9112364a57f18875a89a3047f0fc44d60ac3fc0e
bnguy
Mon Jan 27 14:43:54 2020 -0800
Remove search box in header.html. Add Northstar and NDEx card, Add Scimtar logo in tools.html, Updated MISCE pdf, Updated Home page Description in index.html, Rearrange (Alphabetize) dataset in project.html
diff --git src/hg/cirm/gateway/htdocs/projects.html src/hg/cirm/gateway/htdocs/projects.html
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+++ src/hg/cirm/gateway/htdocs/projects.html
@@ -1,1720 +1,1721 @@
<!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
</th>
-->
<th colspan=3 rowspan=2 class="text-nowrap "></th>
<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="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>."
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="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="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="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="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="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."
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="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="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="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="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="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="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="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="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" 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 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="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 read the RRBS paper (2005).">
<i class="fas fa-info-circle" aria-hidden="true"></i></a>
RRBS
</span>
</div>
</th>
<th style="width: 1%;" class="rotate-45 text-light-green">
<div>
<span>
<a 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 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/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 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="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 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="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="In this project, imaging is only used in the context of
spatial transcriptomics where 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>
</tr>
<tr>
<!--
<td colspan="3"></td>
-->
<td class="text-nowrap">
<b>Research Theme</b>
</td>
<td>
<b>Lab</b>
</td>
<td>
<b>Dataset</b>
</td>
<td class="text-dark-blue text-nowrap"></td>
<td colspan="2" class="text-dark-pink text-center">Genomics</td>
<td colspan="3" class="text-light-blue text-center">Transcriptomics</td>
<td colspan="7" class="text-light-green text-center">Epigenomics</td>
<td colspan="1" class="text-orange"></td>
<td colspan="1" class="text-dark-blue"></td>
</tr>
<!-- EXAMPLE LAB AND DATASET ROW
<tr>
<td></td>
<td class="lab text-nowrap">
Smith
</td>
<td class="datasetid">
labAssaySample
</td>
<td class="text-dark-blue 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-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">
<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-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">
<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">
<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">
<i class="fas fa-square" aria-hidden="true"></i>
</td>
<td class="text-orange text-center">
<i class="fas fa-square" aria-hidden="true"></i>
</td>
</tr>
-->
<tr class="table-active">
- <td colspan="100%">Neurobiology</td>
+ <td colspan="100%">Blood stem cells</td>
</tr>
<tr>
<td></td>
<td class="lab text-nowrap">
- <a href="https://www.uclahealth.org/daniel-geschwind" target="_blank"
- data-toggle="popover" data-trigger="hover" class="popoveradjust"
- data-placement="top" data-container="body" data-html="true"
- title="Daniel Geschwind, UCLA"
- data-content="The Geschwind lab is exploring how multiple distinct mutations
- lead to the convergent pathology of autism spectrum disorder. They are
- analyzing the iPSC organoids from the Pasca lab.">Geschwind</a>
- <i class="fas fa-external-link-alt icon-sm" aria-hidden="true"></i>
- / <a href="http://www.pascalab.org/" target="_blank"
+ <a href="http://baldwin.scripps.edu/" target="_blank"
data-toggle="popover" data-trigger="hover" class="popoveradjust"
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>
+ 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">
- geschwindNeurospheres1
+ <td class="datasetid text-nowrap">
+ baldwin12PairedIpscCellLines1
<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-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 GSE120700"
- data-content="Click database icon to view on GEO.">
- <i class="fas fa-database" aria-hidden="true"></i></a>
+ title=""
+ data-content="A study of the mutagenic effects of the induction process
+ by comparing two different methods of induction using fribroblast-derived
+ iPSC lines."></i>
</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-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">
- <a href="https://kriegsteinlab.ucsf.edu/" target="_blank"
