47089f8fc76c64482a1a76d08e782c472e2ce70d
chmalee
  Mon Apr 18 09:44:16 2016 -0700
Staging GTEx announcement, refs #15645

diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html
index ada96ff..ca02c37 100755
--- src/hg/htdocs/indexNews.html
+++ src/hg/htdocs/indexNews.html
@@ -47,30 +47,59 @@
   <a href="https://www.lens.org/lens/bio" target="_blank">PatSeq</a>
   database mapped to the genome and then colored based on where the sequence appears in
   the patent document. Details pages contain the patent titles with links to the patents in the
   Lens database. The data from PatSeq is divided into two tracks, one includes those sequences
   that were submitted in bulk patents containing 100 or more sequences and the other containing
   all other sequences. These tracks are currently present on the human (hg19), mouse (mm10),
   and Ebola virus (eboVir3) genomes.
   </p>
 
   <p>
   Thanks to our collaborators at the Lens, Osmat Jefferson and Deniz Koellhofer, for providing the
   data and feedback on the visualization. Thank you to Max Haeussler and Matthew Speir, members of
   the UCSC Genome Browser team, for their efforts in creating these tracks.
   </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 original 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 
+  vertical 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
+  across many different tissues for the <em>entire</em> gene. Traditionally the 3 purple bars 
+  would be associated with the intron of TCAP gene, in this case those three bars indicate that 
+  the entire gene is highly expressed in cardiac and skeletal muscle tissue. Clicking on the graph 
+  brings up a description page which displays a more detailed box and whisker plot of the RPKM 
+  data, as well 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>
   <p>
   <font color="#006666" size="4"><b> 15 April 2016 -
   dbSNP 146 Available for hg19 and hg38</b></font>
   <p>
   We are pleased to announce the release of four tracks derived
   from NCBI <a href="http://www.ncbi.nlm.nih.gov/SNP/">
   dbSNP</a> Build 146 data, available on the two most
   recent human assemblies GRCh37/hg19 and GRCh38/hg38.
   NCBI's dbSNP database is a collection of &quot;simple nucleotide
   polymorphisms&quot; (SNPs), which are a class of genetic variations
   that include single nucleotide polymorphisms and small
   insertions/deletions (indels). This immense database contains over
   150 million such SNPs that cover the human genome.
   </p>
@@ -164,57 +193,30 @@
   <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="goldenPath/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="goldenPath/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
@@ -223,30 +225,43 @@
   of the Genome Browser.
   </p>
   <hr>
 
 <!-- start archives -->
 <!--staged for future release
         <p>
 	<font color="#006666" size="4"><b>20 Apr 2016
 	- Data from the Lens PatSeq Database Now Available</b>: </font>
 	We are pleased to announce the release of a set of tracks containing data from the
 	<a href="https://www.lens.org/" target="_blank">Lens</a>
 	PatSeq database in the UCSC Genome Browser.
 	<a href="goldenPath/newsarch.html#042016">Read more</a>.
 
         <p>
+        <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, as well as 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 vertical location in the browser! 
+	<a href="goldenPath/newsarch.html#04192016">Read more</a>.
+
+        <p>
 	<font color="#006666" size="4"><b> 15 April 2016 -
 	dbSNP 146 Available for hg19 and hg38</b>: </font>
 	We are pleased to announce the release of four tracks derived
 	from NCBI <a href="http://www.ncbi.nlm.nih.gov/SNP/">
 	dbSNP</a> Build 146 data.
 	<a href="goldenPath/newsarch.html#041516_2">Read more</a>.
 	</p>
 
 	<p>
 	<font color="#006666" size="4"><b>15 April 2016
 	- Genome Browsers for Gorilla, Rhesus, and Crab-Eating Macacque Now Available.</b></font>
 	<a href="goldenPath/newsarch.html#041516_1">Read more</a>.
 	</p>
 	
 	<p>