Wellcome Trust Sanger Institute, Hinxton, United Kingdom.
European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom.
Elife. 2017 Nov 16;6:e30860. doi: 10.7554/eLife.30860.
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.
我们生成了斑马鱼从单细胞到受精后 5 天的 18 个时间点的 mRNA 表达时间历程，对单个和多个胚胎进行了取样。使用 poly(A) 下拉 RNA-seq 和 3' 端转录本计数方法，我们描绘了 23642 个基因的时空表达谱。我们发现了时空和功能转录共变，将 5024 个未命名基因与特定的发育时间点相关联。具体来说，一类位于 4 号染色体长臂上的、以前未被描述的含有锌指结构域的基因，在合子基因组激活过程中呈现出一个明显的高峰表达。此外，该数据揭示了新的基因和转录本，在发育过程中不同的外显子使用和以前未识别的 3' 末端，新的初级 microRNA，以及在硬骨鱼基因组复制中产生的基因旁系同源物的时间分化。为了使这个数据集成为一个有用的基线参考，数据可以在 Expression Atlas 和 Ensembl 上进行浏览和下载。