+ <a href="https://cornlab.com/" target="_blank"
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>
+ 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/kriegsteinBrainOrganoids1">kriegsteinBrainOrganoids1</a>
+ <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="Single-cell Brain Organoids"
- data-content="874 iPSC-derived brain organoid samples processed
- via single-cell RNA-seq."></i>
+ title=""
+ data-content="Investigating erythoid maturation with 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"
+ <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">
- <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-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">
- kriegsteinBrainOrganoids2
- <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>
- </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>
- </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>
- </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 class="text-orange 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>
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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>
</tr>
<tr>
<td></td>
<td class="lab text-nowrap"></td>
<td class="datasetid">
- <a href="<!--#echo var='ROOT'-->d/kriegstein6k">kriegstein6k</a>
+ <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="RNA-seq from 6,000 primary cells at UCSF."></i>
+ data-content="Investigating CRISPR off-target cleavage sites using
+ GUIDE-seq, Amplicon-seq and Capture-seq."></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"
+ <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">
- <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>
- <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">
- <a href="https://med.stanford.edu/stemcell/about/Laboratories/clarke.html"
- data-toggle="popover" data-trigger="hover" class="popoveradjust"
- data-placement="top" data-container="body" data-html="true"
- title="Michael F. Clarke, Stanford"
- data-content="The Clarke lab is collaborating with the Quake lab
- in exploring chromatin landscapes.">Clarke</a>
- </td>
- <td class="datasetid"></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 class="text-dark-pink 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>
- <td class="text-orange text-center"></td>
- </tr>
- -->
- <tr>
- <td></td>
- <!-- <a href="#" title="Dismissible popover" data-toggle="popover" data-trigger="focus" data-content="C">Click me</a> -->
- <td class="lab text-nowrap">
- <a href="https://quakelab.stanford.edu/" target="_blank"
- data-toggle="popover" data-trigger="hover" class="popoveradjust"
- 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>
- </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"></td>
<td class="text-light-blue text-center">
- <i class="fas fa-square text-light-blue" aria-hidden="true"></i>
+ <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-orange text-center">
+ <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/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"
+ <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="Download from the Stem Cell Hub">
- <i class="fas fa-file-download" aria-hidden="true"></i></a>
+ 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-braille fa-lg" aria-hidden="true"></i>
+ <i class="fas fa-tint 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-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">
- <a href="http://yeolab.github.io/" target="_blank"
+ <a href="http://www.crooks-lab.com/" target="_blank"
data-toggle="popover" data-trigger="hover" class="popoveradjust"
data-placement="top" data-container="body" data-html="true"
- title="Gene Yeo, UCSD"
- data-content="The Yeo lab is exploring how RNA localizes in certain
- parts of the cell, effecting differentiation, stress and neurodegeneration,
- particularly with regards to ALS (amytrophic lateral sclerosis).">Yeo</a>
+ title="Gay Crooks, UCLA"
+ data-content="The Crooks Lab is working to create a comprehensive
+ transcriptome and epigenome map of human hematopoetic stem cell (HSC)
+ ontogeny by comparing human hematopoietic tissues
+ and cells derived from embryonic stem cells (ESCs).">Crooks</a>
<i class="fas fa-external-link-alt icon-sm" aria-hidden="true"></i>
</td>
<td class="datasetid">
- yeoRnaLocalization1
- <i class="fas fa-info-circle popoveradjust"
+ crooksHsc
+ <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="Investigating ALS with Frac-seq"
- data-content="Global subcellular mRNA localization in differentiation, stress,
- and neurodegeneration."></i>
+ title=""
+ data-content="RNA-seq data from fetal liver."></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" 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>
+ <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-orange text-center"></td>
<td class="text-dark-blue text-center"></td>
+ </tr>
+ <tr>
+ <td></td>
+ <td class="lab text-nowrap">
+ <a href="http://stemcellphd.stanford.edu/faculty/irv-weissman.html" target="_blank"
+ data-toggle="popover" data-trigger="hover" class="popoveradjust"
+ data-placement="top" data-container="body" data-html="true"
+ title="Irv Weissman, Stanford"
