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Single-cell RNA-Seq resolves cellular complexity in sensory organs from the neonatal inner ear

Author

Listed:
  • Joseph C. Burns

    (Laboratory of Cochlear Development, National Institute on Deafness and Other Communication Disorders, National Institutes of Health)

  • Michael C. Kelly

    (Laboratory of Cochlear Development, National Institute on Deafness and Other Communication Disorders, National Institutes of Health)

  • Michael Hoa

    (Laboratory of Cochlear Development, National Institute on Deafness and Other Communication Disorders, National Institutes of Health)

  • Robert J. Morell

    (Genomics and Computational Biology Core, National Institute on Deafness and Other Communication Disorders, National Institutes of Health)

  • Matthew W. Kelley

    (Laboratory of Cochlear Development, National Institute on Deafness and Other Communication Disorders, National Institutes of Health)

Abstract

In the inner ear, cochlear and vestibular sensory epithelia utilize grossly similar cell types to transduce different stimuli: sound and acceleration. Each individual sensory epithelium is composed of highly heterogeneous populations of cells based on physiological and anatomical criteria. However, limited numbers of each cell type have impeded transcriptional characterization. Here we generated transcriptomes for 301 single cells from the utricular and cochlear sensory epithelia of newborn mice to circumvent this challenge. Cluster analysis indicates distinct profiles for each of the major sensory epithelial cell types, as well as less-distinct sub-populations. Asynchrony within utricles allows reconstruction of the temporal progression of cell-type-specific differentiation and suggests possible plasticity among cells at the sensory–nonsensory boundary. Comparisons of cell types from utricles and cochleae demonstrate divergence between auditory and vestibular cells, despite a common origin. These results provide significant insights into the developmental processes that form unique inner ear cell types.

Suggested Citation

  • Joseph C. Burns & Michael C. Kelly & Michael Hoa & Robert J. Morell & Matthew W. Kelley, 2015. "Single-cell RNA-Seq resolves cellular complexity in sensory organs from the neonatal inner ear," Nature Communications, Nature, vol. 6(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:6:y:2015:i:1:d:10.1038_ncomms9557
    DOI: 10.1038/ncomms9557
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    Cited by:

    1. Jing Nie & Yoshitomo Ueda & Alexander J. Solivais & Eri Hashino, 2022. "CHD7 regulates otic lineage specification and hair cell differentiation in human inner ear organoids," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    2. Kieran R Campbell & Christopher Yau, 2016. "Order Under Uncertainty: Robust Differential Expression Analysis Using Probabilistic Models for Pseudotime Inference," PLOS Computational Biology, Public Library of Science, vol. 12(11), pages 1-20, November.
    3. Huihui Liu & Hongchao Liu & Longhao Wang & Lei Song & Guixian Jiang & Qing Lu & Tao Yang & Hu Peng & Ruijie Cai & Xingle Zhao & Ting Zhao & Hao Wu, 2023. "Cochlear transcript diversity and its role in auditory functions implied by an otoferlin short isoform," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    4. Ming-Wen Hu & Dong Won Kim & Sheng Liu & Donald J Zack & Seth Blackshaw & Jiang Qian, 2019. "PanoView: An iterative clustering method for single-cell RNA sequencing data," PLOS Computational Biology, Public Library of Science, vol. 15(8), pages 1-17, August.

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