3e8d94c4a57eb234369ec0ceb2835b7e778ef390
ccpowell
  Mon Jun 17 15:33:20 2019 -0700
Releasing encode 3 announcement, refs #23243, refs #21139

diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html
index 34715f0..c0dbcb0 100755
--- src/hg/htdocs/goldenPath/newsarch.html
+++ src/hg/htdocs/goldenPath/newsarch.html
@@ -39,36 +39,34 @@
     </div>
     <div class="col-sm-3">
       <ul>
         <li><a href="#2004">2004 News</a></li>
         <li><a href="#2003">2003 News</a></li>
         <li><a href="#2002">2002 News</a></li>
         <li><a href="#2001">2001 News</a></li>
       </ul>
     </div>
   </div>
 </div>
 
 <!-- ============= 2019 archived news ============= -->
 <a name="2019"></a>
 
-<!--
-<a name="061719"></a>i
-Staging encode3 announcement on the rr
 
+<a name="061719"></a>
 
-<h2> Jun. 13, 2019 &nbsp;&nbsp; New ENCODE 3 transcription factor binding site track sets for human (<em>GRCh37/hg19, GRCh38/hg38</em>)</h2>
+<h2> Jun. 17, 2019 &nbsp;&nbsp; New ENCODE 3 transcription factor binding site track sets for human (<em>GRCh37/hg19, GRCh38/hg38</em>)</h2>
 <p>
 We are pleased to announce two new ENCODE 3 transcription factor binding site track sets for human 
 (GRCh37/hg19, GRCh38/hg38). These track sets show regions of transcription factor binding 
 derived from a large collection of ChIP-seq experiments performed by the ENCODE project between 
 February 2011 and November 2018.
 </p>
 <p>
 The ENCODE TF ChIP-seq data were processed using the
 <a href="https://www.encodeproject.org/chip-seq/transcription_factor/" target="_blank"
 >ENCODE Transcription Factor ChIP-seq Processing Pipeline</a> to generate peaks of TF binding.
 Peaks from 1264 experiments (1256 in hg38) representing 338 transcription factors (340 in hg38) in
 130 cell types (129 in hg38) were used to generate these two track sets.<br> 
 <ul>
   <li>The <b>ENCODE 3 TF ChIP Clusters tracks</b> are collections of ChIP-seq peaks consolidated into a
    summary display or &lsquo;cluster&rsquo; showing occupancy regions for each factor. The cluster
@@ -78,51 +76,52 @@
    TF ChIP Clusters tracks here:
    <a href="../cgi-bin/hgTrackUi?db=hg19&g=encRegTfbsClustered" target="_blank">hg19</a>, 
    <a href="../cgi-bin/hgTrackUi?db=hg38&g=encRegTfbsClustered" target="_blank">hg38</a>.</li>
   <li>The <b>ENCODE 3 TF ChIP Peaks track sets</b> are collections of the underlying ChIP-seq peak tracks
       which can be viewed individually or collectively by cell type or transcription factor. You can read more about the TF ChIP Peaks track sets here:
       <a href="../cgi-bin/hgTrackUi?db=hg19&g=encTfChipPk" target="_blank">hg19</a>,                                    
       <a href="../cgi-bin/hgTrackUi?db=hg38&g=encTfChipPk" target="_blank">hg38</a>.</li>
 </ul>
 </p>
 <p>
 An example of these two track sets is shown in the following sessions where CTCF binds to the MYC Proto-Oncogene
 across a few selected cell types. CTCF is a transcription factor identified as a repressor of MYC
 shown to inhibit cell growth (<a href="https://www.pnas.org/content/100/2/633" 
 target="_blank">Qi et al., 2002</a>).<br>
 <ul>
- <li><a href="../cgi-bin/hgTracks?db=hg38&hideTracks=1&wgEncodeReg=show&wgEncodeReg_hideKids=1&encTfChipPk=pack&encTfChipPk_hideKids=1&encTfChipPkENCFF535MZG=dense&encTfChipPkENCFF535MZG_sel=1&encTfChipPkENCFF579XTC=dense&encTfChipPkENCFF579XTC_sel=1&encTfChipPkENCFF574FIL=dense&encTfChipPkENCFF574FIL_sel=1&encTfChipPkENCFF560GGY=dense&encTfChipPkENCFF560GGY_sel=1&encTfChipPkENCFF552XDP=dense&encTfChipPkENCFF552XDP_sel=1&encTfChipPkENCFF540DVR=dense&encTfChipPkENCFF540DVR_sel=1&encRegTfbsClustered_sel=1&encRegTfbsClustered=full&encRegTfbsClustered.filterBy.name=CTCF&position=chr8%3A127736594-127740958&knownGene=full"
+ <li><a href="../cgi-bin/hgTracks?db=hg19&hideTracks=1&wgEncodeReg=show&wgEncodeReg_hideKids=1&encRegTfbsClustered=dense&encRegTfbsClustered=full&encRegTfbsClustered.filterBy.name=CTCF&wgEncodeTfBindingSuper=show&wgEncodeTfBindingSuper_hideKids=1&encTfChipPk=dense&encTfChipPk_hideKids=1&encTfChipPkENCFF003YLJ=dense&encTfChipPkENCFF003YLJ_sel=1&position=chr8%3A128748315-128753680&knownGene=full&encTfChipPkENCFF016EUX=dense&encTfChipPkENCFF016EUX_sel=1&encTfChipPkENCFF030BPR=dense&encTfChipPkENCFF030BPR_sel=1&encTfChipPkENCFF032DEW=dense&encTfChipPkENCFF032DEW_sel=1&encTfChipPkENCFF777TZZ=dense&encTfChipPkENCFF777TZZ_sel=1&pix=900"
 target="_blank"
      >CTCF transcription factor binding to MYC on hg19</a></li>
- <li><a href="../cgi-bin/hgTracks?db=hg19&hideTracks=1&wgEncodeReg=show&wgEncodeReg_hideKids=1&encRegTfbsClustered_sel=1&encRegTfbsClustered=full&encRegTfbsClustered.filterBy.name=CTCF&wgEncodeTfBindingSuper=show&wgEncodeTfBindingSuper_hideKids=1&encTfChipPk=dense&encTfChipPk_hideKids=1&encTfChipPkENCFF003YLJ=dense&encTfChipPkENCFF003YLJ_sel=1&position=chr8%3A128748315-128753680&knownGene=full&encTfChipPkENCFF016EUX=dense&encTfChipPkENCFF016EUX_sel=1&encTfChipPkENCFF030BPR=dense&encTfChipPkENCFF030BPR_sel=1&encTfChipPkENCFF032DEW=dense&encTfChipPkENCFF032DEW_sel=1&encTfChipPkENCFF777TZZ=dense&encTfChipPkENCFF777TZZ_sel=1" target="_blank"
+ <li><a href="../cgi-bin/hgTracks?db=hg38&hideTracks=1&wgEncodeReg=show&wgEncodeReg_hideKids=1&encTfChipPk=pack&encTfChipPk_hideKids=1&encTfChipPkENCFF535MZG=dense&encTfChipPkENCFF535MZG_sel=1&encTfChipPkENCFF579XTC=dense&encTfChipPkENCFF579XTC_sel=1&encTfChipPkENCFF574FIL=dense&encTfChipPkENCFF574FIL_sel=1&encTfChipPkENCFF560GGY=dense&encTfChipPkENCFF560GGY_sel=1&encTfChipPkENCFF552XDP=dense&encTfChipPkENCFF552XDP_sel=1&encTfChipPkENCFF540DVR=dense&encTfChipPkENCFF540DVR_sel=1&encRegTfbsClustered_sel=1&encRegTfbsClustered=full&encRegTfbsClustered.filterBy.name=CTCF&position=chr8%3A127736594-127740958&knownGene=full&pix=900"
+target="_blank"
      >CTCF transcription factor binding to MYC on hg38</a></li>
 </ul>
 </p>
 <p>
 Thanks to the <a href="https://www.encodeproject.org/" target="_blank">ENCODE Consortium</a>,
 the ENCODE ChIP-seq production laboratories, and the ENCODE Data Coordination Center for generating
 and processing the TF ChIP-seq datasets. The ENCODE accession numbers of the constituent
 datasets are available on the peak details page as links in the Clusters tracks and in the track
 title for the Peaks tracks. Special thanks to Henry Pratt, Jill Moore, Michael Purcaro, and Zhiping
 Weng, PI, at the 
 <a href="https://www.umassmed.edu/zlab/" target="_blank">ENCODE Data Analysis Center (ZLab at UMass Medical Center)</a>
 for providing the peak datasets, metadata, and guidance developing these track sets. Thanks to Kate
 Rosenbloom and Conner Powell of the UCSC Genome Browser group for their work in creating and
 releasing these track sets.
-</p>i
+</p>
+
 
