95cd69f99acb6391ff832a547ad0b38193ca7176
Merge parents 785fe0f 251e118
chmalee
  Fri Apr 15 16:09:39 2016 -0700
Resolving merge conflict on indexNews page, refs #15645

diff --cc src/hg/htdocs/indexNews.html
index a15c46f,6fb09c1..da5d007
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@@@ -75,98 -123,72 +123,99 @@@
    </p>
  
    <p>
    Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser
    <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/gorGor4/">FTP server</a> or the
    <a href="http://hgdownload.soe.ucsc.edu/downloads.html#gorilla">Downloads</a> page.
    Please observe the <a href="credits.html#gorilla_use">conditions for use</a> when
    accessing and using these data sets.  The annotation tracks for this browser were
    generated by UCSC and collaborators worldwide.  See the <a
    href="credits.html#gorilla_credits">Credits</a> page for a detailed list of the
    organizations and individuals who contributed to this release.
    </p>
    - - -
    <p>
    A Genome Browser is now available for the rhesus monkey (<em>Macaca mulatta</em>)
-   assembly released Nov 2015 by the 
- <A HREF="https://www.hgsc.bcm.edu/non-human-primates/rhesus-monkey-genome-project"
- TARGET="_blank">Baylor College of Medicine Human Genome Sequencing Center</A>. 
+   assembly released November 2015 by the 
+   <A HREF="https://www.hgsc.bcm.edu/non-human-primates/rhesus-monkey-genome-project"
+   TARGET="_blank">Baylor College of Medicine Human Genome Sequencing Center</A>. 
    For more information and statistics about this assembly, see the NCBI assembly record
    for <a href="http://www.ncbi.nlm.nih.gov/assembly/2715158" target="_blank"> Mmul_8.0.1</a>.  
- There are 286,263 scaffolds with a total size of 3,236,224,332 bases.
+   There are 23 complete chromosomes alongside 284,705 scaffolds with a total size of
+   3,236,224,332 bases.
    </p>
  
    <p>
    Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser
    <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/rheMac8/">FTP server</a> or the
    <a href="http://hgdownload.soe.ucsc.edu/downloads.html#rhesus">Downloads</a> page.
    Please observe the <a href="credits.html#rhesus_use">conditions for use</a> when
    accessing and using these data sets.  The annotation tracks for this browser were
    generated by UCSC and collaborators worldwide.  See the <a
    href="credits.html#rhesus_credits">Credits</a> page for a detailed list of the
    organizations and individuals who contributed to this release.
    </p>
    - - -
    <p>
-   A Genome Browser is now available for the crab-eating macaque (<em>Ornithorhynchus anatinus</em>)
-   assembly released February 2007 by the 
- <A HREF="http://genome.wustl.edu/genomes/detail/macaca-fascicularis/"
- TARGET=_blank>Genome Sequencing Center at Washington University, St. Louis</A>.
- For more information about this assembly, see
- <A HREF="http://www.ncbi.nlm.nih.gov/assembly/704988" TARGET="_blank">
- Macaca_fascicularis_5.0</A> in the NCBI Assembly database. There are 
- 7,625 scaffolds with a total size of 2,946,843,737 bases.
-  </p>
+   A Genome Browser is now available for the crab-eating macaque (<em>Macaca fascicularis</em>)
+   assembly released June 2013 by the 
+   <A HREF="http://genome.wustl.edu/genomes/detail/macaca-fascicularis/"
+   TARGET=_blank>Genome Sequencing Center at Washington University, St. Louis</A>.
+   For more information about this assembly, see
+   <A HREF="http://www.ncbi.nlm.nih.gov/assembly/704988"
+   TARGET="_blank">Macaca_fascicularis_5.0</A> in the NCBI Assembly database. There are 
+   22 complete chromosomes alongside 7,579 scaffolds with a total size of 2,946,843,737 bases.
+   </p>
  
    <p>
    Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser
    <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/macFas5/">FTP server</a> or the
    <a href="http://hgdownload.soe.ucsc.edu/downloads.html#crab-eating_macaque">Downloads</a> page.
    Please observe the <a href="credits.html#crab-eating_macaque_use">conditions for use</a> when
    accessing and using these data sets.  The annotation tracks for this browser were
    generated by UCSC and collaborators worldwide.  See the <a
    href="credits.html#crab-eating_macaque_credits">Credits</a> page for a detailed list of the
    organizations and individuals who contributed to this release.
    </p>
-   -->
 +  <!-- Staging for Tuesday Announcement of GTEX track
 +  <hr>
 +  <font color="#006666" size="4"><b>19 April 2016
 +  - New Genotyping Tissue Expression Track for hg19 and hg38!</b></font>
 +  <p>
 +  We are excited to announce the release of a new track based on data from the 
 +  <a href="http://commonfund.nih.gov/GTEx/index" TARGET = _BLANK>
 +  Genotyping Tissue Expression Consortium</a> V6 data freeze. This track displays tissue-specific
 +  gene expression for a single gene based on RNA-Seq data. The data for this 
 +  track can be found at the <a href="http://www.gtexportal.org/home" target = _blank>GTEX Portal</a> 
 +  hosted by the Broad Institute.
 +  <p>
 +  This track also features a new display method that extends the traditional Genome Browser 
 +  display &mdash; a bar graph! Each bar graph depicts the expression level (in RPKM) of the 
 +  various tissues assayed by the GTEX Consortium, and is specific to each gene, not the graph's 
 +  location in the browser! 
 +  <p>
 +  <center><img src="images/gtexAnnounceExample.png"></center>
 +  <p>
 +  Notice how the blue gene-model underneath the graph extends past the end of the graph? This gene
 +  model represents the target of the RNA-Seq experiment, and the graph displays the RPKM levels
 +  from across many different tissues for the <em>entire</em> gene. Clicking on the graph through
 +  to the details page displays a more detailed box and whisker plot of the RPKM data, as well
 +  as information as a description about all the methods used in the generation of the data. 
 +  <p>
 +  Credit goes to Kate Rosenbloom for implementing this feature.
 +  -->
+ 
    <hr>
    <font color="#006666" size="4"><b>4 Apr 2016
    - New video shows how to obtain sequence or coordinates for exons. </b></font>
    <p>
    We have released a new <A HREF =
    "http://genome.ucsc.edu/training/vids/index.html#vid08" TARGET =
    _BLANK>video</A> to our YouTube channel.  This newest installment in our effort
    to share the capabilities of the Genome Browser shows how to
    use the Table Browser to obtain either the sequences or the coordinates for
    exons in the genes from a chosen region of the genome.
    </p>
  
    <p>
    We also want to take this opportuinty to remind you that we offer
    on-site <A HREF = "http://genome.ucsc.edu/training/index.html" TARGET =