+ data-content="The Weissman lab is working on identifying and characterizing
+ the progression of discrete changes, genetic and epigenetic, that leads to
+ 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>
+ </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 class="table-active">
<td colspan="100%">Cardiac biology</td>
</tr>
<tr>
<td></td>
<td class="lab text-nowrap">
<a href="http://bruneaulab.gladstone.org/" target="_blank"
data-toggle="popover" data-trigger="hover" class="popoveradjust"
data-placement="top" data-container="body" data-html="true"
title="Benoit Bruneau, UCSF"
data-content="The Bruneau lab is investigating transcriptomic and epigenetic
analysis of iPSC-derived cardiomyocytes at four stages
of differentiation.">Bruneau</a>
<i class="fas fa-external-link-alt icon-sm" aria-hidden="true"></i>
</td>
<td class="datasetid">
bruneauCardioEpigenetics1
<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="A study to discern basic gene regulating mechanisms of iPSC
derived cardiomyocytes at four stages of differentiation."></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"></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>
<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">
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>
</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">
<a href="http://cardiology.ucsd.edu/research/labs/chi-lab/Pages/default.aspx" target="_blank"
data-toggle="popover" data-trigger="hover" class="popoveradjust"
data-placement="top" data-container="body" data-html="true"
title="Neil Chi, UCSD"
data-content="The Chi lab is generating human cardiac stem cells and
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>
</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"></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">
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>
</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">
<a href="http://frazer.ucsd.edu/" target="_blank"
data-toggle="popover" data-trigger="hover" class="popoveradjust"
data-placement="top" data-container="body" data-html="true"
title="Kelly Frazer, UCSD"
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
+ 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"></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>
+ <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-orange text-center"></td>
+ <td class="text-dark-blue text-center"></td>
+ </tr>
+ <tr>
+ <td></td>
+ <td class="lab text-nowrap">
+ <a href="http://www.salk.edu/scientist/katherine-jones/" target="_blank"
+ data-toggle="popover" data-trigger="hover" class="popoveradjust"
+ data-placement="top" data-container="body" data-html="true"
+ title="Kathy Jones, The Salk Institute"
+ 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"></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>
+ <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">
+ <a href="http://snyderlab.stanford.edu/" target="_blank"
+ data-toggle="popover" data-trigger="hover" class="popoveradjust"
+ data-placement="top" data-container="body" data-html="true"
+ title="Mike Snyder, Stanford"
+ data-content="The Snyder lab is investigating drug response of
+ hypertrophic cardiomyopathy (HCM), dialated cardiomyopathy (DCM),
+ and healthy (control) donors with a comprehensive survey combining
+ iPSC-cardiac differentiation, drug treatment and genomic and
+ transcriptomic analysis.">Snyder</a>
+ <i class="fas fa-external-link-alt icon-sm" aria-hidden="true"></i>
+ / <a href="http://med.stanford.edu/wulab.html" target="_blank"
+ data-toggle="popover" data-trigger="hover" class="popoveradjust"
+ data-placement="top" data-container="body" data-html="true"
+ title="Joseph Wu, Stanford"
+ data-content="The Wu lab is investigating patient-specific and
+ disease-specific induced pluripotent stem cells (iPSCs) and their
+ uses in drug discovery and clinical trials.">Wu</a>
+ <i class="fas fa-external-link-alt icon-sm" aria-hidden="true"></i>
+ </td>
+ <td class="datasetid">
+ snyderCardIps1
+ <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="A comprehensive survey combining iPSC-cardiac
+ differentiation, drug treatment, genomic, and transcriptomic
+ analysis applied to these iPSC lines to assess the drug response
+ of each individual patient."></i>
+ </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>
+ <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 class="table-active">
+ <td colspan="100%">Molecular regulators of stem cells</td>
+ </tr>
+ <tr>
+ <td></td>
+ <td class="lab text-nowrap">
+ <a href="http://belmonte.salk.edu/" target="_blank"
+ data-toggle="popover" data-trigger="hover" class="popoveradjust"
+ data-placement="top" data-container="body" data-html="true"
+ title="Juan Carlos Izpisua-Belmonte, The Salk Insitute"
+ data-content="The Belmonte lab is working to characterize the
+ molecular dynamics of cells undergoing 4F-induced reprogramming in vivo in
+ the mouse.">Belmonte</a>
+ <i class="fas fa-external-link-alt icon-sm" aria-hidden="true"></i>
+ </td>
+ <td class="datasetid">
+ belmonteMouseDnmt3a
+ <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="Short-term reprogramming of mouse spleens in-vivo
