Literature DB >> 27039265

Xenopus genomic data and browser resources.

Peter D Vize1, Aaron M Zorn2.   

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.
Copyright © 2016 Elsevier Inc. All rights reserved.

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Year:  2016        PMID: 27039265      PMCID: PMC5045824          DOI: 10.1016/j.ydbio.2016.03.030

Source DB:  PubMed          Journal:  Dev Biol        ISSN: 0012-1606            Impact factor:   3.582


  20 in total

1.  The UCSC Genome Browser Database.

Authors:  D Karolchik; R Baertsch; M Diekhans; T S Furey; A Hinrichs; Y T Lu; K M Roskin; M Schwartz; C W Sugnet; D J Thomas; R J Weber; D Haussler; W J Kent
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

2.  The generic genome browser: a building block for a model organism system database.

Authors:  Lincoln D Stein; Christopher Mungall; ShengQiang Shu; Michael Caudy; Marco Mangone; Allen Day; Elizabeth Nickerson; Jason E Stajich; Todd W Harris; Adrian Arva; Suzanna Lewis
Journal:  Genome Res       Date:  2002-10       Impact factor: 9.043

3.  Visualizing next-generation sequencing data with JBrowse.

Authors:  Oscar Westesson; Mitchell Skinner; Ian Holmes
Journal:  Brief Bioinform       Date:  2012-03-12       Impact factor: 11.622

4.  A New Nomenclature of Xenopus laevis Chromosomes Based on the Phylogenetic Relationship to Silurana/Xenopus tropicalis.

Authors:  Yoichi Matsuda; Yoshinobu Uno; Mariko Kondo; Michael J Gilchrist; Aaron M Zorn; Daniel S Rokhsar; Michael Schmid; Masanori Taira
Journal:  Cytogenet Genome Res       Date:  2015-04-08       Impact factor: 1.636

5.  Database and Informatic Challenges in Representing Both Diploid and Tetraploid Xenopus Species in Xenbase.

Authors:  Peter D Vize; Yu Liu; Kamran Karimi
Journal:  Cytogenet Genome Res       Date:  2015-05-27       Impact factor: 1.636

6.  High-resolution analysis of gene activity during the Xenopus mid-blastula transition.

Authors:  Clara Collart; Nick D L Owens; Leena Bhaw-Rosun; Brook Cooper; Elena De Domenico; Ilya Patrushev; Abdul K Sesay; James N Smith; James C Smith; Michael J Gilchrist
Journal:  Development       Date:  2014-05       Impact factor: 6.868

7.  Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development.

Authors:  Nick D L Owens; Ira L Blitz; Maura A Lane; Ilya Patrushev; John D Overton; Michael J Gilchrist; Ken W Y Cho; Mustafa K Khokha
Journal:  Cell Rep       Date:  2016-01-07       Impact factor: 9.423

8.  Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis.

Authors:  Ozren Bogdanovic; Ana Fernandez-Miñán; Juan J Tena; Elisa de la Calle-Mustienes; Carmen Hidalgo; Ila van Kruysbergen; Simon J van Heeringen; Gert Jan C Veenstra; José Luis Gómez-Skarmeta
Journal:  Genome Res       Date:  2012-05-16       Impact factor: 9.043

9.  Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.

Authors:  Helga Thorvaldsdóttir; James T Robinson; Jill P Mesirov
Journal:  Brief Bioinform       Date:  2012-04-19       Impact factor: 11.622

10.  Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes.

Authors:  J Brad Karpinka; Joshua D Fortriede; Kevin A Burns; Christina James-Zorn; Virgilio G Ponferrada; Jacqueline Lee; Kamran Karimi; Aaron M Zorn; Peter D Vize
Journal:  Nucleic Acids Res       Date:  2014-10-13       Impact factor: 16.971

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  5 in total

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

Authors:  David Jukam; Rishabh R Kapoor; Aaron F Straight; Jan M Skotheim
Journal:  Curr Biol       Date:  2021-08-12       Impact factor: 10.900

2.  Axial Skeletal Malformations in Genetically Modified Xenopus laevis and Xenopus tropicalis.

Authors:  Anne L Zlatow; Sabrina S Wilson; Donna M Bouley; Joanne Tetens-Woodring; Daniel R Buchholz; Sherril L Green
Journal:  Comp Med       Date:  2020-11-17       Impact factor: 0.982

3.  Pa2G4 is a novel Six1 co-factor that is required for neural crest and otic development.

Authors:  Karen M Neilson; Genevieve Abbruzzesse; Kristy Kenyon; Vanessa Bartolo; Patrick Krohn; Dominique Alfandari; Sally A Moody
Journal:  Dev Biol       Date:  2016-12-09       Impact factor: 3.582

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

Authors:  Sergei Reverdatto; Aparna Prasad; Jamie L Belrose; Xiang Zhang; Morgan A Sammons; Kurt M Gibbs; Ben G Szaro
Journal:  BMC Genomics       Date:  2022-01-04       Impact factor: 3.969

5.  Xenbase: a genomic, epigenomic and transcriptomic model organism database.

Authors:  Kamran Karimi; Joshua D Fortriede; Vaneet S Lotay; Kevin A Burns; Dong Zhou Wang; Malcom E Fisher; Troy J Pells; Christina James-Zorn; Ying Wang; V G Ponferrada; Stanley Chu; Praneet Chaturvedi; Aaron M Zorn; Peter D Vize
Journal:  Nucleic Acids Res       Date:  2018-01-04       Impact factor: 16.971

  5 in total

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