PT  - JOURNAL ARTICLE
AU  - Richard J. White
AU  - John E. Collins
AU  - Ian M. Sealy
AU  - Neha Wali
AU  - Christopher M. Dooley
AU  - Zsofia Digby
AU  - Derek L. Stemple
AU  - Daniel N. Murphy
AU  - Thibaut Hourlier
AU  - Anja Füllgrabe
AU  - Matthew P. Davis
AU  - Anton J. Enright
AU  - Elisabeth M. Busch-Nentwich
TI  - A high-resolution mRNA expression time course of embryonic development in zebrafish
AID  - 10.1101/107631
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 107631
4099  - http://biorxiv.org/content/early/2017/02/20/107631.short
4100  - http://biorxiv.org/content/early/2017/02/20/107631.full
AB  - 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 the temporal expression profiles of 23,642 genes. We identify temporal and functional transcript co-variance that associates 5,024 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. The data reveal complex and widespread differential use of exons and previously unidentified 3′ ends across development, new primary microRNA transcripts and temporal divergence of gene paralogues generated in the teleost genome duplication. To make this dataset a useful baseline reference, the data are accessible to browse and download at Expression Atlas and Ensembl.