PUBLICATION
A single-cell transcriptome atlas for zebrafish development
- Authors
- Farnsworth, D.R., Saunders, L.M., Miller, A.C.
- ID
- ZDB-PUB-191130-16
- Date
- 2020
- Source
- Developmental Biology 459(2): 100-108 (Journal)
- Registered Authors
- Farnsworth, Dylan, Miller, Adam
- Keywords
- none
- MeSH Terms
-
- Animals
- Embryonic Development/genetics*
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Developmental
- Larva/genetics
- Male
- Organogenesis/genetics*
- Reproducibility of Results
- Retina/embryology
- Sequence Analysis, RNA/methods
- Single-Cell Analysis/methods*
- Transcriptome*
- Zebrafish/embryology*
- PubMed
- 31782996 Full text @ Dev. Biol.
Citation
Farnsworth, D.R., Saunders, L.M., Miller, A.C. (2020) A single-cell transcriptome atlas for zebrafish development. Developmental Biology. 459(2):100-108.
Abstract
The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge, we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap, we produced an atlas using single-cell RNA-sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single-cell transcriptome atlas encompasses transcriptional profiles from 44,102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single-cell resolution. Furthermore, we highlight the power of this analysis to assign new cell-type or developmental stage-specific expression information to many genes, including those that are currently known only by sequence and/or that lack expression information altogether. The resulting atlas is a resource for biologists to generate hypotheses for functional analysis, which we hope integrates with existing efforts to define the diversity of cell-types during zebrafish organogenesis, and to examine the transcriptional profiles that produce each cell type over developmental time.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping