PUBLICATION
Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo
- Authors
- Wagner, D.E., Weinreb, C., Collins, Z.M., Briggs, J.A., Megason, S.G., Klein, A.M.
- ID
- ZDB-PUB-180428-3
- Date
- 2018
- Source
- Science (New York, N.Y.) 360(6392): 981-987 (Journal)
- Registered Authors
- Megason, Sean
- Keywords
- none
- Datasets
- 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
Citation
Wagner, D.E., Weinreb, C., Collins, Z.M., Briggs, J.A., Megason, S.G., Klein, A.M. (2018) Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo. Science (New York, N.Y.). 360(6392):981-987.
Abstract
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.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping