ZFIN ID: ZDB-PUB-180428-3
Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo
Wagner, D.E., Weinreb, C., Collins, Z.M., Briggs, J.A., Megason, S.G., Klein, A.M.
Date: 2018
Source: Science (New York, N.Y.)   360(6392): 981-987 (Journal)
Registered Authors: Megason, Sean
Keywords: none
Microarrays: GEO:GSE112294
MeSH Terms:
  • Animals
  • Clonal Evolution/genetics*
  • Gene Expression
  • Gene Expression Regulation, Developmental*
  • Glycoproteins/genetics
  • Intercellular Signaling Peptides and Proteins/genetics
  • Sequence Analysis, RNA/methods
  • Single-Cell Analysis/methods
  • Zebrafish/embryology*
  • Zebrafish/genetics*
  • Zebrafish Proteins/genetics*
PubMed: 29700229 Full text @ Science
High-throughput mapping of cellular differentiation hierarchies from single-cell data promises to empower systematic interrogations of vertebrate development and disease. Here we applied single-cell RNA sequencing to >92,000 cells from zebrafish embryos during the first day of development. Using a graph-based approach, we mapped a cell-state landscape that describes axis patterning, germ layer formation, and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon-based barcoding approach (TracerSeq) for reconstructing single-cell lineage histories. Clonally related cells were often restricted by the state landscape, including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in embryos lacking the chordin gene. We provide web-based resources for further analysis of the single-cell data.