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 together, we constructed a much-improved gene
model set (26,500 genes, 41,000 transcripts), identified 150,000 potential cis-regulatory elements,
and measured their activities during embryogenesis. To facilitate the use of these datasets, three tools
have been implemented. For detailed information, please see the notes below.
- Each tool can be opened in a new window by clicking the icon.
Genome Browser (JBrowse):
- By default, five tracks are shown:
- Ensembl gene models
- IGDB gene models (constructed in this study)
- RNA-seq coverage (combined all RNA-seq data in this study)
- ATAC-seq coverage (combined all ATAC-seq data in this study)
- ATAC-seq peaks
- Click the track selector, you can search for various data tracks by categories, samples (embryo
stages, adult tissues), PIs, sources (published papers), targets (mRNA, accessibility, histone
modifications etc), and technologies (RNA-seq, ATAC-seq, Histone ChIP-seq etc).
- Click the track name, you can change many settings (display mode, height, colors, detailed configs)
of the track.
- You can zoom in, zoom out, and move the view.
- You can search for a gene by it's name or IGDB ID, or locate a region by coordinates.
- You can click 'Share' to get the link of the current view, to share with others or open a new
Gene Viewer (Shiny)
- This tool contains all gene models in the IGDB set, including their sequences and corresponding Ensembl
gene ID, name, GO annotation, Interpro protein domain annotation, and TF family, and their orthologs in
human, mouse, zebrafish and fly. You can search by all these terms for genes. For example, if you are
interested in a human gene, then you can easily found its orthologs in medaka and many pieces of related
information by this tool.
- The result pages contains many links to other tools and databases: IGDB IDs link to JBrowse, Ensembl IDs
link to Ensembl pages of the given genes, TF families link to AnimalTFDB pages of the given TF families,
Interpro IDs link to corresponding pages in Interpro database.
- The essential function of this tool is to query and visualize the quantification data of gene
expression. You can obtain TPM, percent, or z-scores of expression data for any gene of interest, and
visualize them using heatmaps or line plots. We also incorporated time course datasets from Nat Commun
2017 and Nature 2018.
Sequence Search (BLAST)
- You can search for medaka sequences by BLAST. Currently we have three BLAST DBs: genome, Ensembl cDNA,
IGDB cDNA. In addition, there also some reference proteomes DBs for searching orthologs.
- In the result page, you can read BLAST reports, get various diagrams, and download fasta sequences or
alignments of hits.
- If you BLASTed the genome database, there will be a JBrowse link to show the hits on the genome.
- If you run the BLAST in a separated window, you can obtain the ID of the result to read later or share
with other people.
- 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.
We alao incorporated multiple published sets from other labs as well, including:
- Uesaka M, Kuratani S, Takeda H, Irie N. 2019. Recapitulation-like developmental transitions
chromatin accessibility in vertebrates. Zoological Lett 5: 33.
- Marlétaz F, Firbas PN, Maeso I, Tena JJ, Bogdanovic O, Perry M, Wyatt CDR, de la Calle-Mustienes E,
S, Burguera D, et al. 2018. Amphioxus functional genomics and the origins of vertebrate gene
regulation. Nature 564: 64–70.
- Ichikawa K, Tomioka S, Suzuki Y, Nakamura R, Doi K, Yoshimura J, Kumagai M, Inoue Y, Uchida Y, Irie
al. 2017. Centromere evolution and CpG methylation during vertebrate speciation. Nat
- Tena JJ, González-Aguilera C, Fernández-Miñán A, Vázquez-Marín J, Parra-Acero H, Cross JW, Rigby
Carvajal JJ, Wittbrodt J, Gómez-Skarmeta JL, et al. 2014. Comparative epigenomics in
related teleost species identifies conserved cis-regulatory nodes active during the vertebrate
period. Genome Res 24:1075–1085.
- Nakamura R, Tsukahara T, Qu W, Ichikawa K, Otsuka T, Ogoshi K, Saito TL, Matsushima K, Sugano S,
S, et al. 2014. Large hypomethylated domains serve as strong repressive machinery for key
developmental genes in vertebrates. Development 141: 2568–2580.