RNA-sequencing of Adult Zebrafish Inner Ear Hair Cells

To understand the basic biological properties of inner ear hair cells (HCs) from non-mammalian vertebrates, we examined the transcriptome of adult zebrafish auditory and vestibular HCs. GFP-labeled HCs were isolated from inner-ear sensory epithelia of a pou4f3 promoter-driven GAP-GFP line of transgenic zebrafish. One thousand HCs 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. The resulting sequenced reads were mapped. Comparisons between HCs and nsSCs allow identification of enriched genes in HCs, which may underlie HC specialization. Our dataset provides an extensive resource for understanding the molecular mechanisms underlying morphology, function, and pathology of adult zebrafish HCs. It also establishes a framework for future characterization of the genes expressed in HCs and for the study of HC evolution. One thousand HCs and 1,000 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. The resulting sequenced reads were mapped. Comparisons between HCs and nsSCs allow identification of enriched genes in HCs, which may underlie HC specialization.