Single-cell RNA-sequencing (scRNA-seq) of GFP+cells isolated from Tg(Brn3c:mGFP) 6 days zebrafish with GFP expression in all hair cells.

Hair cells play key roles in hearing and balance, and hair cell loss would result in hearing loss or vestibular dysfunction. Zebrafsh, owing to their hair cell-enriched organs, have been widely applied in hair cell-related research worldwide. In this study, we analyzed the GFP+cells isolated from Tg(Brn3c:mGFP) larvae with GFP expression in all hair cells using single-cell RNA-sequencing (scRNA-seq). Three subtypes of hair cells, namely macula hair cell (MHC), crista hair cell (CHC), and neuromast hair cell (NHC), were characterized and validated by whole-mount in situ hybridization analysis of marker genes. The hair cell scRNA-seq data revealed hair cell-specifc genes, including hearing loss genes that have been identifed in humans and novel genes potentially involved in hair cell formation and function. Zebrafsh were maintained at 28.5 °C. The Tg(Brn3c:mGFP) transgenic zebrafsh larvae at 6 days post-fertilization (dpf) were anesthetized and then treated with 0.25% trypsin to dissociate into single cells, which were divided into GFP-positive and GFP-negative cells through the fuorescent activated cell sorter, and the RNA expressed in GFP-positive cells were then obtained and sequenced using the 10×Genomics platform