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.
Department of Otolaryngology, Head & Neck Surgery and Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.
Robert
R
Durruthy-Durruthy
Departments of Bioengineering and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Assaf
A
Gottlieb
Department of Otolaryngology, Head & Neck Surgery and Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.
Byron H
BH
Hartman
Department of Otolaryngology, Head & Neck Surgery and Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.
Jörg
J
Waldhaus
Department of Otolaryngology, Head & Neck Surgery and Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.
Roman D
RD
Laske
Departments of Bioengineering and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Russ
R
Altman
Department of Otolaryngology, Head & Neck Surgery and Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address: hellers@stanford.edu.
Stefan
S
Heller
D000818:Animals; D007758:Ear, Inner / Q000166:cytology* / Q000196:embryology*; D004622:Embryo, Mammalian / Q000166:cytology; D005260:Female; D018507:Gene Expression Regulation, Developmental; D008297:Male; D051379:Mice; D058953:Neural Stem Cells / Q000166:cytology*; D025341:Principal Component Analysis; D059010:Single-Cell Analysis; D059467:Transcriptome