ede58f65bb4b32788dcfabafbcb04f1dfab4fe66
mspeir
  Wed Apr 3 13:13:07 2019 -0700
Adding links for assay info icons in table header.

diff --git src/hg/cirm/gateway/htdocs/projects.html src/hg/cirm/gateway/htdocs/projects.html
index ed6e838..bc50ed5 100755
--- src/hg/cirm/gateway/htdocs/projects.html
+++ src/hg/cirm/gateway/htdocs/projects.html
@@ -42,127 +42,132 @@
          - SC Hub File Download
       </div>
       <div class="col-4">
         <i class="fas fa-table fa-lg text-dark-blue" aria-hidden="true"></i>
          - SC Hub Metadata Download
       </div>
     </div>
   </div>
 </div><br>
     <table class="table table-hover table-header-rotated" style="overflow: visible">
         <thead>
             <tr>
                 <th style="width: 1%;" class="text-nowrap"><br>Research Theme</th>
                 <th style="width: 1%;" class="text-nowrap">Lab</th>
                 <th style="width: 1%;" class="text-nowrap ">Data Set</th>
-                <th style="width: 1%;" class="text-dark-blue text-nowrap">Single cell <a href="#"
+                <th style="width: 1%;" class="text-dark-blue text-nowrap">Single cell <a href="https://en.wikipedia.org/wiki/Single-cell_analysis" target="_blank"
                  data-toggle="popover" data-trigger="hover" class="popoveradjust"
-                 data-placement="top"  data-container="body" data-html="true" title=""
-                 data-content="It is possible to assay individual cells from a population to
+                 data-placement="top"  data-container="body" data-html="true" title="It is possible to assay individual cells from a population to
                  learn more about the cells making up a community, also known as studying the
-                 <em>cellular heterogenetity</em>."><i class="fas fa-info-circle"
+                 <em>cellular heterogenetity</em>."
+                 data-content="Click the info icon to read more on Wikipedia."><i class="fas fa-info-circle"
                  aria-hidden="true"></i></a></th>
                 <th style="width: 1%;" class="rotate-45 text-dark-pink"><div><span><a
-                 href="#" data-toggle="popover" data-trigger="hover" class="popoveradjust"
-                 data-placement="top"  data-container="body" data-html="true" title=""
-                 data-content="Whole genome sequencing."><i class="fas fa-info-circle"
+                 href="https://en.wikipedia.org/wiki/Whole_genome_sequencing" target="_blank"  data-toggle="popover" data-trigger="hover" class="popoveradjust"
+                 data-placement="top"  data-container="body" data-html="true" title="Whole genome sequencing."
+                 data-content="Click the info icon to read more on Wikipedia."><i class="fas fa-info-circle"
                  aria-hidden="true"></i></a> WGS</span</div></th>
                 <th style="width: 1%;" class="text-nowrap rotate-45
-                 text-dark-pink"><div><span><a href="#" data-toggle="popover" data-trigger="hover"
+                 text-dark-pink"><div><span><a href="https://www.illumina.com/techniques/sequencing/dna-sequencing/targeted-resequencing/amplicon-sequencing.html"
+                 target="_blank" data-toggle="popover" data-trigger="hover"
                  class="popoveradjust" data-placement="top"  data-container="body"
-                 data-html="true" title="" data-content="A method for sequencing a specific
-                 region of interest. Similar to AMP-seq."><i class="fas
+                 data-html="true" title="A method for sequencing a specific
+                 region of interest. Similar to AMP-seq." data-content="Click the info icon to read more on the Illumina website."><i class="fas
                  fa-info-circle" aria-hidden="true"></i></a> Amplicon-seq</span</div></th>
                 <th style="width: 1%;" class="rotate-45
-                 text-light-blue"><div><span><a href="#" data-toggle="popover" data-trigger="hover"
+                 text-light-blue"><div><span><a href="https://www.ncbi.nlm.nih.gov/pubmed/19015660" target="_blank" data-toggle="popover" data-trigger="hover"
                  class="popoveradjust" data-placement="top"  data-container="body"
-                 data-html="true" title="" data-content="Some RNA-seq is done on bulk tissue,
+                 data-html="true" title="Some RNA-seq is done on bulk tissue,
                  though for this project much of it is done on single cells. The icons in the
                  single cell column indicate how the cells were handled to generate the RNA-seq
-                 data."><i class="fas fa-info-circle" aria-hidden="true"></i></a>
+                 data." data-content="Click info icon to read a review paper of RNA-seq (2009)."><i class="fas fa-info-circle" aria-hidden="true"></i></a>
                  RNA-seq</span></div></th>
                 <th style="width: 1%;" class="rotate-45
