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figure6_test.html
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<!DOCTYPE html>
<html>
<head>
<meta charset="UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=edge"/>
<title>Juicebox</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0"/>
<link rel="icon" type="image/png" href="https://aidenlab.org/favicon.ico">
<!-- Shims for legacy browsers -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/es5-shim/4.5.7/es5-shim.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/es6-shim/0.35.3/es6-shim.js"></script>
<!-- DataTables CSS -->
<link rel="stylesheet" type="text/css"
href="https://cdn.datatables.net/v/dt/dt-1.10.15/sc-1.4.2/se-1.2.2/datatables.min.css"/>
<!-- Bootstrap CSS -->
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css">
<!-- Font Awesome CSS-->
<link rel="stylesheet" type="text/css" href="//maxcdn.bootstrapcdn.com/font-awesome/4.2.0/css/font-awesome.min.css">
<!-- JQuery UI CSS -->
<link rel="stylesheet" type="text/css" href="https://code.jquery.com/ui/1.12.1/themes/redmond/jquery-ui.css"/>
<!-- IGV CSS -->
<link rel="stylesheet" type="text/css" href="https://igv.org/web/jb/release/cell/igv.css">
<!-- site CSS -->
<link rel="stylesheet" type="text/css" href="https://igv.org/web/jb/release/cell/site/css/site.css">
<!-- Juicebox CSS-->
<link rel="stylesheet" type="text/css" href="https://igv.org/web/jb/release/cell/juicebox-bootstrap.css">
<!-- Bootstrap-Select Plugin CSS -->
<link rel="stylesheet"
href="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.12.2/css/bootstrap-select.min.css">
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<!-- Bootstrap JS -->
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<script src="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.12.2/js/bootstrap-select.min.js"></script>
<!-- DataTables JS -->
<script src="https://cdn.datatables.net/v/dt/dt-1.10.15/sc-1.4.2/se-1.2.2/datatables.min.js"></script>
<!-- IGV JS-->
<script src="https://igv.org/web/jb/release/cell/igv.min.js"></script>
<!-- Site JS-->
<script src="https://igv.org/web/jb/release/cell/site/js/site.js"></script>
<!-- Juicebox JS -->
<script src="https://igv.org/web/jb/release/cell/juicebox.js"></script>
<!-- MS polyfill (pointer -> touch -->
<script src="https://igv.org/web/jb/release/current/touchpolyfill.min.js"></script>
</head>
<body style="margin:30px">
<h1 style="text-align: center; font:Helvetica Neue;font-size:36px;line-height: 40px; color: #333333
">Figure 6</h1>
<div class="row">
<div class="col-md-8">
<div>
<p style="font-size:30px" class="panelID">A</p>
</div>
<br>
</div>
</div>
<div class="row">
<div class="col-md-5">
<div class="row">
<div class="col-md-8 col-md-offset-4">
<div>
<img class="img-responsive"
src="https://theaidenlab.github.io/figures/css/img/figure2_static_components/Fig2A_untreated_header.png"
alt="Untreated" width="300">
</div>
<br>
</div>
</div>
<div>
<img src="https://theaidenlab.github.io/figures/css/img/figure6_static_components/6A_extrusion_sim.png"
alt="with extrusion sim" width="600">
</div>
</div>
<div class="col-md-5">
<div class="row">
<div class="col-md-8 col-md-offset-4">
<div>
<img class="img-responsive"
src="https://theaidenlab.github.io/figures/css/img/figure2_static_components/Fig2A_treated_header.png"
alt="6hr Auxin Treated" width="300">
</div>
<br>
</div>
</div>
<div>
<img src="https://theaidenlab.github.io/figures/css/img/figure6_static_components/6A_noextrusion_sim.png"
alt="no extrusion sim" width="600">
</div>
</div>
</div>
<div class="row">
<div class="col-md-5">
<div class="row">
<div class="col-md-10 col-md-offset-2">
<div id="app-container-1">
</div>
<br>
</div>
</div>
</div>
<div class="col-md-5">
<div class="row">
<div class="col-md-10 col-md-offset-2">
<div id="app-container-2">
</div>
<br>
</div>
</div>
</div>
</div>
<div class="row">
<div class="col-md-8">
<div>
<p style="font-size:30px" class="panelID">B</p>
</div>
<br>
</div>
</div>
<div class="row">
<div class="col-md-5">
<div class="row">
<div class="col-md-10 col-md-offset-2">
<div>
<img src="https://theaidenlab.github.io/figures/css/img/figure6_static_components/6B_extrusion_globule.png"
alt="extrusion globule" width="400">
</div>
<br>
</div>
</div>
</div>
<div class="col-md-5">
<div class="row">
<div class="col-md-10 col-md-offset-2">
<div>
<img src="https://theaidenlab.github.io/figures/css/img/figure6_static_components/6B_noextrusion_globule.png"
alt="no extrusion globule" width="400">
</div>
<br>
</div>
</div>
</div>
</div>
<br>
<div>
<p class="legend">(A) We use loop extrusion and compartmentalization to simulate a 2.1 Mb region on chromosome 3 in
HCT-116 RAD21-mAC cells before (left) and after (right) auxin treatment. CTCF and SMC1 ChIP-Seq signals are
normalized and converted into binding probabilities for the simulated extrusion complex (first and second rows).
