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Audiol. Otol."],"abstract":"<jats:sec><jats:title>Introduction<\/jats:title><jats:p>Mutations in microRNA-96 (miR-96), a microRNA expressed within the hair cells (HCs) of the inner ear, result in progressive hearing loss in both mouse models and humans. In this study, we present the first HC-specific RNA-sequencing (RNA-seq) dataset from newborn <jats:italic>Mir96<\/jats:italic><jats:sup><jats:italic>Dmdo<\/jats:italic><\/jats:sup> heterozygous, homozygous mutant, and wildtype mice.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Bulk RNA-seq was performed on HCs of newborn <jats:italic>Mir96<\/jats:italic><jats:sup><jats:italic>Dmdo<\/jats:italic><\/jats:sup> heterozygous, homozygous mutant, and wildtype mice. Differentially expressed gene analysis was conducted on <jats:italic>Mir96<\/jats:italic><jats:sup><jats:italic>Dmdo<\/jats:italic><\/jats:sup> homozygous mutant HCs compared to wildtype littermate controls, followed by GO term and protein-protein interaction analysis on these differentially expressed genes.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We identify 215 upregulated and 428 downregulated genes in the HCs of the <jats:italic>Mir96<\/jats:italic><jats:sup><jats:italic>Dmdo<\/jats:italic><\/jats:sup> homozygous mutant mice compared to their wildtype littermate controls. Many of the significantly downregulated genes in <jats:italic>Mir96<\/jats:italic><jats:sup><jats:italic>Dmdo<\/jats:italic><\/jats:sup> homozygous mutant HCs have established roles in HC development and\/or known roles in deafness including <jats:italic>Myo15a, Myo7a, Ush1c, Gfi1<\/jats:italic>, and <jats:italic>Ptprq<\/jats:italic> and have enrichment in gene ontology (GO) terms with biological functions such as sensory perception of sound. Interestingly, upregulated genes in <jats:italic>Mir96<\/jats:italic><jats:sup><jats:italic>Dmdo<\/jats:italic><\/jats:sup> homozygous mutants, including possible miR-96 direct targets, show higher wildtype expression in supporting cells compared to HCs.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Our data further support a role for miR-96 in HC development, possibly as a repressor of supporting cell transcriptional programs in HCs. The HC-specific <jats:italic>Mir96<\/jats:italic><jats:sup><jats:italic>Dmdo<\/jats:italic><\/jats:sup> RNA-seq data set generated from this manuscript are now publicly available in a dedicated profile in the gene expression analysis resource (gEAR-<jats:ext-link>https:\/\/umgear.org\/p?l=miR96<\/jats:ext-link>).<\/jats:p><\/jats:sec>","DOI":"10.3389\/fauot.2024.1400576","type":"journal-article","created":{"date-parts":[[2024,5,9]],"date-time":"2024-05-09T05:07:25Z","timestamp":1715231245000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":2,"title":["A cell type\u2013specific approach to elucidate the role of miR-96 in inner ear hair cells"],"prefix":"10.3389","volume":"2","author":[{"given":"Kathleen","family":"Gwilliam","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michal","family":"Sperber","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katherine","family":"Perry","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kevin P.","family":"Rose","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Laura","family":"Ginsberg","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nikhil","family":"Paladugu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yang","family":"Song","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Beatrice","family":"Milon","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ran","family":"Elkon","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ronna","family":"Hertzano","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2024,5,9]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"05005","DOI":"10.7554\/eLife.05005.028","article-title":"Predicting effective microRNA target sites in mammalian mRNAs","volume":"4","author":"Agarwal","year":"2015","journal-title":"ELife"},{"key":"B2","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq\u2013a Python framework to work with high-throughput sequencing data","volume":"31","author":"Anders","year":"2015","journal-title":"Bioinformatics"},{"key":"B3","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1007\/s00439-021-02359-z","article-title":"The noncoding genome and hearing loss","volume":"141","author":"Avraham","year":"2022","journal-title":"Hum. 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