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<p style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;">
<b><span style="color: rgb(0, 0, 0); font-size: 16pt; font-family: "Times New Roman", Times, serif;">Xenbase Spring Newsletter, April 2019</span></b></p>
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<b><span style="color: red; font-size: 10pt; font-family: "Times New Roman", Times, serif;"><br>
</span></b></p>
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<b><span style="color: red; font-size: 10pt; font-family: "Times New Roman", Times, serif;">NEW GEO tracks on JBrowse<o:p></o:p></span></b></p>
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<span style="font-size: 11pt;"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">Xenbase developed standardized pipelines to process
</span><b><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">NextGen
</span><i><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">Xenopus</span></i><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;"> Sequence data from GEO/SRA</span></b><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">
(</span><u><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">S</span></u><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">equence
</span><u><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">R</span></u><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">ead
</span><u><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">A</span></u><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">rchive at NCBI). The goal was to wrangle diverse NGS data to make it organized,
</span><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;" class="">consistent and</span><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;"> accessible, so you can compare data from different sources, all</span><b><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">
aligned against latest genomes.</span></b><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;"> We built
</span><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;" class="">new</span><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;"> tools to search and select experiments and load them into JBrowse and two complementary
navigation/selection systems to view processed GEO data on JBrowse: a </span><b><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">faceted browser</span></b><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">
and a </span><b><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">hierarchically organized browser</span></b><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">.</span><o:p></o:p></span></p>
<p style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;">
<span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">Xenbase is the first model organism database to have done this data wrangling for NGS !!!<o:p></o:p></span></p>
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<b><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">Highlights</span></b><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">:<o:p></o:p></span></p>
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<!--[if !supportLists]--><span style="font-size: 11pt; font-family: Arial, sans-serif;"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">•</span><span style="font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10pt; line-height: normal; font-family: "Times New Roman", Times, serif;">
</span></span><!--[endif]--><span style="font-size: 11pt;"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">Xenbase processed
</span><b><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">54% of the GSMs in GEO</span></b><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;"> (964/1547 data sets).</span><o:p></o:p></span></p>
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<!--[if !supportLists]--><span style="font-size: 11pt; line-height: 115%; font-family: Arial, sans-serif;"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">•</span><span style="font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10pt; line-height: normal; font-family: "Times New Roman", Times, serif;">
</span></span><!--[endif]--><b><span style="font-size: 10pt; line-height: 115%; font-family: "Times New Roman", Times, serif;">648 tracks on JBrowse</span></b><span style="font-size: 10pt; line-height: 115%; font-family: "Times New Roman", Times, serif;">:
525 RNA-Seq and 123 ChIP-Seq tracks, more to come!<o:p></o:p></span></p>
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<!--[if !supportLists]--><span style="font-size: 11pt; font-family: Arial, sans-serif;"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">•</span><span style="font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10pt; line-height: normal; font-family: "Times New Roman", Times, serif;">
</span></span><!--[endif]--><span style="font-size: 11pt; font-family: "Times New Roman", serif;"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">Details of each GEO series (called a GSE) are summarized on
</span><b><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">GSE pa</span></b><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">ge (</span><a href="http://www.xenbase.org/geneExpression/viewGse.do?method=display&gseId=75278&beginIndex=1&currentPage=1&gseValue=75278&isWildcardSearchField=F&showAdvanceSearch=false&manipStageFromId=4363448&manipStageToId=536335&manipTypeId=ANYBASE&assayStageFromId=536407&assayStageToId=4363450&selectedCurationStatusId=0&isCuratorField=T&" style="color: rgb(5, 99, 193); text-decoration: underline;" id="LPlnk495649" class="OWAAutoLink" previewremoved="true"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">click
for an example</span></a><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">)</span><o:p></o:p></span></p>
<p style="text-indent: -0.25in; margin: 0in 0in 0.0001pt 0.5in; font-size: 12pt; font-family: Calibri, sans-serif;">
<!--[if !supportLists]--><span style="font-size: 11pt; font-family: Arial, sans-serif;"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">•</span><span style="font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10pt; line-height: normal; font-family: "Times New Roman", Times, serif;">
</span></span><!--[endif]--><span style="font-size: 11pt; font-family: "Times New Roman", serif;"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">Search all the GEO data on Xenbase
</span><a href="http://www.xenbase.org/geneExpression/gseCurationSearch.do?method=search" style="color: rgb(5, 99, 193); text-decoration: underline;" id="LPlnk608744" class="OWAAutoLink" previewremoved="true"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">here</span></a><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">.
</span><b><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">Simple Search and Advanced Search options.</span></b><o:p></o:p></span></p>
<p style="text-indent: -0.25in; margin: 0in 0in 0.0001pt 0.5in; font-size: 12pt; font-family: Calibri, sans-serif;">
<!--[if !supportLists]--><span style="font-size: 11pt; font-family: Arial, sans-serif;"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">•</span><span style="font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10pt; line-height: normal; font-family: "Times New Roman", Times, serif;">
</span></span><!--[endif]--><span style="font-size: 11pt; font-family: "Times New Roman", serif;"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">When you find data you want to compare,
</span><b><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">check box</span><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;"> and click Load to JBrowse</span></b><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">.</span><o:p></o:p></span></p>
<p style="text-indent: -0.25in; margin: 0in 0in 0.0001pt 0.5in; font-size: 12pt; font-family: Calibri, sans-serif;">
<!--[if !supportLists]--><span style="font-size: 11pt; font-family: Arial, sans-serif;"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">•</span><span style="font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10pt; line-height: normal; font-family: "Times New Roman", Times, serif;">
</span></span><!--[endif]--><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">Differential Expressed Genes (DEG) list can be filtered (</span><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">fold change,
FDR, TPM</span><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">) and downloaded.<o:p></o:p></span></p>
<p style="text-indent: -0.25in; line-height: 115%; margin: 0in 0in 0.0001pt 0.5in; font-size: 12pt; font-family: Calibri, sans-serif;">
<!--[if !supportLists]--><span style="font-size: 11pt; line-height: 115%; font-family: Arial, sans-serif;"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">•</span><span style="font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10pt; line-height: normal; font-family: "Times New Roman", Times, serif;">
</span></span><!--[endif]--><span style="font-size: 11pt; line-height: 115%; font-family: "Times New Roman", serif;"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">Processed GEO data files are available to download from
</span><a href="ftp://xenbaseturbofrog.org/genomics/GEO/" style="color: rgb(5, 99, 193); text-decoration: underline;" id="LPlnk425930" class="OWAAutoLink" previewremoved="true"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">Xenbase
FTP</span></a><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">.</span></span><span style="font-size: 11pt; line-height: 115%; font-family: "Times New Roman", serif;"><o:p></o:p></span></p>
<p style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;">
<b><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">3 ways to get to GEO tools.<o:p></o:p></span></b></p>
<p style="text-indent: -0.25in; margin: 0in 0in 0.0001pt 0.5in; font-size: 12pt; font-family: Calibri, sans-serif;">
<!--[if !supportLists]--><span style="font-size: 11pt; font-family: "Times New Roman", serif;"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">1.</span><span style="font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10pt; line-height: normal; font-family: "Times New Roman", Times, serif;">
</span></span><!--[endif]--><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">“GEO data @ Xenbase” link under Expression menu.<o:p></o:p></span></p>
<p style="text-indent: -0.25in; margin: 0in 0in 0.0001pt 0.5in; font-size: 12pt; font-family: Calibri, sans-serif;">
<!--[if !supportLists]--><span style="font-size: 11pt; font-family: "Times New Roman", serif;"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">2.</span><span style="font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10pt; line-height: normal; font-family: "Times New Roman", Times, serif;">
</span></span><!--[endif]--><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">Quick search mini-bar, select “GEO data sets”.<o:p></o:p></span></p>
<p style="text-indent: -0.25in; margin: 0in 0in 0.0001pt 0.5in; font-size: 12pt; font-family: Calibri, sans-serif;">
<!--[if !supportLists]--><span style="font-size: 11pt; font-family: "Times New Roman", serif;"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">3.</span><span style="font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10pt; line-height: normal; font-family: "Times New Roman", Times, serif;">
</span></span><!--[endif]--><span style="font-size: 11pt; font-family: "Times New Roman", serif;"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">Genomes Menu or Genome Browser tile, select either
</span><i><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">X.
</span><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;" class="">laevis</span></i><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;"> ‘J-Strain 9.2’ or
</span><i><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">X.
</span><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;" class="">tropicalis</span></i><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;"> ‘Nigerian 9.1 on JBrowse’, then select the tracks from the left menu,
or click on the floating box in the upper left called “GEO tracks” to open the faceted list view.</span><o:p></o:p></span></p>
<p style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;">
<span style="font-size: 10pt; color: rgb(68, 114, 196); font-family: "Times New Roman", Times, serif;">Coming Soon:
<o:p></o:p></span></p>
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<!--[if !supportLists]--><span style="font-size:11.0pt;
font-family:"Arial",sans-serif;mso-fareast-font-family:Arial;color:#4472C4;
mso-themecolor:accent1"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">•</span><span style="font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10pt; line-height: normal; font-family: "Times New Roman", Times, serif;">
</span></span><!--[endif]--><span style="font-size: 10pt; color: rgb(68, 114, 196); font-family: "Times New Roman", Times, serif;">Webinar on ‘How to Navigate GEO data on Xenbase’, live and recorded.
<o:p></o:p></span></p>
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<!--[if !supportLists]--><span style="font-size:11.0pt;
font-family:"Arial",sans-serif;mso-fareast-font-family:Arial;color:#4472C4;
mso-themecolor:accent1"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">•</span><span style="font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10pt; line-height: normal; font-family: "Times New Roman", Times, serif;">
</span></span><!--[endif]--><span style="font-size: 10pt; color: rgb(68, 114, 196); font-family: "Times New Roman", Times, serif;">Differentially Expressed Genes (DEG) displayed in heatmaps and other interactive data displays.</span><b><span style="font-size: 10pt; color: rgb(68, 114, 196); font-family: "Times New Roman", Times, serif;">
<o:p></o:p></span></b></p>
<p style="text-indent: -0.25in; margin: 0in 0in 0.0001pt 0.5in; font-size: 12pt; font-family: Calibri, sans-serif;">
<!--[if !supportLists]--><span style="font-size:11.0pt;
font-family:"Arial",sans-serif;mso-fareast-font-family:Arial;color:#4472C4;
mso-themecolor:accent1"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">•</span><span style="font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10pt; line-height: normal; font-family: "Times New Roman", Times, serif;">
</span></span><!--[endif]--><span style="font-size: 11pt; color: rgb(68, 114, 196);"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">GEO Processing</span><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">
Pipeline will soon be available on GitHub.</span></span><b><span style="font-size:11.0pt;color:#4472C4;mso-themecolor:accent1"><o:p></o:p></span></b></p>
<p style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;">
<b><span style="font-size:11.0pt;color:#4472C4;mso-themecolor:accent1"><o:p><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;"> </span></o:p></span></b></p>
<p align="center" style="text-align: left; margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;">
<span style="font-size: 11pt;"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;"><b>Int</b><b>erested in a
</b></span><b><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">Xenbase GEO Workshop</span><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;"> at the October 11-14 XERT meeting in Woods Hole?</span><o:p></o:p></b></span></p>
<p align="center" style="text-align: left; margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;">
<span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;"><b>Please let us know if you, your students or postdocs can attend an afternoon workshop on 11/10/19.<o:p></o:p></b></span></p>
<p align="center" style="text-align: left; margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;">
<span style="font-size: 10pt;"><b><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">Email your interest and potential numbers to
</span><a href="mailto:Xenbase@ucalgary.ca" style="color: rgb(5, 99, 193); text-decoration: underline;" id="LPlnk265758" class="OWAAutoLink" previewremoved="true"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">Xenbase@ucalgary.ca</span></a><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">
with </span><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">subject</span></b><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;"><b> line ‘GEO Workshop’.</b></span></span></p>
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<span style="font-size: 10pt;"></p>
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0%;mso-style-textoutline-outlinestyle-dash:solid;mso-style-textoutline-outlinestyle-align:
center;mso-style-textoutline-outlinestyle-compound:simple;mso-effects-shadow-color:
black;mso-effects-shadow-themecolor:dark1;mso-effects-shadow-alpha:40.0%;
mso-effects-shadow-dpiradius:3.0pt;mso-effects-shadow-dpidistance:1.5pt;
mso-effects-shadow-angledirection:2700000;mso-effects-shadow-align:topleft;
mso-effects-shadow-pctsx:100.0%;mso-effects-shadow-pctsy:100.0%;mso-effects-shadow-anglekx:
0;mso-effects-shadow-angleky:0"><o:p></o:p></span></p>
<p align="right" style="text-align: right; margin: 0in 0in 0.0001pt 0.5in; font-size: 12pt; font-family: Calibri, sans-serif;">
<b style="font-family: "Times New Roman", serif; font-size: 12pt; text-align: center;"><span style="font-size:11.0pt;color:red"><o:p><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;"> </span></o:p></span></b><br>
</p>
<p style="text-align: left; margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;">
<a href="http://www.xenbase.org/other/static/HowTo.jsp" style="color: rgb(5, 99, 193); text-decoration: underline;" id="LPlnk266199" class="OWAAutoLink" previewremoved="true"><b><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">JBrowse
Video-Tutorials</span></b></a><b><span style="font-size:11.0pt"><o:p></o:p></span></b></p>
<p style="text-align: left; margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;">
<span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">JBrowse is the genome browser on Xenbase where you can interrogate the latest genome builds for
<o:p></o:p></span></p>
<p style="text-align: left; margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;">
<i><span style="font-size:11.0pt"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">X.
</span><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">tropicalis</span></span></i><span style="font-size:11.0pt"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;"> and
</span><i><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">X.
</span><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">laevis</span></i><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">, transcription factor binding sites, and, as described above, NGS data.
</span><o:p></o:p></span></p>
<p style="text-align: left; margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;">
<span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">Learn how to navigate JBrowse via our helpful video tutorials:
<o:p></o:p></span></p>
<p style="text-align: left; text-indent: -0.25in; margin: 0in 0in 0.0001pt 0.5in; font-size: 12pt; font-family: Calibri, sans-serif;">
<!--[if !supportLists]--><span style="font-size:11.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
mso-bidi-font-family:Symbol"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">·</span><span style="font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10pt; line-height: normal; font-family: "Times New Roman", Times, serif;">
</span></span><!--[endif]--><a href="http://www.xenbase.org/other/static/HowTo.jsp" style="color: rgb(5, 99, 193); text-decoration: underline;" id="LPlnk894686" class="OWAAutoLink" previewremoved="true"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">Introduction
to JBrowse</span></a><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">. How to select tracks, species, genome version and find genes.<o:p></o:p></span></p>
<p style="text-align: left; text-indent: -0.25in; margin: 0in 0in 0.0001pt 0.5in; font-size: 12pt; font-family: Calibri, sans-serif;">
<!--[if !supportLists]--><span style="font-size:11.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
mso-bidi-font-family:Symbol"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">·</span><span style="font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10pt; line-height: normal; font-family: "Times New Roman", Times, serif;">
</span></span><!--[endif]--><a href="http://www.xenbase.org/other/static/HowTo.jsp" style="color: rgb(5, 99, 193); text-decoration: underline;" id="LPlnk194951" class="OWAAutoLink" previewremoved="true"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">JBrowse
1</span></a><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">: How to view all aspects of a gene sequence (e.g., UTR, intron, CDS).<o:p></o:p></span></p>
<p style="text-align: left; text-indent: -0.25in; margin: 0in 0in 0.0001pt 0.5in; font-size: 12pt; font-family: Calibri, sans-serif;">
<!--[if !supportLists]--><span style="font-size:11.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
mso-bidi-font-family:Symbol"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">·</span><span style="font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10pt; line-height: normal; font-family: "Times New Roman", Times, serif;">
</span></span><!--[endif]--><a href="http://www.xenbase.org/other/static/HowTo.jsp" style="color: rgb(5, 99, 193); text-decoration: underline;" id="LPlnk799363" class="OWAAutoLink" previewremoved="true"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">JBrowse
2</span></a><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">: How to save track data for a particular region.<o:p></o:p></span></p>
<p style="text-align: left; text-indent: -0.25in; margin: 0in 0in 0.0001pt 0.5in; font-size: 12pt; font-family: Calibri, sans-serif;">
<!--[if !supportLists]--><span style="font-size:11.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
mso-bidi-font-family:Symbol"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">·</span><span style="font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10pt; line-height: normal; font-family: "Times New Roman", Times, serif;">
</span></span><!--[endif]--><a href="http://www.xenbase.org/other/static/HowTo.jsp" style="color: rgb(5, 99, 193); text-decoration: underline;" title="http://www.xenbase.org/other/static/HowTo.jsp
Cmd+Click or tap to follow the link" id="LPlnk714228" class="OWAAutoLink" previewremoved="true"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">JBrowse
3</span></a><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">: How to add custom tracks from your computer.<o:p></o:p></span></p>
<p align="center" style="text-align: left; margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;">
<span style="font-size: 10pt; color: rgb(68, 114, 196); font-family: "Times New Roman", Times, serif;">Coming soon: JBrowse 4: How to view JBrowse tracks for ChIP-Seq and RNA-Seq data from GEO.<o:p></o:p></span></p>
<p style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;">
<b><span style="font-size:11.0pt;color:red"><o:p><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;"> </span></o:p></span></b></p>
<p style="text-align: left; margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;">
<b><span style="font-size: 10pt; color: red; font-family: "Times New Roman", Times, serif;">NEW
</span></b><b><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">Gene
</span></b><b><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">Expression Ribbon
<o:p></o:p></span></b></p>
<p style="text-align: justify; margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;">
<span style="font-size:11.0pt"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">Each Gene Page now has a ribbon that summarizes
</span><i><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">in situ</span></i><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;"> and RNA-Seq data for embryonic stages, embryonic tissues and adult tissues
of </span><i><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">X.
</span><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">laevis</span></i><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;"> and
</span><i><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">X.
</span><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">tropicalis</span></i><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">.
</span><o:p></o:p></span></p>
<p style="text-align: justify; text-indent: -0.25in; margin: 0in 0in 0.0001pt 0.5in; font-size: 12pt; font-family: Calibri, sans-serif;">
<!--[if !supportLists]--><span style="font-size:11.0pt;
font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">·</span><span style="font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10pt; line-height: normal; font-family: "Times New Roman", Times, serif;">
</span></span><!--[endif]--><span style="font-size:11.0pt;font-family:"Times New Roman",serif"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">Green represents
</span><i><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">in situ
</span></i><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">data from the vast collection of curated gene expression in Xenbase. Mouse over to show
</span><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;" class="">number</span><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;"> of records for expression in that stage or tissue.
</span><o:p></o:p></span></p>
<p style="text-align: justify; text-indent: -0.25in; margin: 0in 0in 0.0001pt 0.5in; font-size: 12pt; font-family: Calibri, sans-serif;">
<!--[if !supportLists]--><span style="font-size:11.0pt;
font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">·</span><span style="font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10pt; line-height: normal; font-family: "Times New Roman", Times, serif;">
</span></span><!--[endif]--><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">Click ‘Xenbase Expression Details’ to go to the full gene expression data.
<o:p></o:p></span></p>
<p style="text-align: justify; text-indent: -0.25in; margin: 0in 0in 0.0001pt 0.5in; font-size: 12pt; font-family: Calibri, sans-serif;">
<!--[if !supportLists]--><span style="font-size:11.0pt;
font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">·</span><span style="font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 10pt; line-height: normal; font-family: "Times New Roman", Times, serif;">
</span></span><!--[endif]--><span style="font-size:11.0pt;font-family:"Times New Roman",serif"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">RNA-Seq data from Sessions
</span><i><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">et al.</span></i><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;"> 2016 (adult tissues) are shown in color gradients of TPM values in
</span><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">top</span><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;"> right half of NF stage and adult tissues ribbon. Mouse over to see the TPM value for
a particular tissue/stage.</span><o:p></o:p></span></p>
<p align="center" style="text-align: center; margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;">
<i><span style="font-size:10.0pt;mso-bidi-font-size:11.0pt"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">Single-cell RNA-Seq data from Briggs et al. 2018 for embryonic tissues are being processed. In the meantime, explore pre-loaded
single cell data via the links to </span><a href="https://kleintools.hms.harvard.edu/tools/spring.html" style="color: rgb(5, 99, 193); text-decoration: underline;" id="LPlnk971124" class="OWAAutoLink" previewremoved="true"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">SPRING</span></a><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">,
a tool to uncover high-dimensional structure in </span><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;" class="">single cell</span><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;"> gene expression built
by the Klein lab at Harvard.</span></span></i></p>
<p align="center" style="text-align: center; margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;">
<i><span style="font-size:10.0pt;mso-bidi-font-size:11.0pt"><span style="font-size: 12pt; font-family: "Times New Roman", Times, serif;"><br>
</span></span></i></p>
<p style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif; display: inline !important;">
</p>
<div style="text-align: left;"><b style="font-size: 12pt;"><span style="font-size: 10pt; color: red;">Updated
</span></b><b style="font-size: 12pt;"><span style="font-size: 10pt;">Marker genes, anatomy tree and more images for
</span></b><span style="font-size: 10pt;"><a href="http://www.xenbase.org/anatomy/anatomy.do?method=display&tabId=2" style="color: rgb(5, 99, 193);" id="LPlnk316079" class="OWAAutoLink" previewremoved="true"><b><span style="font-size: 10pt;">XAO Anatomy Pages</span></b></a><b><span style="font-size: 10pt;">
</span></b></span><b style="font-size: 12pt;"><span style="font-size: 10pt;">(see Fig 3. below left).</span></b></div>
<p></p>
</span>
<p></p>
<p style="text-align: justify; margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;">
<span style="font-size: 10pt;">Each anatomical term we use to describe gene expression has its own XAO page. XAO pages are useful to find out more about a structure, at what time in development it is observed, and which genes are expressed. We’re adding validated
marker genes, exemplary gene expression images, and annotated diagrams as we curate new research articles and data from large screens. Let us know your favorite markers, and we’ll share your insights! Email
</span><a href="mailto:xenbase@ucalgary.ca" style="color: rgb(5, 99, 193); text-decoration: underline;" id="LPlnk500725" class="OWAAutoLink" previewremoved="true"><span style="font-size: 10pt;">xenbase@ucalgary.ca</span></a><span style="color: rgb(5, 99, 193); text-decoration: underline;"><span style="font-size: 10pt;">.</span></span><span style="font-size:11.0pt;color:#0070C0"><o:p></o:p></span></p>
<p></p>
<p style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;">
<b><span style="font-size:11.0pt"><o:p><span style="font-size: 10pt;"> </span></o:p></span></b></p>
<p style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;">
<b><i><span style="font-size: 10pt;">Xenopus</span></i></b><b><span style="font-size: 10pt;"> Stock Center frogs all cataloged on Xenbase<o:p></o:p></span></b></p>
<p style="text-align: justify; margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;">
<span style="font-size:11.0pt"><span style="font-size: 10pt;">Transgenic and mutant
</span><i><span style="font-size: 10pt;">Xenopus</span></i><span style="font-size: 10pt;"> lines and wildtypes strains supplied by the NXR (USA), the NBRP (Japan) and the EXRC (Europe) are
</span></span><a href="http://www.xenbase.org/stockCenter/searchLines.do?method=searchMutantLines&searchSpecies=11" style="color: rgb(5, 99, 193); text-decoration: underline;" id="LPlnk949640" class="OWAAutoLink" previewremoved="true"><span style="font-size: 10pt;">cataloged
and searchable on Xenbase</span></a><span style="font-size: 10pt;">. The stock centers hold over 130 different transgenic lines, and the NXR has developed 74 mutant lines. Many lines are shared between the centers, yet each line has a single entry on Xenbase,
and carry unique RRIDs (identification numbers) depending on supplier. We encourage researchers to use the official standardized name and cite the RRID number in their papers.<o:p></o:p></span></p>
<p style="text-align: justify; margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;">
<span style="font-size:11.0pt"><o:p><span style="font-size: 10pt;"> </span></o:p></span></p>
<p align="center" style="text-align: center; margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;">
<span style="font-size: 10pt;"><span style="font-size: 12pt; font-family: "Times New Roman", Times, serif;"></p>
<p style="text-align: left; margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;">
<b style=""><span style="font-size: 11pt;">New Xenbase paper<o:p></o:p></span></b></p>
<p style="text-align: justify; margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;">
<span style="font-size:11.0pt;
color:#0070C0">Take a look! </span><b><span style="font-size:11.0pt;color:#020202;
mso-font-kerning:18.0pt">Xenbase: Facilitating the use of Xenopus to Model Human Disease</span></b><span style="font-size:11.0pt;color:#020202;mso-font-kerning:
18.0pt;mso-bidi-font-weight:bold">.