+ by low 4F induction using Doxycycline treatment, in DNMT3a
+ deficient mice."></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" 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">
+ <a href="https://fan.genetics.ucla.edu/" target="_blank"
+ data-toggle="popover" data-trigger="hover" class="popoveradjust"
+ data-placement="top" data-container="body" data-html="true"
+ 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">
+ fanIcf1
<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>
+ 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>
+ </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-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">
<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>
+ <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>
+ <td class="text-light-green text-center">
+ <i class="fas fa-square" aria-hidden="true"></i>
+ </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">
- <a href="http://www.salk.edu/scientist/katherine-jones/" target="_blank"
+ <a href="https://sanfordlab.mcdb.ucsc.edu/Sanford_Lab/Welcome.html" target="_blank"
data-toggle="popover" data-trigger="hover" class="popoveradjust"
data-placement="top" data-container="body" data-html="true"
- title="Kathy Jones, The Salk Institute"
- 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>
+ title="Jeremy Sanford, UCSC"
+ data-content="The Sanford lab is studying how alternative pre-mRNA splicing
+ contributes to the regulation of gene expression and protein diversity.">Sanford</a>
<i class="fas fa-external-link-alt icon-sm" aria-hidden="true"></i>
</td>
<td class="datasetid">
- jonesYap1
+ sanfordRnaRegulation1
<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>
+ data-content="CLIP-seq and RNA-seq on human stem cells and human neural
+ progenitor cells."></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" 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 class="text-light-blue 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>
<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 class="table-active">
+ <td colspan="100%">Neurobiology</td>
+ </tr>
<tr>
<td></td>
<td class="lab text-nowrap">
- <a href="http://snyderlab.stanford.edu/" target="_blank"
+ <a href="https://www.uclahealth.org/daniel-geschwind" target="_blank"
data-toggle="popover" data-trigger="hover" class="popoveradjust"
data-placement="top" data-container="body" data-html="true"
- title="Mike Snyder, Stanford"
- data-content="The Snyder lab is investigating drug response of
- hypertrophic cardiomyopathy (HCM), dialated cardiomyopathy (DCM),
- and healthy (control) donors with a comprehensive survey combining
- iPSC-cardiac differentiation, drug treatment and genomic and
- transcriptomic analysis.">Snyder</a>
+ title="Daniel Geschwind, UCLA"
+ data-content="The Geschwind lab is exploring how multiple distinct mutations
+ lead to the convergent pathology of autism spectrum disorder. They are
+ analyzing the iPSC organoids from the Pasca lab.">Geschwind</a>
<i class="fas fa-external-link-alt icon-sm" aria-hidden="true"></i>
- / <a href="http://med.stanford.edu/wulab.html" target="_blank"
+ / <a href="http://www.pascalab.org/" target="_blank"
data-toggle="popover" data-trigger="hover" class="popoveradjust"
data-placement="top" data-container="body" data-html="true"
- title="Joseph Wu, Stanford"
- data-content="The Wu lab is investigating patient-specific and
- disease-specific induced pluripotent stem cells (iPSCs) and their
- uses in drug discovery and clinical trials.">Wu</a>
+ 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">
- snyderCardIps1
+ 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"
+ data-toggle="popover" data-trigger="hover" data-placement="top"
+ data-container="body" data-html="true"
title=""
- data-content="A comprehensive survey combining iPSC-cardiac
- differentiation, drug treatment, genomic, and transcriptomic
- analysis applied to these iPSC lines to assess the drug response
- of each individual patient."></i>
+ 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>
<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 class="table-active">
- <td colspan="100%">Blood stem cells</td>
- </tr>
<tr>
<td></td>
<td class="lab text-nowrap">
- <a href="http://baldwin.scripps.edu/" target="_blank"
+ <a href="https://kriegsteinlab.ucsf.edu/" target="_blank"
data-toggle="popover" data-trigger="hover" class="popoveradjust"
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>
+ 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 text-nowrap">
- baldwin12PairedIpscCellLines1
+ <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="A study of the mutagenic effects of the induction process
- by comparing two different methods of induction using fribroblast-derived
- iPSC lines."></i>
+ 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">
- <i class="fas fa-square" aria-hidden="true"></i>
+ <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-light-blue 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">
- <a href="https://cornlab.com/" target="_blank"
- data-toggle="popover" data-trigger="hover" class="popoveradjust"
- 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="lab text-nowrap"></td>
