63a95bfe1026e5097a22bf8d334c4de4380cb9a5
mspeir
  Wed Apr 3 14:03:49 2019 -0700
Adding links to download files for a dataset to projects page. refs #23124

diff --git src/hg/cirm/gateway/htdocs/projects.html src/hg/cirm/gateway/htdocs/projects.html
index bc50ed5..44f92da 100755
--- src/hg/cirm/gateway/htdocs/projects.html
+++ src/hg/cirm/gateway/htdocs/projects.html
@@ -284,31 +284,36 @@
                  data-toggle="popover" data-trigger="hover" class="popoveradjust"
                  data-placement="top"  data-container="body" data-html="true" title="Single-cell
                  Brain Organoids" data-content="874 iPSC-derived brain organoid samples processed
                  via single-cell RNA-seq." aria-hidden="true"></i><br>&nbsp;&nbsp;
                  <a href="https://www.ncbi.nlm.nih.gov/pubmed/26406371" target="_blank"
                  data-toggle="popover" data-trigger="hover" data-placement="top"
                  data-container="body" data-html="true" title="Pollen AA et al. 2019.
                  Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution. Cell."
                  data-content="View publication from this dataset"><i class="fas fa-file-alt"
                  aria-hidden="true"></i></a>&nbsp;
                 <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE124299"
                 target="_blank" data-toggle="popover" data-trigger="hover" data-placement="top"
                 data-container="body" data-html="true" title="<img
                 src='https://www.ncbi.nlm.nih.gov/geo/img/geo_main.gif' style='height:
                 2em;'>View GSE124299" data-content="Click database icon to view on GEO."><i
-                class="fas fa-database" aria-hidden="true"></i></a></td>
+                class="fas fa-database" aria-hidden="true"></i></a>&nbsp;
+                <a href="../cgi-bin/cdwWebBrowse?browseFiles_facet_op=resetAll&browseFiles_facet_fieldName=&browseFiles_facet_fieldVal=&cdwCommand=browseFiles&cdwFile_filter=data_set_id%3D%27kriegsteinBrainOrganoids1%27%20"
+                 target="_blank" data-toggle="popover" data-trigger="hover" data-placement="top"
+                 data-container="body" data-html="true" title=""
+                 data-content="Download from the Stem Cell Hub">
+                 <i class="fas fa-file-download" aria-hidden="true"></i></a></td>
                 <td class="text-dark-blue text-center"><i class="fas fa-braille fa-lg" aria-hidden="true"></i></td>
                 <td class="text-dark-pink text-center"></td>
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                 <td class="text-light-green text-center"></td>
                 <td class="text-orange text-center"></td>
                 <td class="text-dark-blue text-center"></td>
@@ -361,31 +366,35 @@
                  data-toggle="popover" data-trigger="hover" class="popoveradjust"
                  data-placement="top"  data-container="body" data-html="true" title="single-cell
                  brain development" data-content="376 primary samples of fetal radial glial cells
                  that were processed via single-cell RNA-seq."></i><br>&nbsp;&nbsp;
                  <a href="https://www.ncbi.nlm.nih.gov/pubmed/26406371" target="_blank"
                  data-toggle="popover" data-trigger="hover" data-placement="top"
                  data-container="body" data-html="true" title="Pollen AA et al. 2015. 
                  Molecular identity of human outer radial glia during cortical development. Cell."
                  data-content="View publication from this dataset"><i class="fas fa-file-alt"
                  aria-hidden="true"></i></a>&nbsp;
                 <a href="https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000989"
                 target="_blank" data-toggle="popover" data-trigger="hover" data-placement="top"
                 data-container="body" data-html="true" title="<img
                 src='https://www.ncbi.nlm.nih.gov/projects/gap/images/dbGaP_logo_final.jpg' style='height:
                 2em;'> View phs000989" data-content="Click database icon to view on dbGaP"><i class="fas fa-database"
-                aria-hidden="true"></i></a></td>
+                aria-hidden="true"></i></a>&nbsp;
+                <a href="../cgi-bin/cdwWebBrowse?browseFiles_facet_op=resetAll&browseFiles_facet_fieldName=&browseFiles_facet_fieldVal=&cdwCommand=browseFiles&cdwFile_filter=data_set_id%3D%27kriegsteinRadialGliaStudy1%27%20"
+                 target="_blank" data-toggle="popover" data-trigger="hover" data-placement="top"
+                 data-container="body" data-html="true" title=""
+                 data-content="Download from the Stem Cell Hub"><i class="fas fa-file-download" aria-hidden="true"></i></a></td>
                 <td class="text-dark-blue text-center"><i class="fas fa-braille fa-lg" aria-hidden="true"></i></td>
                 <td class="text-dark-pink text-center"></td>
                 <td class="text-dark-pink text-center"></td>
                 <td class="text-light-blue text-center"><i class="fas fa-square" aria-hidden="true"></i></td>
                 <td class="text-light-blue text-center"></td>
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                 <td class="text-light-green text-center"></td>
                 <td class="text-orange text-center"></td>
                 <td class="text-dark-blue text-center"></td>
@@ -398,31 +407,35 @@
                 <td class="datasetid"><a href="/d/kriegstein6k">kriegstein6k</a> <i class="fas fa-info-circle" aria-hidden="true"
                  data-toggle="popover" data-trigger="hover" class="popoveradjust"
                  data-placement="top"  data-container="body" data-html="true" title=""
                  data-content="RNA-seq from 6,000 primary cells at UCSF."></i><br>&nbsp;&nbsp;
                  <a href="https://www.ncbi.nlm.nih.gov/pubmed/29217575" target="_blank"
                  data-toggle="popover" data-trigger="hover" data-placement="top"
                  data-container="body" data-html="true" title="Nowakowski TJ et al. 2017.
                  Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex. Science."
                  data-content="View publication from this dataset"><i class="fas fa-file-alt"
                  aria-hidden="true"></i></a>&nbsp;
                 <a href="https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000989"
                 target="_blank" data-toggle="popover" data-trigger="hover" data-placement="top"
                 data-container="body" data-html="true" title="<img
                 src='https://www.ncbi.nlm.nih.gov/projects/gap/images/dbGaP_logo_final.jpg' style='height:
                 2em;'> View phs000989" data-content="Click database icon to view on dbGaP"><i class="fas fa-database"
-                aria-hidden="true"></i></a></td>
+                aria-hidden="true"></i></a>&nbsp;
+                <a href="../cgi-bin/cdwWebBrowse?browseFiles_facet_op=resetAll&browseFiles_facet_fieldName=&browseFiles_facet_fieldVal=&cdwCommand=browseFiles&cdwFile_filter=data_set_id%3D%27kriegstein6k%27%20"
+                 target="_blank" data-toggle="popover" data-trigger="hover" data-placement="top"
+                 data-container="body" data-html="true" title=""
+                 data-content="Download from the Stem Cell Hub"><i class="fas fa-file-download" aria-hidden="true"></i></a></td>
                 <td class="text-dark-blue text-center"><i class="fas fa-braille fa-lg" aria-hidden="true"></i></td>
                 <td class="text-dark-pink text-center"></td>
                 <td class="text-dark-pink text-center"></td>
                 <td class="text-light-blue text-center"><i class="fas fa-square" aria-hidden="true"></i></td>
                 <td class="text-light-blue text-center"></td>
                 <td class="text-light-green text-center"></td>
                 <td class="text-light-blue text-center"></td>
                 <td class="text-light-green text-center"></td>
                 <td class="text-light-green text-center"></td>
                 <td class="text-light-green text-center"></td>
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                 <td class="text-light-green text-center"></td>
                 <td class="text-orange text-center"></td>
                 <td class="text-dark-blue text-center"></td>
@@ -475,35 +488,35 @@
                 data-container="body" data-html="true" title="" data-content="View analysis of
                 this dataset"><i class="fa fa-bar-chart" aria-hidden="true"></i></a>
                 &nbsp;-->
                 <a href="https://www.ncbi.nlm.nih.gov/pubmed/26060301" target="_blank"
                 data-toggle="popover" data-trigger="hover" data-placement="top"
                 data-container="body" data-html="true" title="Darmanis S et al. 2015. A survey
                 of human brain transcriptome diversity at the single cell level. PNAS."
