XB-ART-52009Dev Biol. June 15, 2017; 426 (2): 194-199.
Xenopus genomic data and browser resources.
The two species of Xenopus most commonly used in biomedical research are the diploid Xenopus (Silurana) tropicalis and the tetraploid Xenopus laevis. The X. tropicalis genome sequence has been available since 2010 and this year the X. laevis, genome from two distinct genetic backgrounds has been published. Multiple genome assemblies available for both species and transcriptomic and epigenetic data sets are growing rapidly, all of which are available from a variety of web resources. This review describes the contents of these resources, how to locate and download genomic data, and also how to view and manipulate these data on various public genome browsers, with an emphasis on Xenbase, the Xenopus model organism database.
PubMed ID: 27039265
PMC ID: PMC5045824
Article link: Dev Biol.
Grant support: P41 HD064556 NICHD NIH HHS , R01 HD045776 NICHD NIH HHS , P41 HD064556 NICHD NIH HHS , R01 HD045776 NICHD NIH HHS , R01 HD045776 NICHD NIH HHS , P41 HD064556 NICHD NIH HHS
Genes referenced: crebbp gnao1
Article Images: [+] show captions
|Fig. 1. Xenbase GBrowse with NGS data. A. The default view of the cox18 gene in Xenbase, with multiple NGS tracks displayed in a stacked format using a tool called Topoview, developed by FlyBase (http://flybase.org/static_pages/docs/software/topoview.html). Note the large histone H3 lysine 4 methylation (H3K4me1) peak at stage 9 over the transcription start site for this gene. To view additional/alternative tracks, select the “Select Tracks” tab circled in red. B. The Select Tracks view offers an enormous number of supporting NGS data including histone methylation and acetylation, p300 and RNA polymerase binding sites and RNA-seq data. As noted in the text, the content currently varies with the genome build, so exploring other genome versions is worthwhile. To go back to the browser view click on the “Browser” tab on the top left or the “Back to Browser” button at the bottom of the page.|