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Nucleic Acids Res
2015 Jan 01;43Database issue:D756-63. doi: 10.1093/nar/gku956.
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Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes.
Karpinka JB
,
Fortriede JD
,
Burns KA
,
James-Zorn C
,
Ponferrada VG
,
Lee J
,
Karimi K
,
Zorn AM
,
Vize PD
.
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Xenbase (http://www.xenbase.org), the Xenopus frog model organism database, integrates a wide variety of data from this biomedical model genus. Two closely related species are represented: the allotetraploid Xenopus laevis that is widely used for microinjection and tissue explant-based protocols, and the diploid Xenopus tropicalis which is used for genetics and gene targeting. The two species are extremely similar and protocols, reagents and results from each species are often interchangeable. Xenbase imports, indexes, curates and manages data from both species; all of which are mapped via unique IDs and can be queried in either a species-specific or species agnostic manner. All our services have now migrated to a private cloud to achieve better performance and reliability. We have added new content, including providing full support for morpholino reagents, used to inhibit mRNA translation or splicing and binding to regulatory microRNAs. New genomes assembled by the JGI for both species and are displayed in Gbrowse and are also available for searches using BLAST. Researchers can easily navigate from genome content to gene page reports, literature, experimental reagents and many other features using hyperlinks. Xenbase has also greatly expanded image content for figures published in papers describing Xenopus research via PubMedCentral.
Figure 1.
The new Xenbase landing page. The large graphic depicting the Xenopus genomes is dynamic, and displays around 10 recent news stories or papers at any one time. Different Xenbase content is organized into tiles, making up the majority of the page. Across the top of the page are login tools, a search tool and a uniform navigation menu found on every Xenbase page. Down the right-hand side are links to many internal and external resources.
Figure 2.
The new morpholino support interface. We store data on over 1000 morpholino reagents, gathered from large-scale screens and the Xenopus literature. (A) Each morpholino sequence is aligned to the genome via BLAST and the results for both on-target and potential off-target matches displayed. Various other data, such as publications, utilizing the reagent are also illustrated. (B) Morpholino sequences are also available as a track in our GBrowse implementation. When a user clicks on a morpholino in the browser details on the alignment are displayed in a pop-up window.
Armisen,
Abundant and dynamically expressed miRNAs, piRNAs, and other small RNAs in the vertebrate Xenopus tropicalis.
2009, Pubmed,
Xenbase
Armisen,
Abundant and dynamically expressed miRNAs, piRNAs, and other small RNAs in the vertebrate Xenopus tropicalis.
2009,
Pubmed
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Xenbase
Bachy,
Defining pallial and subpallial divisions in the developing Xenopus forebrain.
2002,
Pubmed
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Xenbase
Blitz,
Biallelic genome modification in F(0) Xenopus tropicalis embryos using the CRISPR/Cas system.
2013,
Pubmed
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Xenbase
Bowes,
Xenbase: gene expression and improved integration.
2010,
Pubmed
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Xenbase
Ciau-Uitz,
Tel1/ETV6 specifies blood stem cells through the agency of VEGF signaling.
2010,
Pubmed
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Xenbase
Domínguez,
Characterization of the hypothalamus of Xenopus laevis during development. II. The basal regions.
2014,
Pubmed
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Xenbase
Dubaissi,
Embryonic frog epidermis: a model for the study of cell-cell interactions in the development of mucociliary disease.
2011,
Pubmed
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Xenbase
Guo,
Efficient RNA/Cas9-mediated genome editing in Xenopus tropicalis.
2014,
Pubmed
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Xenbase
Hagenlocher,
Ciliogenesis and cerebrospinal fluid flow in the developing Xenopus brain are regulated by foxj1.
2013,
Pubmed
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Xenbase
Heasman,
Morpholino oligos: making sense of antisense?
2002,
Pubmed
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Xenbase
Heasman,
Beta-catenin signaling activity dissected in the early Xenopus embryo: a novel antisense approach.
2000,
Pubmed
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Xenbase
James-Zorn,
Xenbase: expansion and updates of the Xenopus model organism database.
2013,
Pubmed
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Xenbase
Lee,
Cluap1 is essential for ciliogenesis and photoreceptor maintenance in the vertebrate eye.
2014,
Pubmed
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Xenbase
Lei,
Efficient targeted gene disruption in Xenopus embryos using engineered transcription activator-like effector nucleases (TALENs).
2012,
Pubmed
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Xenbase
Leung,
Uncoupling VEGFA functions in arteriogenesis and hematopoietic stem cell specification.
2013,
Pubmed
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Xenbase
Morona,
Embryonic genoarchitecture of the pretectum in Xenopus laevis: a conserved pattern in tetrapods.
2011,
Pubmed
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Xenbase
Müller,
Textpresso: an ontology-based information retrieval and extraction system for biological literature.
2004,
Pubmed
Nakayama,
Simple and efficient CRISPR/Cas9-mediated targeted mutagenesis in Xenopus tropicalis.
2013,
Pubmed
,
Xenbase
Parain,
A large scale screen for neural stem cell markers in Xenopus retina.
2012,
Pubmed
,
Xenbase
Pedrioli,
miR-31 functions as a negative regulator of lymphatic vascular lineage-specific differentiation in vitro and vascular development in vivo.
2010,
Pubmed
,
Xenbase
Segerdell,
Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase.
2013,
Pubmed
,
Xenbase
Tang,
Xenopus microRNA genes are predominantly located within introns and are differentially expressed in adult frog tissues via post-transcriptional regulation.
2008,
Pubmed
,
Xenbase
Walentek,
A novel serotonin-secreting cell type regulates ciliary motility in the mucociliary epidermis of Xenopus tadpoles.
2014,
Pubmed
,
Xenbase