                 data-content="View publication from this dataset"><i class="fas fa-file-alt"
                 aria-hidden="true"></i></a>&nbsp;
                 <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE67835"
                 target="_blank" data-toggle="popover" data-trigger="hover" data-placement="top"
                 data-container="body" data-html="true" title="<img
                 src='https://www.ncbi.nlm.nih.gov/geo/img/geo_main.gif' style='height:
                 2em;'>View GSE67835" data-content="Click database icon to view on GEO."><i
                 class="fas fa-database" aria-hidden="true"></i></a>&nbsp;
-                <a href="../cgi-bin/cdwWebBrowse?cdwCommand=browseFiles&browseFiles_facet_op=add&browseFiles_facet_fieldName=data_set_id&browseFiles_facet_fieldVal=quakeBrainGeo1"
+                <a href="../cgi-bin/cdwWebBrowse?browseFiles_facet_op=resetAll&browseFiles_facet_fieldName=&browseFiles_facet_fieldVal=&cdwCommand=browseFiles&cdwFile_filter=data_set_id%3D%27quakeBrainGeo1%27%20"
                  target="_blank" data-toggle="popover" data-trigger="hover" data-placement="top"
                  data-container="body" data-html="true" title=""
                  data-content="Download from the Stem Cell Hub">
-                 <i class="fas fa-file-download" aria-hidden="true"></i>
+                 <i class="fas fa-file-download" aria-hidden="true"></i></a>
                 </td>
                 <td class="text-dark-blue text-center"><i class="fas fa-braille fa-lg" aria-hidden="true"></i></td>
                 <td class="text-dark-pink text-center"></td>
                 <td class="text-dark-pink text-center"></td>
                 <td class="text-light-blue text-center"><i class="fas fa-square text-light-blue"
                 aria-hidden="true"></i></a></td>
                 <td class="text-light-blue text-center"></td>
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                 <td class="text-light-green text-center"></td>
@@ -518,31 +531,36 @@
                  data-placement="top"  data-container="body" data-html="true" title=""
                  data-content="Characterizing the effects of glioblastoma on
                  normal brain."></i><br>&nbsp;&nbsp;
                 <a href="https://www.ncbi.nlm.nih.gov/pubmed/29091775/" target="_blank"
                 data-toggle="popover" data-trigger="hover" data-placement="top"
                 data-container="body" data-html="true" title="Darmanis, S., et al. (2017).
                 Single-Cell RNA-Seq Analysis of Infiltrating Neoplastic Cells at the Migrating
                 Front of Human Glioblastoma. Cell Rep."
                 data-content="View publication from this dataset"><i class="fas fa-file-alt"
                 aria-hidden="true"></i></a>&nbsp;
                 <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84465"
                 target="_blank" data-toggle="popover" data-trigger="hover" data-placement="top"
                 data-container="body" data-html="true" title="<img
                 src='https://www.ncbi.nlm.nih.gov/geo/img/geo_main.gif' style='height:
                 2em;'>View GSE84465" data-content="Click database icon to view on GEO."><i
-                class="fas fa-database" aria-hidden="true"></i></td>
+                class="fas fa-database" aria-hidden="true"></i>&nbsp;
+                <a href="../cgi-bin/cdwWebBrowse?browseFiles_facet_op=resetAll&browseFiles_facet_fieldName=&browseFiles_facet_fieldVal=&cdwCommand=browseFiles&cdwFile_filter=data_set_id%3D%27quakeGlioblastomaGeo1%27%20"
+                 target="_blank" data-toggle="popover" data-trigger="hover" data-placement="top"
+                 data-container="body" data-html="true" title=""
+                 data-content="Download from the Stem Cell Hub">
+                 <i class="fas fa-file-download" aria-hidden="true"></i></a></td>
                 <td class="text-dark-blue text-center"><i class="fas fa-braille fa-lg" aria-hidden="true"></i></td>
                 <td class="text-dark-pink text-center"></td>
                 <td class="text-dark-pink text-center"></td>
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@@ -798,31 +816,31 @@
                 <td class="text-light-blue text-center"><i class="fas fa-square" aria-hidden="true"></i></td>
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                 <td class="text-dark-blue text-center"></td>
             </tr>
 
             <tr>
-                <td colspan="100%">Blood stem cells and therapeutics</td>
+                <td colspan="100%">Blood stem cells</td>
             </tr>
 
             <tr>
                 <td></td>
                 <td class="lab text-nowrap"><a href="http://baldwin.scripps.edu/"
