Xenopus genomic data and browser resources

Developmental Biology

Volumn 426, Issue 2, 2017, Pages 194-199

  Vize, Peter D ^a   Zorn, Aaron M ^b  

^a UNIVERSITY OF CALGARY   (Canada)

^b CINCINNATI CHILDREN S HOSPITAL RESEARCH FOUNDATION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

DNA SEQUENCE; GENE MAPPING; GENE NOMENCLATURE; GENETIC DATABASE; GENETIC RESOURCE; GENOMICS; INFORMATION SYSTEM; NEXT GENERATION SEQUENCING; NONHUMAN; PRIORITY JOURNAL; REVIEW; SEQUENCE ANALYSIS; WEB BROWSER; XENBASE; XENOPUS LAEVIS; XENOPUS TROPICALIS; ANIMAL; GENE EXPRESSION; GENETICS; GENOME; MICROCOMPUTER; NOMENCLATURE; PROCEDURES; XENOPUS;

ANIMALS; DATABASES, GENETIC; GENE EXPRESSION; GENOME; GENOMICS; MICROCOMPUTERS; TERMINOLOGY AS TOPIC; WEB BROWSER; XENOPUS; XENOPUS LAEVIS;

EID: 84962456170     PISSN: 00121606     EISSN: 1095564X     Source Type: Journal    
DOI: 10.1016/j.ydbio.2016.03.030     Document Type: Review

References (21)