Nenni et al. (2019).</span><span style="font-size:11.0pt"> <span style="color: rgb(2, 2, 2); background-image: initial; background-">
Front. Physiol. </span></span><a href="https://www.frontiersin.org/articles/10.3389/fphys.2019.00154/abstract" style="color: rgb(5, 99, 193); text-decoration: underline;" id="LPlnk493870" class="OWAAutoLink" previewremoved="true"><span style="font-size: 11pt; background-image: initial; background-">doi:
10.3389/fphys.2019.00154</span></a><span style="font-size: 11pt; color: rgb(2, 2, 2); background-image: initial; background-">.
</span><span style="font-size:11.0pt">This review by Xenbase, which assessed 1000+ articles, describes the breadth of recent Xenopus-Human disease modeling and describes the integration of the H<span style="color: rgb(62, 61, 64); background-image: initial; background-">uman
Disease Ontology (DO) into Xenbase Disease Pages.</span> <o:p></o:p></span></p>
<p style="text-align: justify; margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;">
<span style="font-size: 11pt; color: rgb(2, 2, 2); background-image: initial;"><o:p style=""> </o:p></span></p>
<p style="text-align: left; margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;">
<b style=""><span style="font-size: 11pt;">Disease Ontology Pages with interactive tree viewers.
</span></b><b style=""><span style="font-size:9.0pt">(see Fig 3. below right)</span></b><b style=""><span style="font-size:11.0pt"><o:p></o:p></span></b></p>
<p style="text-align: justify; margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;">
<span style="font-size: 11pt;">To further support human disease modeling in Xenopus, we have added dynamic tree viewers to the Disease Ontology (DO) Disease Pages.
</span><span style="font-size: 9pt;">(Note: OMIM is not an ontology, so OMIM Disease Pages do not have ontology tree viewer).</span><span style="font-size: 11pt;"><o:p></o:p></span></p>
<p style="text-align: justify; text-indent: -0.25in; margin: 0in 0in 0.0001pt 0.5in; font-size: 12pt; font-family: Calibri, sans-serif;">
<!--[if !supportLists]--><span style="font-size:11.0pt;
font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol">·<span style="font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: "Times New Roman";"> </span></span><span style="font-size:11.0pt;font-family:"Times New Roman",serif">The
DO tree viewer shows how diseases are related, e.g., ‘diabetes mellitus’ has five subtypes, ‘gestational’, ‘neonatal’, ‘type 1’ and ‘type 2’, and ‘prediabetes syndrome’.
<o:p></o:p></span></p>
<p style="text-align: justify; text-indent: -0.25in; margin: 0in 0in 0.0001pt 0.5in; font-size: 12pt; font-family: Calibri, sans-serif;">
<!--[if !supportLists]--><span style="font-size:11.0pt;
font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol">·<span style="font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: "Times New Roman";">
</span></span><!--[endif]--><span style="font-size:11.0pt;font-family:"Times New Roman",serif">To explore the ontology in tree-view, click the nodes.
<o:p></o:p></span></p>
<p style="text-align: justify; text-indent: -0.25in; margin: 0in 0in 0.0001pt 0.5in; font-size: 12pt; font-family: Calibri, sans-serif;">
<!--[if !supportLists]--><span style="font-size:11.0pt;
font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol">·<span style="font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: "Times New Roman";">
</span></span><!--[endif]--><span style="font-size:11.0pt;font-family:"Times New Roman",serif">Solid blue nodes indicate more subtypes, e.g., type1 diabetes has 24 subtypes!<o:p></o:p></span></p>
<p style="text-align: justify; text-indent: -0.25in; margin: 0in 0in 0.0001pt 0.5in; font-size: 12pt; font-family: Calibri, sans-serif;">
<!--[if !supportLists]--><span style="font-size:11.0pt;
font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol">·<span style="font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: "Times New Roman";">
</span></span><!--[endif]--><span style="font-size:11.0pt;font-family:"Times New Roman",serif">Numbers in parenthesis show the number of Xenopus papers that refer to that disease.