<td class="datasetid">
- <a href="<!--#echo var='ROOT'-->d/cornErythroidMaturation">cornErythroidMaturation</a>
+ kriegsteinBrainOrganoids2
<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"
+ 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=""
- data-content="Download from the Stem Cell Hub">
- <i class="fas fa-file-download" aria-hidden="true"></i></a>
+ 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>
+ </td>
+ <td class="text-dark-blue text-center">
+ <i class="fas fa-braille fa-lg" aria-hidden="true"></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" 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">
- <i class="fas fa-square" aria-hidden="true"></i>
- </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/cornOffTarget">cornOffTarget</a>
- <i class="fas fa-info-circle popoveradjust" aria-hidden="true"
- data-toggle="popover" data-trigger="hover"
+ <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=""
- data-content="Investigating CRISPR off-target cleavage sites using
- GUIDE-seq, Amplicon-seq and Capture-seq."></i>
+ 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%27cornOffTarget%27%20"
+ <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"></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 class="text-dark-blue text-center">
+ <i class="fas fa-braille fa-lg" aria-hidden="true"></i>
</td>
- <td class="text-light-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-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">
- <i class="fas fa-square" aria-hidden="true"></i>
- </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">
- cornHSPC
+ <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="Single cell RNA-seq of hematopoietic stem cells using
- 10X to identify hematopoietic stem and progenitor cells."></i>
+ 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-tint fa-lg" aria-hidden="true"></i>
+ <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-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">
- <a href="http://www.crooks-lab.com/" target="_blank"
+ <a href="https://med.stanford.edu/stemcell/about/Laboratories/clarke.html"
data-toggle="popover" data-trigger="hover" class="popoveradjust"
data-placement="top" data-container="body" data-html="true"
- title="Gay Crooks, UCLA"
- data-content="The Crooks Lab is working to create a comprehensive
- transcriptome and epigenome map of human hematopoetic stem cell (HSC)
- ontogeny by comparing human hematopoietic tissues
- and cells derived from embryonic stem cells (ESCs).">Crooks</a>
- <i class="fas fa-external-link-alt icon-sm" aria-hidden="true"></i>
- </td>
- <td class="datasetid">
- crooksHsc
- <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 data from fetal liver."></i>
+ title="Michael F. Clarke, Stanford"
+ data-content="The Clarke lab is collaborating with the Quake lab
+ in exploring chromatin landscapes.">Clarke</a>
</td>
+ <td class="datasetid"></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-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">
<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>
- <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-orange text-center"></td>
- <td class="text-dark-blue text-center"></td>
</tr>
+ -->
<tr>
<td></td>
+ <!-- <a href="#" title="Dismissible popover" data-toggle="popover" data-trigger="focus" data-content="C">Click me</a> -->
<td class="lab text-nowrap">
- <a href="http://stemcellphd.stanford.edu/faculty/irv-weissman.html" target="_blank"
+ <a href="https://quakelab.stanford.edu/" target="_blank"
data-toggle="popover" data-trigger="hover" class="popoveradjust"
data-placement="top" data-container="body" data-html="true"
- title="Irv Weissman, Stanford"
- data-content="The Weissman lab is working on identifying and characterizing
- the progression of discrete changes, genetic and epigenetic, that leads to
- the generation of cancer stem cells (CSCs) from a variety of blood and solid
- tissue cancers.">Weissman</a>
+ 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">
- weissmanHsc1
- <i class="fas fa-info-circle popoveradjust" aria-hidden="true"
- data-toggle="popover" data-trigger="hover"
+ <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="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>
+ 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>
</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>
+ <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 class="table-active">
- <td colspan="100%">Molecular regulators of stem cells</td>
- </tr>
<tr>
<td></td>
- <td class="lab text-nowrap">
- <a href="http://belmonte.salk.edu/" target="_blank"
- data-toggle="popover" data-trigger="hover" class="popoveradjust"
- data-placement="top" data-container="body" data-html="true"
- title="Juan Carlos Izpisua-Belmonte, The Salk Insitute"
- data-content="The Belmonte lab is working to characterize the
- molecular dynamics of cells undergoing 4F-induced reprogramming in vivo in
- the mouse.">Belmonte</a>
- <i class="fas fa-external-link-alt icon-sm" aria-hidden="true"></i>
- </td>
+ <td class="lab text-nowrap"></td>
<td class="datasetid">
- belmonteMouseDnmt3a