                  target="_blank" data-toggle="popover" data-trigger="hover" data-placement="top"
                  data-container="body" data-html="true" title="Kristin Baldwin, Scripps"
                  data-content="The Baldwin lab is studying a matched set of iPSC lines
                  from patients with cardiovascular disease.">Baldwin</a>
                  <i class="fas fa-external-link-alt icon-sm" aria-hidden="true"></i></td>
                 <td class="datasetid text-nowrap">baldwin12PairedIpscCellLines1 <i class="fas fa-info-circle" aria-hidden="true"
                  data-toggle="popover" data-trigger="hover" class="popoveradjust"
                  data-placement="top"  data-container="body" data-html="true" title=""
                  data-content="A study of the mutagenic effects of the induction process
                  by comparing two different methods of induction using fribroblast-derived
@@ -844,55 +862,65 @@
                 <td class="text-dark-blue text-center"></td>
             </tr>
             <tr>
                 <td></td>
                 <td class="lab text-nowrap"><a href="https://cornlab.com/" target="_blank"
                  data-toggle="popover" data-trigger="hover" data-placement="top"
                  data-container="body" data-html="true" title="Jacob Corn, UC Berkeley"
                  data-content="The Corn lab is investigating fixing sickle cell
                  anemia with CRISPR. Aim 1 of the Corn lab is to use RNA-seq to explore
                  erythroid (red blood cell) maturation. Aim 2 is using boutique DNA-seq methods
                  to investigate effets of using CRISPR.">Corn</a>
                  <i class="fas fa-external-link-alt icon-sm" aria-hidden="true"></i></td>
                 <td class="datasetid"><a href="/d/cornErythroidMaturation">cornErythroidMaturation</a> <i class="fas fa-info-circle" aria-hidden="true"
                  data-toggle="popover" data-trigger="hover" class="popoveradjust"
                  data-placement="top"  data-container="body" data-html="true" title=""
-                 data-content="Investigating erythoid maturation with RNA-seq."></i></td>
+                 data-content="Investigating erythoid maturation with RNA-seq."></i><br>&nbsp;&nbsp;
+                <a href="../cgi-bin/cdwWebBrowse?browseFiles_facet_op=resetAll&browseFiles_facet_fieldName=&browseFiles_facet_fieldVal=&cdwCommand=browseFiles&cdwFile_filter=data_set_id%3D%27cornErythroidMaturation%27%20"
+                 target="_blank" data-toggle="popover" data-trigger="hover" data-placement="top"
+                 data-container="body" data-html="true" title=""
+                 data-content="Download from the Stem Cell Hub">
+                 <i class="fas fa-file-download" aria-hidden="true"></i></a></td>
                 <td class="text-dark-blue text-center"></td>
                 <td class="text-dark-pink text-center"></td>
                 <td class="text-dark-pink text-center"></td>
                 <td class="text-light-blue text-center"><i class="fas fa-square" aria-hidden="true"></i></td>
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             </tr>
             <tr>
                 <td></td>
                 <td class="lab text-nowrap"></td>
                 <td class="datasetid"><a href="/d/cornOffTarget">cornOffTarget</a> <i class="fas fa-info-circle" aria-hidden="true"
                 data-toggle="popover"
                  data-trigger="hover" class="popoveradjust" data-placement="top"
                  data-container="body" data-html="true" title="" data-content="Investigating
-                 CRISPR off-target cleavage sites using GUIDE-seq, Amplicon-seq and Capture-seq."></i></td>
+             >RISPR off-target cleavage sites using GUIDE-seq, Amplicon-seq and Capture-seq."></i><br>&nbsp;&nbsp;
+                <a href="../cgi-bin/cdwWebBrowse?browseFiles_facet_op=resetAll&browseFiles_facet_fieldName=&browseFiles_facet_fieldVal=&cdwCommand=browseFiles&cdwFile_filter=data_set_id%3D%27cornOffTarget%27%20"
+                 target="_blank" data-toggle="popover" data-trigger="hover" data-placement="top"
+                 data-container="body" data-html="true" title=""
+                 data-content="Download from the Stem Cell Hub">
+                 <i class="fas fa-file-download" aria-hidden="true"></i></a></td>
                 <td class="text-dark-blue text-center"></td>
                 <td class="text-dark-pink text-center"></td>
                 <td class="text-dark-pink text-center"><i class="fas fa-square" aria-hidden="true"></i></td>
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@@ -1106,73 +1134,85 @@
                  data-content="Single cell transcriptome analysis of human pancreas
                  reveals transcriptional signatures of aging and somatic mutation patterns."
