fce3010f837ef9eacc71b4a8153dda3db6037d6e bnguy Mon Feb 24 15:06:21 2020 -0800 Remove icons and changes to single cell column on project.html, index page now has clickable icons, add credit images to orgs page diff --git src/hg/cirm/gateway/htdocs/projects.html src/hg/cirm/gateway/htdocs/projects.html index 58da43f..8656f32 100755 --- src/hg/cirm/gateway/htdocs/projects.html +++ src/hg/cirm/gateway/htdocs/projects.html @@ -1,62 +1,26 @@ <!DOCTYPE html> <!--#set var="TITLE" value="CIRM Stem Cell Hub Projects" --> <!--#include virtual="setRoot.html" --> <!--#include virtual="${ROOT}inc/header.html" --> <div class="cirm-page-body"> <div class="cirm-page-title back-light-blue" style="//background: #1E90FF;"> <h5 class="cirm-page-title-text">Projects initiated and funded by the CESCG</h5> </div> - - <div class="row" style="background:#fff; border:1px solid #ed217c; padding: 10px; margin: 10px 0; position: relative"> - <div class="col-12"> - <div class="row"> - <p class="lead text-dark-blue">Legend:</p> - </div> - <div class="row"> - <div class="col-4"> - <i class="fas fa-braille fa-lg text-dark-blue" aria-hidden="true"></i> - - Plate-based sequencing (e.g. SMART-seq2) - </div> - <div class="col-4"> - <i class="fas fa-tint fa-lg text-dark-blue" aria-hidden="true"></i> - - Droplet-based sequencing (e.g. 10X) - </div> - <div class="col-4"> - <i class="fas fa-database fa-lg text-dark-blue" aria-hidden="true"></i> - - Online Data Archive (e.g. GEO) - </div> - </div> - <div class="row"> - <div class="col-4"> - <i class="fas fa-file-alt fa-lg text-dark-blue" aria-hidden="true"></i> - - PubMed Link - </div> - <div class="col-4"> - <i class="fas fa-file-download fa-lg text-dark-blue" aria-hidden="true"></i> - - 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> <!--<div class="table-responsive scrollable-table" style="/*padding-right: 80px;*/">--> <div style="padding-right: 80px"> <table class="table table-hover table-header-rotated" style="overflow: visible"> <thead> <tr> <!-- <th style="width: 1%;" class="text-nowrap"> Research Theme </th> <th style="width: 1%;" class="text-nowrap"> Lab </th> <th style="width: 1%;" class="text-nowrap "> Data Set @@ -412,39 +376,30 @@ 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="<!--#echo var='ROOT'-->d/cornErythroidMaturation">cornErythroidMaturation</a> <i class="fas fa-info-circle popoveradjust" aria-hidden="true" data-toggle="popover" data-trigger="hover" data-placement="top" data-container="body" data-html="true" title="" data-content="Investigating erythoid maturation with RNA-seq."></i> - <br> - <!-- SCHub Icon/Link --> - <a href="<!--#echo var='ROOT'-->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" class="popoveradjust" - 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> <td class="text-light-blue 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> <td class="text-light-green text-center"></td> <td class="text-light-green text-center"></td> <td class="text-light-green text-center"></td> @@ -453,39 +408,30 @@ <i class="fas fa-square" aria-hidden="true"></i> </td> <td class="text-dark-blue text-center"></td> </tr> <tr> <td></td> <td class="lab text-nowrap"></td> <td class="datasetid"> <a href="<!--#echo var='ROOT'-->d/cornOffTarget">cornOffTarget</a> <i class="fas fa-info-circle popoveradjust" aria-hidden="true" data-toggle="popover" data-trigger="hover" 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> - <br> - <!-- SCHub Icon/Link --> - <a href="<!--#echo var='ROOT'-->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" class="popoveradjust" - 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> <td class="text-light-blue 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-green text-center"></td> <td class="text-light-green text-center"></td> <td class="text-light-green text-center"></td> @@ -498,31 +444,31 @@ <td class="text-dark-blue text-center"></td> </tr> <tr> <td></td> <td class="lab text-nowrap"></td> <td class="datasetid"> cornHspc <i class="fas fa-info-circle popoveradjust" aria-hidden="true" data-toggle="popover" data-trigger="hover" data-placement="top" data-container="body" data-html="true" title="" data-content="Single cell RNA-seq of hematopoietic stem cells using 10X to identify hematopoietic stem and progenitor cells."></i> </td> <td class="text-dark-blue text-center"> - <i class="fas fa-tint fa-lg" aria-hidden="true"></i> + <i class="fas fa-square" 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-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> <td class="text-light-green 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> @@ -584,31 +530,31 @@ the generation of cancer stem cells (CSCs) from a variety of blood and solid tissue cancers.">Weissman</a> <i class="fas fa-external-link-alt icon-sm" aria-hidden="true"></i> </td> <td class="datasetid"> weissmanHsc1 <i class="fas fa-info-circle popoveradjust" aria-hidden="true" data-toggle="popover" data-trigger="hover" data-placement="top" data-container="body" data-html="true" title="" data-content="Single-cell RNA-seq of the rare, blood-forming haematopoietic stem cells (HSCs) in bone marrow. Bone marrow cells were separated using FACS with sorting on standard, in-house developed markers."></i> </td> <td class="text-dark-blue text-center"> - <i class="fas fa-braille fa-lg" aria-hidden="true"></i> + <i class="fas fa-square" 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-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> <td class="text-light-green 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> @@ -660,31 +606,31 @@ </tr> <tr> <td></td> <td class="lab text-nowrap"></td> <td class="datasetid"> bruneauTbx5 <i class="fas fa-info-circle popoveradjust" aria-hidden="true" data-toggle="popover" data-trigger="hover" data-placement="top" data-container="body" data-html="true" title="" data-content="Using two different cardiac differentiation protocols, human gene expression programs are defined that are susceptible to TBX5 dosage at single cell resolution in iPSC-derived cardiomyocytes."></i> </td> <td class="text-dark-blue text-center"> - <i class="fas fa-tint fa-lg" aria-hidden="true"></i> + <i class="fas fa-square" 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-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> <td class="text-light-green text-center"></td> <td class="text-light-green text-center"></td> <td class="text-light-green text-center"> <i class="fas fa-square" aria-hidden="true"></i> @@ -704,31 +650,31 @@ functional cardiomyocytes for cardiac and vascular regenerative repairs.">Chi</a> <i class="fas fa-external-link-alt icon-sm" aria-hidden="true"></i> </td> <td class="datasetid"> chiCardiomyocyte1 <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="Analysis of in vitro and in vivo human cardiovascular lineages" data-content="Discovery of gene regulatory networks that facilitate the differentiation of human pluripotent stem cells (hPSC) into ventricular and atrial cardiomyocyte (CM) lineages using single cell RNA-seq (scRNA-Seq) on cells derived from human hearts at different developmental stages."></i> </td> <td class="text-dark-blue text-center"> - <i class="fas fa-tint fa-lg" aria-hidden="true"></i> + <i class="fas fa-square" 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="fa fa-square" aria-hidden="true"></i> </td> <td class="text-light-blue 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> <td class="text-light-green text-center"></td> <td class="text-light-green text-center"></td> <td class="text-light-green text-center"> <i class="fas fa-square" aria-hidden="true"></i> @@ -738,31 +684,31 @@ <td class="text-dark-blue text-center"></td> </tr> <tr> <td></td> <td class="lab text-nowrap"></td> <td class="datasetid"> chiMouseCardiomyocyte <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="To discover transcriptional networks that regulate the differentiation of mouse cardiovascular lineages."></i> </td> <td class="text-dark-blue text-center"> - <i class="fas fa-tint fa-lg" aria-hidden="true"></i> + <i class="fas fa-square" 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-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> <td class="text-light-green 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> @@ -779,31 +725,31 @@ data-content="The Frazer lab is focused on performing high-throughput phenotypic characterization of iPSC-derived cardiomyocytes from a diverse set of ethnicities to enable further genetic studies investigating the segregation of traits.">Frazer</a> <i class="fas fa-external-link-alt icon-sm" aria-hidden="true"></i></td> <td class="datasetid"> frazerCardIps1 <i class="fas fa-info-circle popoveradjust" aria-hidden="true" data-toggle="popover" data-trigger="hover" data-placement="top" data-container="body" data-html="true" title="" data-content="Generation of human iPSC and iPSC-derived cardiomyocytes from 222 individuals."></i> </td> <td class="text-dark-blue text-center"> - <i class="fas fa-tint fa-lg" aria-hidden="true"></i> + <i class="fas fa-square" 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-blue text-center"></td> <td class="text-light-green text-center"> <i class="fas fa-square" aria-hidden="true"></i> </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> <td class="text-light-green text-center"></td> @@ -824,31 +770,31 @@ data-content="The Jones lab is investigating the role of transcriptional regulators Yap1 and P-TEFb in human embryonic stem cell differentiation towards cardiomyocytes.">Jones</a> <i class="fas fa-external-link-alt icon-sm" aria-hidden="true"></i> </td> <td class="datasetid"> jonesYap1 <i class="fas fa-info-circle popoveradjust" aria-hidden="true" data-toggle="popover" data-trigger="hover" data-placement="top" data-container="body" data-html="true" title="" data-content="Studying the role of Yap1 and P-TEFb in hESC Differentiation towards cardiomyocytes."></i> </td> <td class="text-dark-blue text-center"> - <i class="fas fa-tint fa-lg" aria-hidden="true"></i> + <i class="fas fa-square" 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-blue text-center"></td> <td class="text-light-green text-center"> <i class="fas fa-square" aria-hidden="true"></i> </td> <td class="text-light-green text-center"> <i class="fas fa-square" aria-hidden="true"></i> </td> <td class="text-light-green text-center"></td> @@ -965,31 +911,31 @@ title="Guoping Fan, UCLA" data-content="The Fan lab is working on identifying convergent target genes and signaling pathways perturbed in human overgrowth syndrome.">Fan</a> <i class="fas fa-external-link-alt icon-sm" aria-hidden="true"></i> </td> <td class="datasetid"> <a href="<!--#echo var='ROOT'-->d/fanIcf1">fanIcf1</a> <i class="fas fa-info-circle popoveradjust" aria-hidden="true" data-toggle="popover" data-trigger="hover" data-placement="top" data-container="body" data-html="true" title="" data-content="WGBS, RRBS, WGS, ChIP-seq, and RNA-seq on iPSCs generated from patients with human overgrowth syndrome."></i> </td> <td class="text-dark-blue text-center"> - <i class="fas fa-braille fa-lg" aria-hidden="true"></i> + <i class="fas fa-square" aria-hidden="true"></i> </td> <td class="text-dark-pink text-center"> <i class="fas fa-square" aria-hidden="true"></i> </td> <td class="text-dark-pink text-center"> <i class="fas fa-square" aria-hidden="true"></i> </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-blue text-center"></td> <td class="text-light-green text-center"> <i class="fas fa-square" aria-hidden="true"></i> </td> @@ -1105,63 +1051,30 @@ data-placement="top" data-container="body" data-html="true" title="Sergiu Pasca, Stanford" data-content="The Pasca lab is growing brain organoids with neurological disorders including deletions, duplications and triplications of 16p11.2, Timothy syndrome, epilepsy and mental retardation limited to female (EFMR).">Pasca</a> <i class="fas fa-external-link-alt icon-sm" aria-hidden="true"></i> </td> <td class="datasetid"> geschwindNeurospheres1 <i class="fas fa-info-circle popoveradjust" aria-hidden="true" data-toggle="popover" data-trigger="hover" data-placement="top" data-container="body" data-html="true" title="" data-content="Using iPSC-based models and neurosphere RNA-seq data to study autism spectrum disorder."></i> - <br> - <!-- PubMed Icon/Link --> - <a href="https://www.ncbi.nlm.nih.gov/pubmed/30573846" target="_blank" - data-toggle="popover" data-trigger="hover" class="popoveradjust" - data-placement="top" data-container="body" data-html="true" - title="Yoon SJ et al. 2019. Reliability of human cortical organoid generation. - Nat Methods." - data-content="View publication from this dataset"> - <i class="fas fa-file-alt" aria-hidden="true"></i></a> - <!-- GEO Icon/Link --> - <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93811" target="_blank" - data-toggle="popover" data-trigger="hover" class="popoveradjust" - 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 GSE93811" - data-content="Click database icon to view on GEO."> - <i class="fas fa-database" aria-hidden="true"></i></a> - <!-- GEO Icon/Link --> - <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE107771" target="_blank" - data-toggle="popover" data-trigger="hover" class="popoveradjust" - 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 GSE107771" - data-content="Click database icon to view on GEO."> - <i class="fas fa-database" aria-hidden="true"></i></a> - <!-- GEO Icon/Link --> - <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE120700" target="_blank" - data-toggle="popover" data-trigger="hover" class="popoveradjust" - 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 GSE120700" - data-content="Click database icon to view on GEO."> - <i class="fas fa-database" aria-hidden="true"></i></a> </td> <td class="text-dark-blue text-center"></td> <td class="text-dark-pink text-center"> <i class="fas fa-square" aria-hidden="true"></i> </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-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> <td class="text-light-green text-center"></td> @@ -1178,219 +1091,128 @@ data-toggle="popover" data-trigger="hover" class="popoveradjust" data-placement="top" data-container="body" data-html="true" title="Arnold Kriegstein, UCSF" data-content="The Kriegstein lab is using single-cell RNA profiling to learn about the diverse population of cortical neurons.">Kriegstein</a> <i class="fas fa-external-link-alt icon-sm" aria-hidden="true"></i> </td> <td class="datasetid"> <a href="<!--#echo var='ROOT'-->d/kriegsteinBrainOrganoids1">kriegsteinBrainOrganoids1</a> <i class="fas fa-info-circle popoveradjust" aria-hidden="true" data-toggle="popover" data-trigger="hover" 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."></i> - <br> - <!-- PubMed Icon/Link --> - <a href="https://www.ncbi.nlm.nih.gov/pubmed/30735633" target="_blank" - data-toggle="popover" data-trigger="hover" class="popoveradjust" - 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> - <!-- GEO Icon/Link --> - <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE124299" target="_blank" - data-toggle="popover" data-trigger="hover" class="popoveradjust" - 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> - <!-- SCHub Icon/Link --> - <a href="<!--#echo var='ROOT'-->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" class="popoveradjust" - 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> + <i class="fas fa-square" 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-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> <td class="text-light-green 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> <td class="text-orange text-center"></td> <td class="text-dark-blue text-center"></td> </tr> <tr> <td></td> <td class="lab text-nowrap"></td> <td class="datasetid"> <a href="<!--#echo var='ROOT'-->d/kriegsteinBrainOrganoids2">kriegsteinBrainOrganoids2</a> <i class="fas fa-info-circle popoveradjust" aria-hidden="true" data-toggle="popover" data-trigger="hover" data-placement="top" data-container="body" data-html="true" title="Single-cell Brain Organoids" data-content="Establishing Cerebral Organoids as Models of Human-Specific - Brain Evolution"></i><br> - <!-- PubMed Icon/Link --> - <a href="https://www.ncbi.nlm.nih.gov/pubmed/30735633" target="_blank" - data-toggle="popover" data-trigger="hover" class="popoveradjust" - 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> - <!-- GEO Icon/Link --> - <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE124299" target="_blank" - data-toggle="popover" data-trigger="hover" class="popoveradjust" - 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> + Brain Evolution"></i> </td> <td class="text-dark-blue text-center"> - <i class="fas fa-braille fa-lg" aria-hidden="true"></i> + <i class="fas fa-square" 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-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> <td class="text-light-green 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> <td class="text-orange text-center"></td> <td class="text-dark-blue text-center"></td> </tr> <tr> <td></td> <td class="lab text-nowrap"></td> <td class="datasetid"> <a href="<!--#echo var='ROOT'-->d/kriegsteinRadialGliaStudy1" >kriegsteinRadialGliaStudy1</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="Single-cell Study of Brain Development" data-content="376 primary samples of fetal radial glial cells that were processed via single-cell RNA-seq."></i> - <br> - <!-- PubMed Icon/Link --> - <a href="https://www.ncbi.nlm.nih.gov/pubmed/26406371" target="_blank" - data-toggle="popover" data-trigger="hover" class="popoveradjust" - 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> - <!-- dbGap Icon/Link --> - <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" class="popoveradjust" - 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> - <!-- SCHub Icon/Link --> - <a href="<!--#echo var='ROOT'-->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" class="popoveradjust" - 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> + <i class="fas fa-square" 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> <td class="text-light-green text-center"></td> <td class="text-light-green text-center"></td> <td class="text-light-green text-center"></td> <td class="text-orange text-center"></td> <td class="text-dark-blue text-center"></td> </tr> <tr> <td></td> <td class="lab text-nowrap"></td> <td class="datasetid"> <a href="<!--#echo var='ROOT'-->d/kriegstein6k">kriegstein6k</a> <i class="fas fa-info-circle popoveradjust" aria-hidden="true" data-toggle="popover" data-trigger="hover" data-placement="top" data-container="body" data-html="true" title="" data-content="RNA-seq from 6,000 primary cells at UCSF."></i> - <br> - <!