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4Dnucleome_browser.html
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4Dnucleome_browser.html
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<!DOCTYPE html>
<!--
~ The MIT License (MIT)
~
~ Copyright (c) 2016-2017 The Regents of the University of California
~
~ Permission is hereby granted, free of charge, to any person obtaining a copy of this software and
~ associated documentation files (the "Software"), to deal in the Software without restriction, including
~ without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
~ copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the
~ following conditions:
~
~ The above copyright notice and this permission notice shall be included in all copies or substantial
~ portions of the Software.
~
~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING
~ BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
~ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
~ CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
~ ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
~ THE SOFTWARE.
~
-->
<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">
<!-- Underscore JS -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/underscore.js/1.8.3/underscore-min.js"></script>
<!-- JQuery JS -->
<script src="https://code.jquery.com/jquery-1.12.4.min.js"></script>
<!-- JQuery UI JS -->
<script src="https://code.jquery.com/ui/1.12.1/jquery-ui.min.js"></script>
<!-- Tether JS (Use with Alpha 4.0.0-alpha.6 Bootstrap) -->
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<!-- Bootstrap JS -->
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"></script>
<!-- Bootstrap-Select Plugin JS -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.12.2/js/bootstrap-select.min.js"></script>
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<script src="https://cdn.datatables.net/v/dt/dt-1.10.15/sc-1.4.2/se-1.2.2/datatables.min.js"></script>
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<script src="https://igv.org/web/jb/release/cell/igv.min.js"></script>
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<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
">4D Loop Browser</h1>
<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-5">
<div class="row">
<div class="col-md-10 col-md-offset-2">
<div id="app-container-3">
</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-4">
</div>
<br>
</div>
</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-5">
</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-6">
</div>
<br>
</div>
</div>
</div>
</div>
<div>
<p class="legend"> We use loop resolution Hi-C to track the formation of loop domains across the genome
as cohesin is reintroduced. (Top Left) Contact map for 6hr auxin treated RAD21-mAC cells. (Top Right)
Contact map for RAD21-mAC cells with 6hr auxin treatment + 20 minute auxin withdrawal. (Middle Left)
Contact map for RAD21-mAC cells with 6hr auxin treatment + 40 minute auxin withdrawal. (Middle Right)
Contact map for RAD21-mAC cells with 6hr auxin treatment + 60 minute auxin withdrawal. (Bottom Left)
Contact map for RAD21-mAC cells with 6hr auxin treatment + 180 minute auxin withdrawal. (Bottom Right)
Contact map for untreated RAD21-mAC cells. </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">
$(document).ready(function () {
var browser1, browser2, browser3, browser4, browser5, browser6;
var windowSize = 445;
hic.loadDataset({
url: "https://s3.amazonaws.com/hicfiles/hiseq/degron/treated_6hr/unsynchronized/combined.hic",
nvi: "33255540403%2C36479"
})
.then(function (dataset) {
browser1 = hic.createBrowser($('#app-container-1'), {
miniMode: true,
width: windowSize,
height: windowSize,
dataset: dataset,
href: "?state=8%2C8%2C7%2C13380%2C13380%2C4.88%2CKR&colorScale=116&name=Rao%20et%20al.%20%7C%20Biorxiv%202017%20Combined%20Treated%20(6%20hr)"
});
if (browser2) hic.syncBrowsers([browser1, browser2, browser3, browser4, browser5, browser6]);
})
.catch(function (error) {
console.log(error);
});
hic.loadDataset({
url: "https://s3.amazonaws.com/hicfiles/hiseq/degron/time_course/deep/20min_withdraw_combined.hic",
})
.then(function (dataset) {
browser2 = hic.createBrowser($('#app-container-2'), {
miniMode: true,
width: windowSize,
height: windowSize,
dataset: dataset,
href: "?state=8%2C8%2C7%2C13380%2C13380%2C4.88%2CKR&colorScale=34&name=Rao%20et%20al.%20%7C%20Biorxiv%202017%20Combined%20Treated%20(20min%20withdraw)"
});
if (browser3) hic.syncBrowsers([browser1, browser2, browser3, browser4, browser5, browser6]);
})
.catch(function (error) {
console.log(error);
});
hic.loadDataset({
url: "https://s3.amazonaws.com/hicfiles/hiseq/degron/time_course/deep/40min_withdraw_combined.hic",
})
.then(function (dataset) {
browser3 = hic.createBrowser($('#app-container-3'), {
miniMode: true,
width: windowSize,
height: windowSize,
dataset: dataset,
href: "?state=8%2C8%2C7%2C13380%2C13380%2C4.88%2CKR&colorScale=33&name=Rao%20et%20al.%20%7C%20Biorxiv%202017%20Combined%20Treated%20(40min%withdraw)"
});
if (browser4) hic.syncBrowsers([browser1, browser2, browser3, browser4, browser5, browser6]);
})
.catch(function (error) {
console.log(error);
});
hic.loadDataset({
url: "https://s3.amazonaws.com/hicfiles/hiseq/degron/time_course/deep/60min_withdraw_combined.hic",
})
.then(function (dataset) {
browser4 = hic.createBrowser($('#app-container-4'), {
miniMode: true,
width: windowSize,
height: windowSize,
dataset: dataset,
href: "?state=8%2C8%2C7%2C13380%2C13380%2C4.88%2CKR&colorScale=31&name=Rao%20et%20al.%20%7C%20Biorxiv%202017%20Combined%20Treated%20(60min%20withdraw)"
});
if (browser5) hic.syncBrowsers([browser1, browser2, browser3, browser4, browser5, browser6]);
})
.catch(function (error) {
console.log(error);
});
hic.loadDataset({
url: "https://s3.amazonaws.com/hicfiles/hiseq/degron/time_course/deep/180min_withdraw_combined.hic",
})
.then(function (dataset) {
browser5 = hic.createBrowser($('#app-container-5'), {
miniMode: true,
width: windowSize,
height: windowSize,
dataset: dataset,
href: "?state=8%2C8%2C7%2C13380%2C13380%2C4.88%2CKR&colorScale=34&name=Rao%20et%20al.%20%7C%20Biorxiv%202017%20Combined%20Treated%20(180min%20withdraw)"
});
if (browser6) hic.syncBrowsers([browser1, browser2, browser3, browser4, browser5, browser6]);
})
.catch(function (error) {
console.log(error);
});
hic.loadDataset({
url: "https://s3.amazonaws.com/hicfiles/hiseq/degron/untreated/unsynchronized/combined.hic",
nvi: "30439217680%2C36479"
})
.then(function (dataset) {
browser6 = hic.createBrowser($('#app-container-6'), {
miniMode: true,
width: windowSize,
height: windowSize,
dataset: dataset,
href: "?state=8%2C8%2C7%2C13380%2C13380%2C4.88%2CKR&colorScale=120&name=Rao%20et%20al.%20%7C%20Biorxiv%202017%20Combined%20Untreated"
});
if (browser1) hic.syncBrowsers([browser1, browser2, browser3, browser4, browser5, browser6]);
})
.catch(function (error) {
console.log(error);
});
});
</script>
</body>
</html>