                  ></i><br>&nbsp;&nbsp;
                 <a href="https://www.ncbi.nlm.nih.gov/pubmed/28965763" target="_blank"
                 data-toggle="popover" data-trigger="hover" data-placement="top"
                 data-container="body" data-html="true" title="Enge M et al. 2017. Single-Cell
                 Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and
                 Somatic Mutation Pattern. Cell."
                 data-content="View publication from this dataset"><i class="fas fa-file-alt"
                 aria-hidden="true"></i></a>&nbsp;
                 <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81547"
                 target="_blank" data-toggle="popover" data-trigger="hover" data-placement="top"
                 data-container="body" data-html="true" title="<img
                 src='https://www.ncbi.nlm.nih.gov/geo/img/geo_main.gif' style='height:
                 2em;'>View GSE81547" data-content="Click database icon to view on GEO."><i
-                class="fas fa-database" aria-hidden="true"></i></a>
+                class="fas fa-database" aria-hidden="true"></i></a>&nbsp;
+                <a href="../cgi-bin/cdwWebBrowse?browseFiles_facet_op=resetAll&browseFiles_facet_fieldName=&browseFiles_facet_fieldVal=&cdwCommand=browseFiles&cdwFile_filter=data_set_id%3D%27quakePancreas1%27%20"
+                 target="_blank" data-toggle="popover" data-trigger="hover" data-placement="top"
+                 data-container="body" data-html="true" title=""
+                 data-content="Download from the Stem Cell Hub">
+                 <i class="fas fa-file-download" aria-hidden="true"></i></a>
                 </td>
                 <td class="text-dark-blue text-center"><i class="fas fa-braille fa-lg" aria-hidden="true"></i></td>
                 <td class="text-dark-pink text-center"></td>
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                 <td class="text-dark-blue text-center"></td>
             </tr>
             <tr>
                 <td></td>
                 <td class="lab text-nowrap"></td>
                 <!--<td class="datasetid"><a href="/d/quakeFetalPancreasSpatial">quakeFetalPancreasSpatial</a>-->
                 <td class="datasetid">quakeFetalPancreasSpatial
                 <i class="fas fa-info-circle" aria-hidden="true"
                  data-toggle="popover" data-trigger="hover" class="popoveradjust"
                  data-placement="top"  data-container="body" data-html="true" title=""
-                 data-content=""></i>
-                <!--
+                 data-content="Analysis of the spatial distribution of single mRNA
+                 molecules measured by in situ sequencing on human fetal
+                 pancreas at three developmental time points–80, 87 and
+                 117 days post-fertilization"></i>
                 <br>&nbsp;&nbsp;
-                <a href="https://www.ncbi.nlm.nih.gov/pubmed/26060301" target="_blank"
+                <a href="https://www.nature.com/articles/s41598-019-41951-2" target="_blank"
                 data-toggle="popover" data-trigger="hover" data-placement="top"
-                data-container="body" data-html="true" title="Enge M et al. 2017. Single-Cell
-                Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and
-                Somatic Mutation Pattern. Cell."
+                data-container="body" data-html="true" title="Riu L et al. 2019.
+                Modeling Spatial Correlation of Transcripts with Application to Developing Pancreas. Nature Scientific Reports."
                 data-content="View publication from this dataset"><i class="fas fa-file-alt"
-                aria-hidden="true"></i></a>&nbsp;
+                aria-hidden="true"></i></a>
+                <!--&nbsp;
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+                -->&nbsp;
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