-- PubMed Icon/Link --> - <a href="https://www.ncbi.nlm.nih.gov/pubmed/29217575" target="_blank" - data-toggle="popover" data-trigger="hover" class="popoveradjust" - 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> - <!-- dbGaP Icon/Link --> - <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" class="popoveradjust" - 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> - <!-- SCHub Icon/Link --> - <a href="<!--#echo var='ROOT'-->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" class="popoveradjust" - 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> + <i class="fas fa-square" 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> <td class="text-light-green text-center"></td> <td class="text-light-green text-center"></td> <td class="text-light-green text-center"></td> @@ -1437,111 +1259,63 @@ data-placement="top" data-container="body" data-html="true" title="Stephen Quake, Stanford University" data-content="The Quake lab is working on characterizing cell subpopulations of healthy and pathological tissues of the brain and pancreas. He is also looking at gene and epigenetic properties of organ lineages to compare stem cell differentiation hierarchy to normal tissues to elucidate mechanisms of pathogenesis.">Quake</a> <i class="fas fa-external-link-alt icon-sm" aria-hidden="true"></i> </td> <td class="datasetid"> <a href="<!--#echo var='ROOT'-->d/quakeBrainGeo1">quakeBrainGeo1</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="Examination of cell types in healthy human brain samples."></i><br> - <!-- PubMed Icon/Link --> - <a href="https://www.ncbi.nlm.nih.gov/pubmed/26060301" target="_blank" - data-toggle="popover" data-trigger="hover" class="popoveradjust" - 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> - <!-- GEO Icon/Link --> - <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE67835" target="_blank" - data-toggle="popover" data-trigger="hover" class="popoveradjust" - 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> - <!-- SCHub Icon/Link --> - <a href="<!--#echo var='ROOT'-->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" class="popoveradjust" - 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> + data-content="Examination of cell types in healthy human brain samples."></i> </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 text-light-blue" aria-hidden="true"></i> </td> <td class="text-light-blue 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> <td class="text-light-green 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> <td class="text-orange text-center"></td> <td class="text-dark-blue text-center"></td> </tr> <tr> <td></td> <td class="lab text-nowrap"></td> <td class="datasetid"> <a href="<!--#echo var='ROOT'-->d/quakeGlioblastomaGeo1">quakeGlioblastomaGeo1</a> <i class="fas fa-info-circle popoveradjust" aria-hidden="true" data-toggle="popover" data-trigger="hover" data-placement="top" data-container="body" data-html="true" title="" - data-content="Characterizing the effects of glioblastoma on normal brain."></i><br> - <!-- PubMed Icon/Link --> - <a href="https://www.ncbi.nlm.nih.gov/pubmed/29091775/" target="_blank" - data-toggle="popover" data-trigger="hover" class="popoveradjust" - 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> - <!-- GEO Icon/Link --> - <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84465" target="_blank" - data-toggle="popover" data-trigger="hover" class="popoveradjust" - 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></a> - <!-- SCHub Icon/Link --> - <a href="<!--#echo var='ROOT'-->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" class="popoveradjust" - 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> + data-content="Characterizing the effects of glioblastoma on normal brain."></i> </td> <td class="text-dark-blue text-center"> - <i class="fas fa-braille fa-lg" aria-hidden="true"></i> + <i class="fas fa-square" 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-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> <td class="text-light-green text-center"></td> <td class="text-light-green text-center"></td> <td class="text-light-s text-center"></td> <td class="text-light-green text-center"></td> @@ -1586,31 +1360,31 @@ <td class="text-orange text-center"></td> <td class="text-dark-blue text-center"></td> </tr> <tr> <td></td> <td class="lab text-nowrap"></td> <td class="datasetid"> yeoCorticalOrganoid <i class="fas fa-info-circle popoveradjust" aria-hidden="true" data-toggle="popover" data-trigger="hover" data-placement="top" data-container="body" data-html="true" title="Yeo Lab single cell RNA-seq of cortical organoids" data-content="Single cell 10x platform RNA-seq data from cortical organoids derived from patients with Myotonic Dystrophy and controls."