Xenopus Genomic Data and Browser Resources

Overview

Journal Dev Biol

Publisher Elsevier

Specialties Biology
Reproductive Medicine

Date 2016 Apr 4

PMID 27039265

Citations 7

Authors

Peter D Vize

Aaron M Zorn

Affiliations

Soon will be listed here.

Abstract

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.

Citing Articles

Methods for Tattooing Xenopus laevis with a Rotary Tattoo Machine.

Suber J, Landino J J Vis Exp. 2024; (208).

PMID: 39007614 PMC: 11292787. DOI: 10.3791/67086.

Transcriptomic Analysis Identifies Candidate Genes for Differential Expression during Inner Ear Development.

Virk S, Trujillo-Provencio C, Serrano E bioRxiv. 2024; .

PMID: 38260420 PMC: 10802236. DOI: 10.1101/2023.12.29.573599.

Developmental and Injury-induced Changes in DNA Methylation in Regenerative versus Non-regenerative Regions of the Vertebrate Central Nervous System.

Reverdatto S, Prasad A, Belrose J, Zhang X, Sammons M, Gibbs K BMC Genomics. 2022; 23(1):2.

PMID: 34979916 PMC: 8725369. DOI: 10.1186/s12864-021-08247-0.

The DNA-to-cytoplasm ratio broadly activates zygotic gene expression in Xenopus.

Jukam D, Kapoor R, Straight A, Skotheim J Curr Biol. 2021; 31(19):4269-4281.e8.

PMID: 34388374 PMC: 8511243. DOI: 10.1016/j.cub.2021.07.035.

Axial Skeletal Malformations in Genetically Modified and .

Zlatow A, Wilson S, Bouley D, Tetens-Woodring J, Buchholz D, Green S Comp Med. 2020; 70(6):532-541.

PMID: 33203505 PMC: 7754201. DOI: 10.30802/AALAS-CM-20-000069.

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