<o:p></o:p></span></p>
<p style="text-align: justify; text-indent: -0.25in; margin: 0in 0in 0.0001pt 0.5in; font-size: 12pt; font-family: Calibri, sans-serif;">
<!--[if !supportLists]--><span style="font-size:11.0pt;
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</span></span><!--[endif]--><span style="font-size:11.0pt;font-family:"Times New Roman",serif">Literature tab lists all of the articles, and you can navigate back to the Article Page.
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</span></span><!--[endif]--><span style="font-size: 11pt; font-family: "Times New Roman", serif;">Genes associated with the disease are also shown, and link back to the Xenbase Gene Pages.</span><span style="font-style: italic; font-size: 11pt;">
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<b><i><span style="font-size:11.0pt">Lastly…<o:p></o:p></span></i></b></p>
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<b><span style="background-image: initial; background-">microPublication Biology</span></b><b><span style="font-size: 11pt;"> (µP for short)</span></b><span style="font-size:11.0pt;color:#0070C0"> Call for papers</span><span style="font-size:11.0pt">!<b><o:p></o:p></b></span></p>
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<span style="font-size:11.0pt;line-height:150%">µP<span style="background-image: initial; background-"> is currently accepting single-experiment submissions
</span>of high-quality <i>Xenopus</i> research<span style="background-image: initial; background-">:
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<span style="font-size: 11pt; background-image: initial; background-">-<b>Expression patterns</b> (RT-PCR, WISH, IHC)</span><span style="font-size: 11pt; background-image: initial; background-"> -<b>Phenotypic data</b> (e.g., toxicology, SEM, histology)
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<span style="font-size: 11pt; background-image: initial; background-">-<b>Sequence data</b> (SNPs, polymorphisms) -<b>Genotypic data</b> (mutants or Tg lines)<o:p></o:p></span></p>
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<span style="font-size: 11pt; line-height: 150%; background-image: initial; background-">-<b>Methods</b> (new or updated protocols)<o:p></o:p></span></p>
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<span style="font-size:11.0pt">E<span style="background-image: initial; background-">ach
<b>open-access</b> </span>µP <span style="background-image: initial; background-">
article is <b>peer-reviewed</b>, assigned a <b>DOI</b>, and published <b>online as HTML and PDF</b>. <o:p></o:p></span></span></p>
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<span style="font-size: 11pt; background-image: initial; background-">This is an especially accessible format to get undergraduate student research published quickly!<o:p></o:p></span></p>
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<span style="font-size: 11pt; background-image: initial; background-">Go </span><span style="font-size: 11pt; background-image: initial; background-">to</span><span style="font-size: 11pt; color: rgb(0, 112, 192); background-image: initial; background-">
<span style="color: rgb(0, 112, 192); text-decoration: underline;"><a href="https://www.micropublication.org/submit.html" style="color: rgb(5, 99, 193); text-decoration: underline;" id="LPlnk103475" class="OWAAutoLink" previewremoved="true">https://www.micropublication.org/submit.html</a> <span style="font-family: "Times New Roman", serif; font-size: 14.6667px;">to
submit your uPub manuscript.</span></span></span></p>
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<a id="LPUrlAnchor_15543245686910.0399102205730284" href="https://www.micropublication.org/submit.html" target="_blank" style="text-decoration: none;">Submit - MICROPUBLICATION:BIOLOGY</a></div>
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www.micropublication.org</div>
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Get your findings out to the scientific community microPublication Biology is currently accepting submissions under the topics Expression pattern, Phenotypic data, Genotypic data, Sequence data, Methods, and Software.Other data types will be incorporated in
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Questions? Comments? great Ideas? Email us <b style="font-family: "Times New Roman", serif; font-size: 13.3333px;">
<span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;"> </span><a href="mailto:Xenbase@ucalgary.ca" id="LPlnk265758" class="OWAAutoLink" previewremoved="true" style="color: rgb(5, 99, 193);"><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;">Xenbase@ucalgary.ca</span></a><span style="font-size: 10pt; font-family: "Times New Roman", Times, serif;"> Follow
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