></i> </td> <td class="text-dark-blue text-center"> - <i class="fas fa-tint fa-lg" aria-hidden="true"></i> + <i class="fas fa-square" 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-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> <td class="text-light-green 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> @@ -1660,58 +1434,33 @@ data-content="The Quake lab is working on characterizing cell subpopulations of healthy and pathological tissues of the brain and pancreas. They are also looking at gene and epigenetic properties of organ lineages to compare stem cell differentiation hierarchy to normal tissues to elucidate mechanisms of pathogenesis.">Quake</a> <i class="fas fa-external-link-alt icon-sm" aria-hidden="true"></i> </td> <td class="datasetid"> <a href="<!--#echo var='ROOT'-->d/quakeAdultAgingPancreas1">quakeAdultAgingPancreas1</a> <i class="fas fa-info-circle popoveradjust" aria-hidden="true" data-toggle="popover" data-trigger="hover" data-placement="top" data-container="body" data-html="true" title="" data-content="Single cell transcriptome analysis of human pancreas reveals transcriptional signatures of aging and somatic mutation patterns."></i> - <br> - <!-- PubMed Icon/Link --> - <a href="https://www.ncbi.nlm.nih.gov/pubmed/28965763" target="_blank" - data-toggle="popover" data-trigger="hover" class="popoveradjust" - 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> - <!-- GEO Icon/Link --> - <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81547" target="_blank" - data-toggle="popover" data-trigger="hover" class="popoveradjust" - 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> - <!-- SCHub Icon/Link --> - <a href="<!--#echo var='ROOT'-->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" class="popoveradjust" - 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> + <i class="fas fa-square" 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-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> <td class="text-light-green 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> @@ -1723,47 +1472,30 @@ <td class="lab text-nowrap"></td> <!-- <td class="datasetid"> FYI the following SSI command comment was disabled to avoid nesting comments. replace ~~ with dash dash to restore it <a href="<!~~ #echo var='ROOT'~~>d/quakeFetalPancreasSpatial">quakeFetalPancreasSpatial</a>--> <td class="datasetid"> <a href="<!--#echo var='ROOT'-->d/quakeFetalPancreasSpatial">quakeFetalPancreasSpatial</a> <i class="fas fa-info-circle popoveradjust" aria-hidden="true" data-toggle="popover" data-trigger="hover" data-placement="top" data-container="body" data-html="true" title="" 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> - <!-- PubMed Icon/Link --> - <a href="https://www.nature.com/articles/s41598-019-41951-2" target="_blank" - data-toggle="popover" data-trigger="hover" class="popoveradjust" - data-placement="top" data-container="body" data-html="true" - title="Riu L et al. 2019. Modeling Spatial Correlation of Transcripts - with Application to Developing Pancreas. Nat Sci Rep." - data-content="View publication from this dataset"> - <i class="fas fa-file-alt" aria-hidden="true"></i></a> - <!-- SCHub Icon/Link --> - <a href="<!--#echo var='ROOT'-->cgi-bin/cdwWebBrowse?browseFiles_facet_op=resetAll&browseFiles_facet_fieldName=&browseFiles_facet_fieldVal=&cdwCommand=browseFiles&cdwFile_filter=data_set_id%3D%27quakeFetalPancreasSpatial%27%20" - target="_blank" - data-toggle="popover" data-trigger="hover" class="popoveradjust" - 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"></td> <td class="text-light-blue 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> <td class="text-light-green 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> <td class="text-orange text-center"></td> @@ -1771,31 +1503,31 @@ <i class="fas fa-square" aria-hidden="true"></i> </td> </tr> <tr> <td></td> <td class="lab text-nowrap"></td> <td class="datasetid"> <a href="<!--#echo var='ROOT'-->d/quakeTumorProfiling1">quakeTumorProfiling1</a> <i class="fas fa-info-circle popoveradjust" data-toggle="popover" data-trigger="hover" data-placement="top" data-container="body" data-html="true" title="Quake lab tumours RNA-seq" data-content="Profiling tumor cells with single cell RNA-seq"></i> </td> <td class="text-dark-blue text-center"> - <i class="fas fa-braille fa-lg" aria-hidden="true"></i> + <i class="fas fa-square" 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-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> <td class="text-light-green 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>