-                 text-light-blue"><div><span><a href="#" data-toggle="popover" data-trigger="hover"
+                 text-light-blue"><div><span><a href="https://www.ncbi.nlm.nih.gov/pubmed/22081020" target="_blank" data-toggle="popover" data-trigger="hover"
                  class="popoveradjust" data-placement="top"  data-container="body"
-                 data-html="true" title="" data-content="Genotyping method. Based on capturing and
-                 sequencing specifc regions of the genome."><i class="fas
+                 data-html="true" title="Genotyping method. Based on capturing and
+                 sequencing specifc regions of the genome." data-content="Click info icon to read the Capture-seq paper (2011)."><i class="fas
                  fa-info-circle" aria-hidden="true"></i></a> Capture-seq</span></div></th>
                 <th style="width: 1%;" class="rotate-45
-                 text-light-blue"><div><span><a href="#" data-toggle="popover" data-trigger="hover"
+                 text-light-blue"><div><span><a href="https://www.ncbi.nlm.nih.gov/pubmed/23783272" target="_blank" data-toggle="popover" data-trigger="hover"
                  class="popoveradjust" data-placement="top"  data-container="body"
-                 data-html="true" title="" data-content="A method to distinguish RNA from different
-                 subcellular fractionations"><i class="fas
+                 data-html="true" title="A method to distinguish RNA from different
+                 subcellular fractionations." data-content="Click info icon to read the Frac-seq paper (2013)."><i class="fas
                  fa-info-circle" aria-hidden="true"></i></a> Frac-seq</span></div></th>
                 <th style="width: 1%;" class="text-nowrap rotate-45
-                 text-light-green"><div><span><a href="#" data-toggle="popover" data-trigger="hover"
+                 text-light-green"><div><span><a href="https://en.wikipedia.org/wiki/ChIP-sequencing" target="_blank" data-toggle="popover" data-trigger="hover"
                  class="popoveradjust" data-placement="top"  data-container="body"
-                 data-html="true" title="" data-content="Used to profile histone modifications."
+                 data-html="true" title="Used to profile histone modifications." data-content="Click the info icon to read more on Wikipedia."
                  ><i class="fas
                  fa-info-circle" aria-hidden="true"></i></a> broad-ChIP-seq</span></div></th>
                 <th style="width: 1%;" class="text-nowrap rotate-45
-                 text-light-green"><div><span><a href="#" data-toggle="popover" data-trigger="hover"
+                 text-light-green"><div><span><a href="https://en.wikipedia.org/wiki/ChIP-sequencing" target="_blank" data-toggle="popover" data-trigger="hover"
                  class="popoveradjust" data-placement="top"  data-container="body"
-                 data-html="true" title="" data-content="Used to profile transcription factor (TF)
-                 binding sites."><i class="fas
+                 data-html="true" title="Used to profile transcription factor (TF)
+                 binding sites." data-content="Click the info icon to read more on Wikipedia."><i class="fas
                  fa-info-circle" aria-hidden="true"></i></a> narrow-ChIP-seq</span></div></th>
                 <th style="width: 1%;" class="rotate-45 text-light-green"><div><span><a
-                 href="https://www.ncbi.nlm.nih.gov/pubmed/28973448" data-toggle="popover"r
+                 href="https://www.ncbi.nlm.nih.gov/pubmed/28973448" target="_blank" data-toggle="popover"
                  data-trigger="hover" class="popoveradjust"
                  data-placement="top"  data-container="body" data-html="true" title="Targeted
                  chromatin ligation sequencing. Used in epigenetics to capture histone
                  modification patterns low-cell count experiments." data-content="Click the
-                 info icon to see the paper (2017)"><i
+                 info icon to read the TCL-seq paper (2017)."><i
                  class="fas fa-info-circle" aria-hidden="true"></i></a> TCL-seq</span></div></th>
                 <th style="width: 1%;" class="rotate-45 text-light-green"><div><span><a
-                 href="" data-toggle="popover" data-trigger="hover" class="popoveradjust"
-                 data-placement="top"  data-container="body" data-html="true" title=""
-                 data-content="Whole genome bisulfite sequencing. A method for looking at
-                 methylation throughout the genome."><i class="fas fa-info-circle"
+                 href="https://en.wikipedia.org/wiki/Whole_genome_bisulfite_sequencing" target="_blank" data-toggle="popover" data-trigger="hover" class="popoveradjust"
+                 data-placement="top"  data-container="body" data-html="true" title="Whole genome bisulfite sequencing. A method for looking at
+                 methylation throughout the genome."
