Dynamic transcriptional and chromatin accessibility landscape of medaka embryogenesis

Website:

• http://tulab.genetics.ac.cn/medaka_omics/

Download:

• GSE136018 in GEO
• IGDB ID - Ensembl ID mapping table
• BSgenome package for the medaka genome

Citation:

• Li Y, Liu Y, Yang H, Zhang T, Naruse K, Tu Q. 2020. Dynamic transcriptional and chromatin accessibility landscape of medaka embryogenesis. Genome Res 30: 924–937. [DOI]

Here we report a dynamic transcriptome landscape of medaka embryogenesis profiled by long-read RNA-seq, short-read RNA-seq, and ATAC-seq. Integrating these datasets, we constructed a much-improved gene model set including about 17,000 novel isoforms and identified 1600 transcription factors, 1100 long non-coding RNAs, and 150,000 potential cis-regulatory elements as well. We built a user-friend medaka omics data portal to present these datasets. This resource provides the first comprehensive omics datasets of medaka embryogenesis. We term these three assays as the minimum ENCODE toolbox and propose the use of it as the initial and essential profiling genomic assays for model organisms that have limited data available. This work will be of great value for the research community using medaka as the model organism and many others as well.