+ <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="Short-term reprogramming of mouse spleens in-vivo
- by low 4F induction using Doxycycline treatment, in DNMT3a
- deficient mice."></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" 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">
- <a href="https://fan.genetics.ucla.edu/" target="_blank"
+ 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="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">
- fanIcf1
- <i class="fas fa-info-circle popoveradjust" aria-hidden="true"
- data-toggle="popover" data-trigger="hover"
+ 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="WGBS, RRBS, WGS, ChIP-seq, and RNA-seq on iPSCs generated
- from patients with human overgrowth syndrome."></i>
+ 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">
- <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"></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>
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- <td class="text-light-green text-center">
- <i class="fas fa-square" aria-hidden="true"></i>
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- <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">
- <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>
<td class="text-orange text-center"></td>
<td class="text-dark-blue text-center"></td>
</tr>
<tr>
<td></td>
<td class="lab text-nowrap">
- <a href="https://sanfordlab.mcdb.ucsc.edu/Sanford_Lab/Welcome.html" target="_blank"
+ <a href="http://yeolab.github.io/" target="_blank"
data-toggle="popover" data-trigger="hover" class="popoveradjust"
data-placement="top" data-container="body" data-html="true"
- title="Jeremy Sanford, UCSC"
- data-content="The Sanford lab is studying how alternative pre-mRNA splicing
- contributes to the regulation of gene expression and protein diversity.">Sanford</a>
+ title="Gene Yeo, UCSD"
+ data-content="The Yeo lab is exploring how RNA localizes in certain
+ parts of the cell, effecting differentiation, stress and neurodegeneration,
+ particularly with regards to ALS (amytrophic lateral sclerosis).">Yeo</a>
<i class="fas fa-external-link-alt icon-sm" aria-hidden="true"></i>
</td>
<td class="datasetid">
- sanfordRnaRegulation1
- <i class="fas fa-info-circle popoveradjust" aria-hidden="true"
+ yeoRnaLocalization1
+ <i class="fas fa-info-circle popoveradjust"
data-toggle="popover" data-trigger="hover"
data-placement="top" data-container="body" data-html="true"
- title=""
- data-content="CLIP-seq and RNA-seq on human stem cells and human neural
- progenitor cells."></i>
+ title="Investigating ALS with Frac-seq"
+ data-content="Global subcellular mRNA localization in differentiation, stress,
+ and neurodegeneration."></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" 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>
<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 class="table-active">
<td colspan="100%">Pancreas</td>
</tr>
<tr>
<td></td>
<td class="lab text-nowrap">
<a href="https://quakelab.stanford.edu/" target="_blank"
data-toggle="popover" data-trigger="hover" class="popoveradjust"
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. 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/quakePancreas1">quakePancreas1</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>
</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">
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">
quakeFetalPancreasSpatial
<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>
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<td class="text-dark-pink text-center"></td>
<td class="text-dark-pink text-center"></td>
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<td class="text-light-green text-center"></td>
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<td class="text-orange text-center"></td>
<td class="text-dark-blue text-center">
<i class="fas fa-square" aria-hidden="true"></i>
</td>
</tr>
<tr class="table-active">
<td colspan="100%">Therapeutics</td>
</tr>
<tr class="last-row">
<td></td>
<td class="lab text-nowrap">
<a href="http://www.scripps.edu/loring/" target="_blank"
data-toggle="popover" data-trigger="hover" class="popoveradjust"
data-placement="top" data-container="body" data-html="true"
title="Jeanne Loring, Scripps"
data-content="The Loring lab is carrying out preclinical studies to develop
an autologous cell therapy for Parkinson's disease.">Loring</a>
<i class="fas fa-external-link-alt icon-sm" aria-hidden="true"></i>
</td>
<td class="datasetid">
loringParkinsons1
<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="Genomics-based assays to determine if cells remain
genomically-intact during differentiation for transplantation."></i>
</td>
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<td class="text-dark-pink text-center">
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<td class="text-light-green text-center"></td>
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<td class="text-light-green text-center"></td>
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<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>
</tbody>
</table>
</div>
</div>
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