Reconstruction of the Mouse Otocyst and Early Neuroblast Lineage at Single-Cell Resolution

The otocyst harbors progenitors for most cell types of the mature inner ear. Developmental lineage analyses and gene expression studies suggest that distinct progenitor populations are compartmentalized to discrete axial domains in the early otocyst. Here, we conducted highly parallel quantitative RT-PCR measurements on 382 individual cells from the developing otocyst and neuroblast lineages to assay 96 genes representing established otic markers, signaling-pathway-associated transcripts, and novel otic-specific genes. By applying multivariate cluster, principal component, and network analyses to the data matrix, we were able to readily distinguish the delaminating neuroblasts and to describe progressive states of gene expression in this population at single-cell resolution. It further established a three-dimensional model of the otocyst in which each individual cell can be precisely mapped into spatial expression domains. Our bioinformatic modeling revealed spatial dynamics of different signaling pathways active during early neuroblast development and prosensory domain specification. [Display omitted] [Display omitted] •Early otic neuroblast lineage progression at single-cell resolution•Bioinformatic analyses describe time and space in development•Refinement of expression domains of many known and novel otic genes•Spatial dynamics of signaling pathways during development Multivariate mathematical techniques combined with known gene expression data models the relative location and differentiation status of individual cells to create a 3D model of the inner-ear primordium.