI culture. 200ng of total RNA from each sample was subjected to analyse on the ClaromTM S Mouse GeneChip (Thermo Fisher) according to the manufacturer protocol.