--->
 <a name="060619"></a>
 <h2>June 6, 2019 &nbsp;&nbsp; New Genome Browser: Chinese Hamster Ovary (CHO) cell line, criGriChoV2 (<em>Cricetulus griseus</em>)</h2>
 <p>
 A genome browser is now available for the <em>Chinese Hamster Ovary cell line</em> assembly released in June 2017 by the
 <a href="https://www.eaglegenomics.com/eagle-case-studies/horizon-case-study/" target="_blank">Eagle Genomics Ltd</a> (CHOK1S_HZDv1).
 <h3>About the assembly:</h3>
 <ul>
   <li><b>UCSC Genome Browser assembly ID:</b> <a href=../cgi-bin/hgTracks?db=criGriChoV2>criGriChoV2</a></li>
   <li><b>Sequencing/Assembly provider ID:</b> <a href="https://www.eaglegenomics.com/" target="_blank">
   Eagle Genomics Ltd</a></li>
   <li><b>Assembly date:</b> June 2017</li>
   <li><b>Accession ID:</b> GCA_900186095.1</li>
   <li><b>NCBI Genome information:</b><a href="https://www.ncbi.nlm.nih.gov/genome/2791" 
 target="_blank" > 2791</a> <em>(Cricetulus griseus)</em></li>
   <li><b>NCBI Assembly information:</b><a href="https://www.ncbi.nlm.nih.gov/assembly/1422381"