Molecular characterization of hindbrain vestibular neurons in the larval zebrafish (scRNA-Seq)

The molecular logic that specifies and assembles closely-related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate, topography, and circuit assembly. We used single-cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely-related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons, labeled by Tg(-6.7Tru.Hcrtr2:GAL4-VP16);Tg(UAS:E1b-Kaede), harvested from zebrafish embryos between 72-74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting (FACS) according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or after a previously identified "midpoint" in hindbrain vestibular neuron development (36 hpf), labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.