PUBLICATION

A high-resolution mRNA expression time course of embryonic development in zebrafish

Authors
White, R.J., Collins, J.E., Sealy, I.M., Wali, N., Dooley, C.M., Digby, Z., Stemple, D.L., Murphy, D.N., Billis, K., Hourlier, T., Füllgrabe, A., Davis, M.P., Enright, A.J., Busch-Nentwich, E.M.
ID
ZDB-PUB-171117-18
Date
2017
Source
eLIFE   6: (Journal)
Registered Authors
Busch-Nentwich, Elisabeth, Dooley, Christopher, Stemple, Derek L.
Keywords
RNA-seq, developmental biology, embryogenesis, evolutionary biology, genomics, stem cells, transcriptome, zebrafish
MeSH Terms
  • Animals
  • Embryonic Development*
  • Gene Expression Profiling
  • Gene Expression Regulation, Developmental*
  • RNA, Messenger/biosynthesis*
  • Sequence Analysis, RNA
  • Time Factors
  • Zebrafish/embryology*
PubMed
29144233 Full text @ Elife
Abstract
We have produced an mRNA expression time course of zebrafish development across 18 time points from 1 cell to 5 days post-fertilisation sampling individual and pools of embryos. Using poly(A) pulldown stranded RNA-seq and a 3' end transcript counting method we characterise temporal expression profiles of 23,642 genes. We identify temporal and functional transcript co-variance that associates 5024 unnamed genes with distinct developmental time points. Specifically, a class of over 100 previously uncharacterised zinc finger domain containing genes, located on the long arm of chromosome 4, is expressed in a sharp peak during zygotic genome activation. In addition, the data reveal new genes and transcripts, differential use of exons and previously unidentified 3' ends across development, new primary microRNAs and temporal divergence of gene paralogues generated in the teleost genome duplication. To make this dataset a useful baseline reference, the data can be browsed and downloaded at Expression Atlas and Ensembl.
Genes / Markers
Figures
Figure Gallery
Expression
Phenotype
Mutation and Transgenics
Human Disease / Model Data
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping
Errata and Notes