RNA-seq transcriptomic analysis of adult zebrafish inner ear hair cells

Cody L. Barta, Huizhan Liu, Lei Chen, Kimberlee P. Giffen, Yi Li, Ken Kramer, Kirk Beisel, David Z. He

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

Although hair cells are the sensory receptors of the auditory and vestibular systems in the ears of all vertebrates, hair cell properties are different between non-mammalian vertebrates and mammals. To understand the basic biological properties of hair cells from non-mammalian vertebrates, we examined the transcriptome of adult zebrafish auditory and vestibular hair cells. GFP-labeled hair cells were isolated from inner-ear sensory epithelia of a pou4f3 promoter-driven GAP-GFP line of transgenic zebrafish. One thousand hair cells and 1,000 non-sensory surrounding cells (nsSCs) were separately collected for each biological replicate, using the suction pipette technique. RNA sequencing of three biological replicates for the two cell types was performed and analyzed. Comparisons between hair cells and nsSCs allow identification of enriched genes in hair cells, which may underlie hair cell specialization. Our dataset provides an extensive resource for understanding the molecular mechanisms underlying morphology, function, and pathology of adult zebrafish hair cells. It also establishes a framework for future characterization of genes expressed in hair cells and the study of hair cell evolution.

Original languageEnglish (US)
Article number180005
JournalScientific data
Volume5
DOIs
StatePublished - Feb 6 2018

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RNA
Cells
Cell
pathology
specialization
resources
Gene
Genes
Mammals
Pathology
Resources
Sequencing
Suction
Specialization
Promoter
Receptor

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Information Systems
  • Education
  • Computer Science Applications
  • Statistics, Probability and Uncertainty
  • Library and Information Sciences

Cite this

RNA-seq transcriptomic analysis of adult zebrafish inner ear hair cells. / Barta, Cody L.; Liu, Huizhan; Chen, Lei; Giffen, Kimberlee P.; Li, Yi; Kramer, Ken; Beisel, Kirk; He, David Z.

In: Scientific data, Vol. 5, 180005, 06.02.2018.

Research output: Contribution to journalArticle

Barta, Cody L. ; Liu, Huizhan ; Chen, Lei ; Giffen, Kimberlee P. ; Li, Yi ; Kramer, Ken ; Beisel, Kirk ; He, David Z. / RNA-seq transcriptomic analysis of adult zebrafish inner ear hair cells. In: Scientific data. 2018 ; Vol. 5.
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AU - Beisel, Kirk

AU - He, David Z.

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