+                 data-content="Click the info icon to read more on Wikipedia."><i class="fas fa-info-circle"
                  aria-hidden="true"></i></a> WGBS</span></div></th>
                 <th style="width: 1%;" class="rotate-45 text-light-green"><div><span><a
                  href="https://www.ncbi.nlm.nih.gov/pubmed/16224102" target="_blank"
                  data-toggle="popover" data-trigger="hover" class="popoveradjust"
                  data-placement="top"  data-container="body" data-html="true"
                  title="Reduced-representation Bisulifite Sequencing to determine methylation of
-                 promoter sites" data-content="Click the info icon to see the paper (2005)"><i
+                 promoter sites" data-content="Click the info icon to read the RRBS paper (2005)."><i
                  class="fas fa-info-circle" aria-hidden="true"></i></a> RRBS</th>
                 <th style="width: 1%;" class="rotate-45 text-light-green"><div><span><a
-                 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4374986/" target="_blank"
+                 href="https://www.ncbi.nlm.nih.gov/pubmed/25559105" target="_blank"
                  data-toggle="popover" data-trigger="hover" class="popoveradjust"
                  data-placement="top"  data-container="body" data-html="true"
                  title="Transposase-Accessible Chromatin with high throughput sequencing"
-                 data-content="Click the info icon to see the ATAC-seq publication."><i class="fas
+                 data-content="Click the info icon to read the ATAC-seq paper (2015)."><i class="fas
                  fa-info-circle" aria-hidden="true"></i></a> ATAC-seq</span></div></th>
                 <th style="width: 1%;" class="rotate-45 text-light-green"><div><span><a
-                 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3149993/" target="_blank"
+                 href="https://www.ncbi.nlm.nih.gov/pubmed/20461051" target="_blank"
                  data-toggle="popover" data-trigger="hover" class="popoveradjust"
                  data-placement="top"  data-container="body" data-html="true" title="Assay to
                  determine spatial organization of chromatin" data-content="Click the info icon
-                 to see the Hi-C paper (2010)."><i class="fas fa-info-circle"
+                 to read the Hi-C paper (2010)."><i class="fas fa-info-circle"
                  aria-hidden="true"></i></a> Hi-C</span></div></th>
                 <th style="width: 1%;" class="rotate-45 text-orange"><div><span><a
-                 href="http://www.nature.com/nbt/journal/v33/n2/full/nbt.3117.html"
+                 href="https://www.ncbi.nlm.nih.gov/pubmed/25513782"
                  target="_blank" data-toggle="popover" data-trigger="hover" class="popoveradjust"
                  data-placement="top"  data-container="body" data-html="true" title="Genome-wide
                  Unbiased Identifications of double strand breaks (DSBs) Evaluated by Sequencing"
-                 data-content="Click the info icon to see the paper (2014)."><i class="fas
+                 data-content="Click the info icon to read the GUIDE-seq paper (2014)."><i class="fas
                  fa-info-circle" aria-hidden="true"></i></a> GUIDE-seq</span></div></th>
                 <th style="width: 1%;" class="rotate-45 text-dark-blue"><div><span><a
-                 href="#"
+                 href="https://www.ncbi.nlm.nih.gov/pubmed/27365449"
                  target="_blank" data-toggle="popover" data-trigger="hover" class="popoveradjust"
-                 data-placement="top"  data-container="body" data-html="true" title=""
-                 data-content="Includes a number of different imaging techniques and data types."><i class="fas
+                 data-placement="top"  data-container="body" data-html="true"
+                 title="In this project, imaging is only used in the context of
+                 spatial transcriptomics. Flourescent probes are used to
+                 measure both the relative expression of specific genes and where these genes
+                 are being activated."
+                 data-content="Click info icon to read the Spatial Transcriptomics paper (2016)."><i class="fas
                  fa-info-circle" aria-hidden="true"></i></a> Imaging</span></div></th>
             </tr>
         </thead>
 
         <tbody>
             <tr style="font-size: 75%">
                 <td colspan="3"></td>
 	            <td class="text-dark-blue text-nowrap"></td>
                 <td colspan="2" class="text-dark-pink"></td>
                 <td colspan="3" class="text-light-blue"></td>
                 <td colspan="3" class="text-light-green text-center">Histone modification</td>
                 <td colspan="2" class="text-light-green text-center">Methylome</td>
                 <td colspan="2" class="text-light-green text-nowrap text-center">Chromatin<br>modeling</td>
                 <td colspan="1" class="text-orange text-nowrap text-center">Gene editing<br>profiling</td>
                 <td colspan="1" class="text-dark-blue"></td>