docs/docs/assays.hande.hande_template.html
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<p>
<a href="index.html">CIDC Documentation</a>
</p>
<h1>
H & E assay template
</h1>
<p>
<b>Description:</b> Hemotoxylin and Eosin staining (H&E) submission.
</p>
</div>
<div class="container">
<div class="accordion" id="H&E_accordion">
<div class="card">
<div class="card-header" id="H&E">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#H&E_card" aria-expanded="false" aria-controls="H&E_card">
Worksheet - H&E
</button>
</h2>
</div>
<div id="H&E_card" class="collapse" aria-labelledby="H&E" data-parent="#H&E_accordion">
<div class="card-body">
<div class="accordion" id="H&E_preamble_accordion">
<div class="card">
<div class="card-header" id="H&E_preamble">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#H&E_preamble_card" aria-expanded="false" aria-controls="H&E_preamble_card">
Preamble Rows
</button>
</h2>
</div>
<div id="H&E_preamble_card" class="collapse" aria-labelledby="H&E_preamble" data-parent="#H&E_preamble_accordion">
<div class="card-body">
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="protocol identifier">
protocol identifier
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Trial identifier used by lead organization, ie. Center for Experimental Therapeutics Program (CTEP) ID or Industry Sponsored ID. This is usually a short identifier. Example: E4412.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="assay creator">
assay creator
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Indicates what site is filling out the assay.
</td>
<td>
<
string
>
<ul>
<li>"DFCI"</li>
<li>"Mount Sinai"</li>
<li>"Stanford"</li>
<li>"MD Anderson"</li>
<li>"Adaptive"</li>
<li>"Broad"</li>
</ul>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
<div class="accordion" id="H&E_body_accordion">
<div class="card">
<div class="card-header" id="H&E_body">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#H&E_body_card" aria-expanded="false" aria-controls="H&E_body_card">
Data Columns
</button>
</h2>
</div>
<div id="H&E_body_card" class="collapse" aria-labelledby="H&E_body" data-parent="#H&E_body_accordion">
<div class="card-body">
<h5 class="text-muted">Samples</h4>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="cimac id">
cimac id
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as CTTTPPPSS.AA for trial code TTT, participant PPP, sample SS, and aliquot AA.
</td>
<td>
<
string
>
as regex <br> <code>^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$</code>
</td>
</tr>
<tr>
<td>
<span id="file type">
file type
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
</td>
<td>
<
string
>
<ul>
<li>"svs"</li>
<li>"jpg"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="image file">
image file
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Path to file, relative to the intake bucket.
</td>
<td>
<a href="local_file.html#file_path">
local file#file path
</a>
</td>
</tr>
<tr>
<td>
<span id="tumor tissue (% total area)">
tumor tissue (% total area)
</span>
</td>
<td width=55%>
</td>
<td>
<
number
>
</td>
</tr>
<tr>
<td>
<span id="viable tumor (% area)">
viable tumor (% area)
</span>
</td>
<td width=55%>
</td>
<td>
<
number
>
</td>
</tr>
<tr>
<td>
<span id="viable stroma (% area)">
viable stroma (% area)
</span>
</td>
<td width=55%>
</td>
<td>
<
number
>
</td>
</tr>
<tr>
<td>
<span id="necrosis (% area)">
necrosis (% area)
</span>
</td>
<td width=55%>
</td>
<td>
<
number
>
</td>
</tr>
<tr>
<td>
<span id="fibrosis (% area)">
fibrosis (% area)
</span>
</td>
<td width=55%>
</td>
<td>
<
number
>
</td>
</tr>
<tr>
<td>
<span id="comment">
comment
</span>
</td>
<td width=55%>
A text comment regarding this slide.
</td>
<td>
<
string
>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</div>
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