1. Bogdanovic, O., Fernandez-Minan, A., Tena, J.J., de la Calle-Mustienes, E., Hidalgo, C., van Kruysbergen, I., van Heeringen, S.J., Veenstra, G.J., Gomez-Skarmeta, J.L., Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis. Genome Res. 22 (2012), 2043–2053.
2. Bowes, J.B., Snyder, K.A., Segerdell, E., Gibb, R., Jarabek, C., Noumen, E., Pollet, N., Vize, P.D., Xenbase: a Xenopus biology and genomics resource. Nucleic Acids Res. 36 (2008), D761–D776.
3. Collart, C., Owens, N.D., Bhaw-Rosun, L., Cooper, B., De Domenico, E., Patrushev, I., Sesay, A.K., Smith, J.N., Smith, J.C., Gilchrist, M.J., High-resolution analysis of gene activity during the Xenopus mid-blastula transition. Development 141 (2014), 1927–1939.
4. Giardine, B., Riemer, C., Hardison, R.C., Burhans, R., Elnitski, L., Shah, P., Zhang, Y., Blankenberg, D., Albert, I., Taylor, J., Miller, W., Kent, W.J., Nekrutenko, A., Galaxy: a platform for interactive large-scale genome. Genome Res. 15 (2005), 1451–1455.
5. Grainger, R.M., Xenopus tropicalis as a model organism for genetics and genomics: past, present, and future. Methods Mol. Biol. 917 (2012), 3–15.
6. Hellsten, U., Khokha, M.K., Grammer, T.C., Harland, R.M., Richardson, P., Rokhsar, D.S., Accelerated gene evolution and subfractionalization in the pseudotetraploid frog Xenopus laevis. BMC Biol., 5, 2007, 31.
7. Hellsten, U., Harland, R.M., Gilchrist, M.J., Hendrix, D., Jurka, J., Kapitonov, V., Ovcharenko, I., Putnam, N.H., Shu, S., Taher, L., Blitz, I.L., Blumberg, B., Dichmann, D.S., Dubchak, I., Amaya, E., Detter, J.C., Fletcher, R., Gerhard, D.S., Goodstein, D., Graves, T., Grigoriev, I.V., Grimwood, J., Kawashima, T., Lindquist, E., Lucas, S.M., Mead, P.E., Mitros, T., Ogino, H., Ohta, Y., Poliakov, A.V., Pollet, N., Robert, J., Salamov, A., Sater, A.K., Schmutz, J., Terry, A., Vize, P.D., Warren, W.C., Wells, D., Wills, A., Wilson, R.K., Zimmerman, L.B., Zorn, A.M., Grainger, R., Grammer, T., Khokha, M.K., Richardson, P.M., Rokhsar, D.S., The genome of the Western Clawed Frog Xenopus tropicalis. Science 328 (2010), 633–636.
8. Izutsu, Y., Maeno, M., Analyses of immune responses to ontogeny-specific antigens using an inbred strain of Xenopus laevis (J Strain). Methods Mol. Med. 105 (2005), 149–158.
9. James-Zorn, C., Ponferrada, V.G., Burns, K.A., Fortriede, J.D., Lotay, V.S., Liu, Y., Karpinka, J.B., Karimi, K., Zorn, A.M., Vize, P.D., Xenbase: core features, data acquisition, and data processing. Genesis 53 (2015), 486–497.
10. Karolchik, D., Baertsch, R., Diekhans, M., Furey, T.S., Hinrichs, A., Lu, Y.T., Roskin, K.M., Schwartz, M., Sugnet, C.W., Thomas, D.J., Weber, R.J., Haussler, D., Kent, W.J., University of California Santa Cruz, The UCSC Genome browser database. Nucleic Acids Res. 31 (2003), 51–54.
11. Karpinka, J.B., Fortriede, J.D., Burns, K.A., James-Zorn, C., Ponferrada, V.G., Lee, J., Karimi, K., Zorn, A.M., Vize, P.D., Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes. Nucleic Acids Res. 43 (2015), D756–D763.
12. Matsuda, Y., Uno, Y., Kondo, M., Gilchrist, M.J., Zorn, A.M., Rokhsar, D.S., Schmid, M., Taira, M., A new nomenclature of Xenopus laevis chromosomes based on the phylogenetic relationship to Silurana/Xenopus tropicalis. Cytogenet. Genome Res. 145 (2015), 187–191.
13. Owens, N.D., Blitz, I.L., Lane, M.A., Patrushev, I., Overton, J.D., Gilchrist, M.J., Cho, K.W., Khokha., M.K., Measuring absolute RNA copy numbers at high temporal resolution reveals transcriptome kinetics in development. Cell Rep. 14 (2016), 632–647.
14. Peshkin, L., Wühr, M., Pearl, E., Haas, W., Freeman, R.M., Gerhart, J.C., Klein, A.M., Horb, M., Gygi, S.P., Kirschner, M.W., On the relationship of protein and mRNA dynamics in vertebrate embryonic development. Dev. Cell 35 (2015), 383–394.
15. Session, A.M., Uno, Y., Kwon, T., Chapman, J.A., Toyoda, A., Takahashi, S., Fukui, A., Hikosaka, A., Suzuki, A., Kondo, M., van Heeringen, S.J., Quigley, I., Heinz, S., Ogino, H., Ochi, H., Hellsten, U., Lyons, J.B., Simakov, O., Putnam, N., Stites, J., Kuroki, Y., Tanaka, T., Michiue, T., Watanabe, M., Bogdanovic, O., Lister, R., Georgiou, G., Paranjpe, S.S., van Kruijsbergen, I., Shu, S., Carlson, J., Kinoshita, T., Ohta, Y., Mawaribuchi, S., Jenkins, J., Grimwood, J., Schmutz, J., Mitros, T., Mozaffari, S.V., Suzuki, Y., Haramoto, Y., Yamamoto, T.S., Takagi, C., Heald, R., Miller, K., Haudenschild, C., Kitzman, J., Nakayama, T., Izutsu, Y., Robert, J., Fortriede, J., Burns, K., Lotay, V., Karimi, K., Yasuoka, Y., Dichmann, D.S., Flajnik, M.F., Houston, D.W., Shendure, J., DuPasquier, L., Vize, P.D., Zorn, A.M., Ito, M., Marcotte, E.M., Wallingford, J.B., Ito, Y., Asashima, M., Ueno, N., Matsuda, Y., Veenstra, G.J., Fujiyama, A., Harland, R.M., Taira, M., Rokhsar, D.S., 2016. Genome evolution in the allotetraploid frog Xenopus laevis. Nature 538, 336-343.PMID:27762356 PMCID:PMC5313049.
16. Stein, L.D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J.E., Harris, T.W., Arva, A., Lewis, S., The generic genome browser: a building block for a model organism system database. Genome Res. 12 (2002), 1599–1610.
17. Tan, M.H., Au, K.F., Yablonovitch, A.L., Wills, A.E., Chuang, J., Baker, J.C., Wong, W.H., Li, J.B., RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. Genome Res. 23 (2013), 201–216.
18. Thorvaldsdóttir, H., Robinson, J.T., Mesirov, J.P., Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief. Bioinform. 14 (2013), 178–192.
19. van Heeringen, S.J., Akkers, R.C., van Kruijsbergen, I., Arif, M.A., Hanssen, L.L., Sharifi, N., Veenstra, G.J., Principles of nucleation of H3K27 methylation during embryonic development. Genome Res. 24 (2014), 401–410.
20. Vize, P.D., Liu, Y., Karimi, K., Database and informati challenges in representing both diploid and tetraploid Xenopus species in Xenbase. Cytogenet. Genome Res. 145 (2015), 278–282.
21. Westesson, O., Skinner, M., Holmes, I., Visualizing next-generation sequencing data with JBrowse. Brief. Bioinform. 14 (2013), 172–177.