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.
Highlights
Background & SummaryHair cells are the sensory receptors of the auditory and vestibular systems in the ears of all vertebrates
In addition to the apical stereocilia bundle, hair cells contain structural and functional specializations in the basolateral and synaptic membranes, which are responsible for electrical activities and synaptic transmission[2,3,4]
Hair cells of non-mammals are electrically tuned to specific frequencies and possess an active process in the stereocilia bundle to amplify sound signals[5,6]
Summary
Hair cells are the sensory receptors of the auditory and vestibular systems in the ears of all vertebrates. Since hair cells in those studies were obtained from zebrafish larvae, whose gene expression profile is known to be different from that of adult hair cells, we examined the inner ear hair cell-specific transcriptome of adult zebrafish using RNA-seq. Study design workflow for cell isolation and collection for transcriptome analysis of GFPpositive hair cells (we used HCs in all figures) and GFP-negative nsSCs isolated from adult zebrafish inner ear. (a) Workflow of experimental design for RNA-seq and transcriptome analysis for 1,000 individually collected hair cells and nsSCs. We describe transcriptome-wide profiling of hair cells and non-sensory surrounding cells (nsSCs) from the adult zebrafish inner ear. Careful and stringent technical design at each experimental stage has allowed generation of a high-quality RNA-seq dataset which has tremendous value for future characterization of all genes expressed in zebrafish hair cells. The present dataset is useful for comparative studies of hair cells between zebrafish and mouse
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