Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database.

Xenbase is the Xenopus model organism database ( www.xenbase.org ), a web-accessible resource that integrates the diverse genomic and biological data for Xenopus research. It hosts a variety of content including current and archived genomes for both X. laevis and X. tropicalis, bioinformatic tools for comparative genetic analyses including BLAST and GBrowse, annotated Xenopus literature, and catalogs of reagents including antibodies, ORFeome clones, morpholinos, and transgenic lines. Xenbase compiles gene-specific pages which include manually curated gene expression images, functional information including gene ontology (GO), disease associations, and links to other major data sources such as NCBI:Entrez, UniProtKB, and Ensembl. We also maintain the Xenopus Anatomy Ontology (XAO) which describes anatomy throughout embryonic development. This chapter provides a full description of the many features of Xenbase, and offers a guide on how to use various tools to perform a variety of common tasks such as identifying nucleic acid or protein sequences, finding gene expression patterns for specific genes, stages or tissues, identifying literature on a specific gene or tissue, locating useful reagents and downloading our extensive content, including Xenopus gene-Human gene disease mapping files.

[1]  J. Faber,et al.  Normal table of Xenopus laevis (Daudin). A systematical and chronological survey of the development from the fertilized egg till the end of metamorphosis. , 1956 .

[2]  T. Elsdale,et al.  Sexually Mature Individuals of Xenopus laevis from the Transplantation of Single Somatic Nuclei , 1958, Nature.

[3]  J. Gurdon.  The developmental capacity of nuclei taken from differentiating endoderm cells of Xenopus laevis. , 1960, Journal of embryology and experimental morphology.

[4]  S. Moody.  Fates of the blastomeres of the 32-cell-stage Xenopus embryo. , 1987, Developmental biology.

[5]  S. Moody,et al.  Fates of the blastomeres of the 16-cell stage Xenopus embryo. , 1987, Developmental biology.

[6]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[7]  S. Moody,et al.  The cleavage stage origin of Spemann's Organizer: analysis of the movements of blastomere clones before and during gastrulation in Xenopus. , 1994, Development.

[8]  S. Ekker,et al.  Effective targeted gene ‘knockdown’ in zebrafish , 2000, Nature Genetics.

[9]  C. Wylie,et al.  Beta-catenin signaling activity dissected in the early Xenopus embryo: a novel antisense approach. , 2000, Developmental biology.

[10]  S. Nutt,et al.  Comparison of morpholino based translational inhibition during the development of Xenopus laevis and Xenopus tropicalis , 2001, Genesis.

[11]  Nancy Papalopulu,et al.  Techniques and probes for the study of Xenopus tropicalis development , 2002, Developmental dynamics : an official publication of the American Association of Anatomists.

[12]  Michael J Gilchrist,et al.  Defining Synphenotype Groups in Xenopus tropicalis by Use of Antisense Morpholino Oligonucleotides , 2006, PLoS genetics.

[13]  Erik Segerdell,et al.  An ontology for Xenopus anatomy and development , 2008, BMC Developmental Biology.

[14]  D. Raciti,et al.  Organization of the pronephric kidney revealed by large-scale gene expression mapping , 2008, Genome Biology.

[15]  Erik Segerdell,et al.  Xenbase: a Xenopus biology and genomics resource , 2007, Nucleic Acids Res..

[16]  L. Stein,et al.  JBrowse: a next-generation genome browser. , 2009, Genome research.

[17]  Michael J Gilchrist,et al.  Abundant and dynamically expressed miRNAs, piRNAs, and other small RNAs in the vertebrate Xenopus tropicalis. , 2009, Genome research.

[18]  Russell B. Fletcher,et al.  The Genome of the Western Clawed Frog Xenopus tropicalis , 2010, Science.

[19]  Leonid Peshkin,et al.  Mapping gene expression in two Xenopus species: evolutionary constraints and developmental flexibility. , 2011, Developmental cell.

[20]  N. Pollet,et al.  Databases of gene expression in Xenopus development. , 2012, Methods in molecular biology.

[21]  K. Parain,et al.  A large scale screen for neural stem cell markers in Xenopus retina , 2012, Developmental neurobiology.

[22]  J. Zuo,et al.  VEGFA-dependent and -independent pathways synergise to drive Scl expression and initiate programming of the blood stem cell lineage in Xenopus , 2013, Development.

[23]  Erik Segerdell,et al.  Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase , 2013, J. Biomed. Semant..

[24]  Xiaohui Xie,et al.  Biallelic genome modification in F0 Xenopus tropicalis embryos using the CRISPR/Cas system , 2013, Genesis.

[25]  Anushya Muruganujan,et al.  Large-scale gene function analysis with the PANTHER classification system , 2013, Nature Protocols.

[26]  Ting Wang,et al.  Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser , 2013, Bioinform..

[27]  Kamran Karimi,et al.  The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud , 2014, Database J. Biol. Databases Curation.

[29]  Maura Lane,et al.  CRISPR/Cas9: An inexpensive, efficient loss of function tool to screen human disease genes in Xenopus. , 2015, Developmental biology.

[30]  M. Schmid,et al.  A New Nomenclature of Xenopus laevis Chromosomes Based on the Phylogenetic Relationship to Silurana/Xenopus tropicalis , 2015, Cytogenetic and Genome Research.

[31]  Yun Shen,et al.  The Xenopus ORFeome: A resource that enables functional genomics , 2015, Developmental biology.

[32]  G. Wheeler,et al.  A Database of microRNA Expression Patterns in Xenopus laevis , 2015, PloS one.

[33]  O. Kretz,et al.  Direct reprogramming of fibroblasts into renal tubular epithelial cells by defined transcription factors , 2016, Nature Cell Biology.

[34]  Kevin A. Burns,et al.  Genome evolution in the allotetraploid frog Xenopus laevis , 2016, Nature.

[35]  Ken W. Y. Cho,et al.  Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development. , 2016, Cell reports.

[36]  S. Moody,et al.  Using Xenopus to understand human disease and developmental disorders , 2017, Genesis.

[37]  Cynthia L. Smith,et al.  Naming CRISPR alleles: endonuclease-mediated mutation nomenclature across species , 2017, Mammalian Genome.

[38]  M. Levin,et al.  The Zahn drawings: new illustrations of Xenopus embryo and tadpole stages for studies of craniofacial development , 2017, Development.