Each peak is assigned a forward (green) or reverse (red) orientation based on the corresponding CTCF motif.
ChIP-Seq data for 9 histone modifications were used to classify loci into two compartments (red and blue, fifth
row). Histone modification data for H3K36me3 and H3K4me1 is shown, illustrating the correspondence between the
classification tracks and the underlying ChIP-Seq signals (third and fourth rows). The simulations yield an
ensemble of polymer configurations. We show contact maps from the simulated ensemble (top) and from the
corresponding Hi-C experiments (bottom). The simulations accurately capture the positions of loops and domains,
as well as the loss of loop domains after the depletion of cohesin. In addition, our simulation accurately
captures compartmentalization patterns seen before and after auxin treatment.</p>
</div>
<div>
<p class="legend">(B) Examples of globules from simulations of compartmentalization with extrusion (left) and
without (right). Notably, the globule without extrusion shows stronger segregation of compartment types.</p>
</div>
<br>
<style type="text/css">
.row {
display: flex;
}
.legend {
text-align: left;
font: Helvetica Neue;
font-size: 36;
px color: #333333;
}
.col-md-2 {
display: inline-flex;
flex-direction: column;
justify-content: center;
}
</style>
<script type="text/javascript">
$(document).ready(function () {
var browser1, browser2;
var windowSize = 445;
igv.xhr.loadJson("config/hicFileConfigs.txt", {})
.then(function (config) {
hic.loadDataset({
url: config["degron/untreated/unsynchronized/combined.hic"],
nvi: "30439217680%2C36479"
})
.then(function (dataset) {
browser1 = hic.createBrowser($('#app-container-1'), {
miniMode: true,
width: windowSize,
height: windowSize,
dataset: dataset,
initialImage: {
left: 19108.5484,
top: 19108.5484,
imageURL: "img/fig6A-1.png"
},
href: "?state=3%2C3%2C7%2C19215%2C19215%2C1.55%2CKR&colorScale=72&name=Rao%20et%20al.%20%7C%20Biorxiv%202017%20Combined%20Untreated&tracks=https%3A%2F%2Fs3.amazonaws.com%2Fhicfiles%2Fhiseq%2Fdegron%2Fchipseq%5Fdata%2Funtreated%2FH3K36me3%5FFE.bw%7CUntreated%20H3K36me3%7C0-3%7Crgb(0%2C150%2C0)%7C%7C%7Chttps%3A%2F%2Fs3.amazonaws.com%2Fhicfiles%2Fhiseq%2Fdegron%2Fchipseq%5Fdata%2Funtreated%2FH3K4me1%5FFE.bw%7CUntreated%20H3K4me1%7C0-7%7Crgb(0%2C150%2C0)"
});
if (browser2) hic.syncBrowsers([browser1, browser2]);
})
.catch(function (error) {
console.log(error);
});
hic.loadDataset({
url: config["degron/treated_6hr/unsynchronized/combined.hic"],
nvi: "33255540403%2C36479"
})
.then(function (dataset) {
browser2 = hic.createBrowser($('#app-container-2'), {
miniMode: true,
width: windowSize,
height: windowSize,
dataset: dataset,
initialImage: {
left: 19109.8387,
top: 19109.8387,
imageURL: "img/fig6A-2.png"
},
href: "?state=3%2C3%2C7%2C19215%2C19215%2C1.55%2CKR&colorScale=31&name=Rao%20et%20al.%20%7C%20Biorxiv%202017%20Combined%20Treated%20(6%20hr)&tracks=https%3A%2F%2Fs3.amazonaws.com%2Fhicfiles%2Fhiseq%2Fdegron%2Fchipseq%5Fdata%2Ftreated%2FH3K36me3%5FFE.bw%7C6hr%20Treated%20H3K36me3%7C0-3%7Crgb(0%2C150%2C0)%7C%7C%7Chttps%3A%2F%2Fs3.amazonaws.com%2Fhicfiles%2Fhiseq%2Fdegron%2Fchipseq%5Fdata%2Ftreated%2FH3K4me1%5FFE.bw%7C6hr%20Treated%20H3K4me1%7C0-7%7Crgb(0%2C150%2C0)"
});
if (browser1) hic.syncBrowsers([browser1, browser2]);
})
.catch(function (error) {
console.log(error);
});
});
});
</script>
</body>
</html>