[Xenopus] Xenbase Fall 2014 Newsletter

[xenbase]

Xenbase Fall 2014 Newsletter

Highlights of the new Xenbase v3.3

Morpholinos have launched on Xenbase!!  Morpholino antisense oligos (MOs) are widely used in Xenopus to suppress gene function. Xenbase has introduced a comprehensive catalog of ~1585 published MOs so researchers can quickly identify effective Xenopus specific reagents.

Access the new MO database from Xenbase menus and front page

MOs are mapped to genome and can be viewed on GBrowse

Search MOs via gene symbol, sequence or name used in the publication

Each MO has a dedicated page, showing its alignment to genome (see e.g. Nodal5.2 MO2)

Target/Off Target hits illustrated

MOs are listed as reagents at bottom on gene page

MOs used in publications are listed on article’s Xenbase page.

New MOs will be added as articles are published and curated.



Genome Builds & Gene Models: Latest Updates from JGI & Adam Sessions (Rokhsar Group)

X. laevis v7.2 annotation/gene model is now shown on the v7.1 genome build on GBrowse

X. laevis L and S (long and short) genomes now on GBrowse

We are working on reconciling X. laevis L & S alleles on gene pages

X. tropicalis genome build v8.0 has more gene names assigned on GBrowse

GBrowse snapshots are bigger and crisper on gene pages

 Human Disease Associations:

Single-gene disease associations are now on ~14,600 gene pages, facilitating direct comparison of information from Xenopus genes with their human orthologs (e.g. tgfb1). Diseases can be searched using OMIM ID from the main search menu.

 HomoloGene:

New HomoloGene link is on ‘Genes’ tile of the Xenbase front page. This link goes directly to a Xenopus search of this NCBI resource that helps construct putative homology groups from the complete gene sets of a wide range of eukaryotic species.

Transgenes Naming Guidelines:

Xenbase has drafted the ‘Xenopus Transgenic Nomenclature Guidelines’ in consultation with the NXR, EXRC and NBRP, and gene nomenclature committee. These guidelines are based on the well-established rules for zebrafish and mouse, with the goal of increasing experimental reproducibility and data clarity cross model organisms. Authors are strongly encouraged to follow the guidelines when naming transgenes or mutant or transgenic Xenopus lines. Contact  Xenbase (xenbase at ucalgary.ca) with comments/questions and for help naming your constructs. See http://www.xenbase.org/gene/static/tgNomenclature.jsp

 Coming Soon: Xenbase Forums

A discussion forum/community bulletin board to discuss and ask advice on all aspects of Xenopus research (e.g., experimental design & data analysis for ChipSeq, RNASeq, Morpholinos, ISH, genes etc.).

More details of the recent updates to Xenbase are detailed in Karpinka et al (2014). Xenbase, the Xenopus Model Organism Database; new virtualized system, data types and genomes. Nucl. Acids Res. first published online October 13, 2014 doi:10.1093/nar/gku956

http://nar.oxfordjournals.org/content/early/2014/10/13/nar.gku956.full?sid=e82f949b-5e2a-4933-ab1e-d39051c74116

Image or Data Submissions? Questions or Comments? Contact us at xenbase at ucalgary.ca





http://www.xenbase.org

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