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<!--StartFragment--><p class="MsoNormal" align="center" style="text-align:center"><span style="font-size:14.0pt">Xenbase Fall 2014 Newsletter</span></p><p class="MsoNormal" align="center" style="text-align:center">Highlights of the new Xenbase v3.3</p><p class="MsoNormal"><a href="http://www.xenbase.org/reagents/morpholino.do"><span style="font-size:10.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:
"Times New Roman"">Morpholinos</span></a><span style="font-size:10.0pt"> have launched
on Xenbase!! </span><span style="font-size:10.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:
"Times New Roman";color:#252525;background:white">Morpholino antisense oligos</span><span style="font-size:10.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:
"Times New Roman""> (MOs) <span style="color:#252525;background:white">are
widely used in </span></span><i><span style="font-size: 10pt; border: 1pt none windowtext; padding: 0in; background-color: white; background-position: initial initial; background-repeat: initial initial; ">Xenopus</span></i><span style="font-size: 10pt; background-color: white; background-position: initial initial; background-repeat: initial initial; "> to suppress gene function</span><span style="font-size:10.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:
"Times New Roman";color:#252525;background:white">. Xenbase has introduced a comprehensive
</span><span style="font-size: 10pt; background-color: white; background-position: initial initial; background-repeat: initial initial; ">catalog of </span><span style="font-size:10.0pt">~1585 </span><span style="font-size: 10pt; background-color: white; background-position: initial initial; background-repeat: initial initial; ">published MOs so researchers can quickly identify effective </span><i><span style="font-size:10.0pt">Xenopus</span></i><span style="font-size:10.0pt"> specific reagents</span><span style="font-size:10.0pt;
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";
color:#252525;background:white">.</span><span style="font-size:10.0pt"><o:p></o:p></span></p><p class="MsoNormal" style="text-indent:.5in"><span style="font-size:10.0pt">Access
the new </span><a href="http://www.xenbase.org/reagents/morpholino.do"><span style="font-size:10.0pt">MO database</span></a><span style="font-size:10.0pt"> from
Xenbase menus and front page<o:p></o:p></span></p><p class="MsoNormal" style="text-indent:.5in"><span style="font-size:10.0pt">MOs are
mapped to genome and can be viewed on GBrowse<o:p></o:p></span></p><p class="MsoNormal" style="text-indent:.5in"><span style="font-size:10.0pt">Search
MOs via gene symbol, sequence or name used in the publication<o:p></o:p></span></p><p class="MsoNormal" style="text-indent:.5in"><span style="font-size:10.0pt">Each
MO has a dedicated page, showing its alignment to genome (see e.g. </span><a href="http://www.xenbase.org/reagents/displayMorpholino.do?featureId=17250012"><span style="font-size:10.0pt">Nodal5.2 MO2</span></a><span style="font-size:10.0pt">)<o:p></o:p></span></p><p class="MsoNormal" style="text-indent:.5in"><span style="font-size:10.0pt">Target/Off
Target hits illustrated<o:p></o:p></span></p><p class="MsoNormal" style="text-indent:.5in"><span style="font-size:10.0pt">MOs are
listed as reagents at bottom on gene page<o:p></o:p></span></p><p class="MsoNormal" style="text-indent:.5in"><span style="font-size:10.0pt">MOs used
in publications are listed on article’s Xenbase page.<o:p></o:p></span></p><p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt">New
MOs will be added as articles are published and curated. </span><span style="font-size:10.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:
"Times New Roman""><o:p></o:p></span></p><p class="MsoNormal"><br></p><p class="MsoNormal"><span style="font-size:10.0pt">Genome Builds & Gene
Models: Latest Updates from JGI & Adam Sessions (Rokhsar Group)<o:p></o:p></span></p><p class="MsoNormal" style="margin-left:.5in"><i><span style="font-size:10.0pt">X. laevis</span></i><span style="font-size:10.0pt"> v7.2
annotation/gene model is now shown on the v7.1 genome build on </span><a href="http://gbrowse.xenbase.org/fgb2/gbrowse/xl7_1/?name=Scaffold9843:209,774..1,209,773"><span style="font-size:10.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:
"Times New Roman";background:white">GBrowse</span></a><span style="font-size:
10.0pt"><o:p></o:p></span></p><p class="MsoNormal" style="margin-left:.5in"><i><span style="font-size:10.0pt">X. laevis</span></i><span style="font-size:10.0pt"> L
and S (long and short) genomes now on GBrowse<o:p></o:p></span></p><p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt">We
are working on reconciling <i>X. laevis</i>
L & S alleles on gene pages<o:p></o:p></span></p><p class="MsoNormal" style="margin-left:.5in"><i><span style="font-size:10.0pt">X. tropicalis</span></i><span style="font-size:10.0pt">
genome build v8.0 has more gene names assigned on </span><a href="http://gbrowse.xenbase.org/fgb2/gbrowse/xt8_0/?"><span style="font-size:
10.0pt">GBrowse</span></a><span style="font-size:10.0pt"> <o:p></o:p></span></p><p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt">GBrowse
</span><span style="font-size:10.0pt;mso-fareast-font-family:"Times New Roman";
mso-bidi-font-family:"Times New Roman";background:white">snapshots are bigger
and crisper </span><span style="font-size:10.0pt">on gene pages<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size:10.0pt"> </span><span style="font-size: 10pt; ">Human
Disease Associations:</span></p><p class="MsoNormal" style="margin-left:.5in"><span style="font-size: 10pt; background-color: white; background-position: initial initial; background-repeat: initial initial; ">Single-gene disease</span><span style="font-size:
10.0pt"> associations are now on ~14,600 gene pages,</span><span style="font-size: 10pt; background-color: white; background-position: initial initial; background-repeat: initial initial; "> facilitating direct comparison
of information from <i><span style="border:none windowtext 1.0pt;
mso-border-alt:none windowtext 0in;padding:0in">Xenopus</span></i> genes
with their human orthologs</span><span style="font-size:10.0pt"> (e.g. </span><a href="http://www.xenbase.org/gene/showgene.do?method=display&geneId=488110"><span style="font-size:10.0pt">tgfb1</span></a><span style="font-size:10.0pt">).</span><span style="font-size: 10pt; background-color: white; background-position: initial initial; background-repeat: initial initial; "> </span><span style="font-size:
10.0pt">Diseases can be searched using OMIM ID from the main search menu.</span><span style="font-size:10.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:
"Times New Roman""><o:p></o:p></span></p><p class="MsoNormal"><span style="font-size:10.0pt"> </span><span style="font-size: 10pt; ">HomoloGene:</span></p><p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt">New
HomoloGene link is on ‘Genes’ tile of the Xenbase front page. This link goes
directly to a <i>Xenopus</i> search of this
NCBI resource that helps </span><span style="font-size:10.0pt;mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:"Times New Roman"">construct putative
homology groups from the complete gene sets of a wide range of eukaryotic
species.</span></p><p class="MsoNormal"><span style="font-size:10.0pt">Transgenes Naming Guidelines:<o:p></o:p></span></p><p class="MsoNormal" style="margin-left:.5in"><span style="font-size: 10pt; background-color: white; background-position: initial initial; background-repeat: initial initial; ">Xenbase has drafted the ‘</span><a href="http://www.xenbase.org/gene/static/tgNomenclature.jsp"><i><span style="font-size:10.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:
"Lucida Grande";border:none windowtext 1.0pt;mso-border-alt:none windowtext 0in;
padding:0in;background:white">Xenopus</span></i><span style="font-size:10.0pt;
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Lucida Grande";
background:white"> Transgenic Nomenclature Guidelines’</span></a><span style="font-size: 10pt; background-color: white; background-position: initial initial; background-repeat: initial initial; "> 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 <i><span style="border:none windowtext 1.0pt;mso-border-alt:
none windowtext 0in;padding:0in">Xenopus</span></i> lines. Contact Xenbase (</span><span style="font-size:10.0pt"><a href="mailto:xenbase@ucalgary.ca">xenbase@ucalgary.ca</a>)</span><span style="font-size: 10pt; background-color: white; background-position: initial initial; background-repeat: initial initial; "> with comments/questions and for
help naming your constructs. See </span><a href="http://www.xenbase.org/gene/static/tgNomenclature.jsp"><span style="font-size:10.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:
"Times New Roman";color:#1155CC;mso-bidi-font-weight:bold">http://www.xenbase.org/gene/static/tgNomenclature.jsp</span></a><span style="font-size: 10pt; background-color: white; background-position: initial initial; background-repeat: initial initial; "><o:p></o:p></span></p><p class="MsoNormal"><span style="font-size:10.0pt"> </span><span style="font-size: 10pt; ">Coming Soon: Xenbase Forums</span></p><p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt">A discussion
forum/community bulletin board to discuss and ask advice on all aspects of <i>Xenopus</i> research (e.g., experimental
design & data analysis for ChipSeq, RNASeq, Morpholinos, ISH, genes etc.).</span></p><p class="MsoNormal"><span style="font-size:10.0pt">More details of the recent
updates to Xenbase are detailed in Karpinka et al (2014). Xenbase, the <i>Xenopus</i> Model Organism Database; new
virtualized system, data types and genomes. </span><cite><span style="font-size:10.0pt;font-family:Cambria;mso-ascii-theme-font:minor-latin;
mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin">Nucl.
Acids Res. </span></cite><span class="cit-sep"><i><span style="font-size:10.0pt;
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman"">first
published online </span></i></span><span class="cit-ahead-of-print-date"><i><span style="font-size:10.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:
"Times New Roman"">October 13, 2014 </span></i></span><span class="cit-sep"><i><span style="font-size:10.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:
"Times New Roman"">doi:</span></i></span><span class="cit-doi"><i><span style="font-size:10.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:
"Times New Roman"">10.1093/nar/gku956</span></i></span><span style="font-size:
10.0pt"><o:p></o:p></span></p><p class="MsoNormal"><span style="font-size:10.0pt"><a href="http://nar.oxfordjournals.org/content/early/2014/10/13/nar.gku956.full?sid=e82f949b-5e2a-4933-ab1e-d39051c74116">http://nar.oxfordjournals.org/content/early/2014/10/13/nar.gku956.full?sid=e82f949b-5e2a-4933-ab1e-d39051c74116</a></span></p><p class="MsoNormal"><span style="font-size:10.0pt">Image or Data Submissions? Questions
or Comments? Contact us at </span><span style="font-size:10.0pt"><a href="mailto:xenbase@ucalgary.ca?subject=feedback%20for%20Xenbase">xenbase@ucalgary.ca</a></span><span style="font-size:
10.0pt"> <o:p></o:p></span></p><p class="MsoNormal"><br></p><div apple-content-edited="true"><span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px; "><br style="color: rgb(0, 0, 0); font-family: 'Helvetica Neue'; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span style="color: rgb(0, 0, 0); font-family: 'Helvetica Neue'; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "></span><span style="color: rgb(0, 0, 0); font-family: 'Helvetica Neue'; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "></span><span style="color: rgb(0, 0, 0); font-family: 'Helvetica Neue'; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "></span><span style="color: rgb(0, 0, 0); font-family: 'Helvetica Neue'; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span><img height="48" width="256" id="6be872c4-abd4-4051-a604-e3c65287b126" apple-width="yes" apple-height="yes" src="cid:3393311928_31261500"></span><span class="Apple-style-span" style="color: rgb(0, 0, 0); font-family: 'Helvetica Neue'; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; border-collapse: separate; border-spacing: 0px; -webkit-text-decorations-in-effect: none; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Helvetica Neue'; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Helvetica Neue'; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><br><a href="http://www.xenbase.org">http://www.xenbase.org</a><br></span></span></span>
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