docs/docs/assays.nanostring.nanostring_template.html
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<a href="index.html">CIDC Documentation</a>
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<h1>
Nanostring assay template
</h1>
<p>
<b>Description:</b> Nanostring sequencing submission.
</p>
</div>
<div class="container">
<div class="accordion" id="nanostring_accordion">
<div class="card">
<div class="card-header" id="nanostring">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#nanostring_card" aria-expanded="false" aria-controls="nanostring_card">
Worksheet - nanostring
</button>
</h2>
</div>
<div id="nanostring_card" class="collapse" aria-labelledby="nanostring" data-parent="#nanostring_accordion">
<div class="card-body">
<div class="accordion" id="nanostring_preamble_accordion">
<div class="card">
<div class="card-header" id="nanostring_preamble">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#nanostring_preamble_card" aria-expanded="false" aria-controls="nanostring_preamble_card">
Preamble Rows
</button>
</h2>
</div>
<div id="nanostring_preamble_card" class="collapse" aria-labelledby="nanostring_preamble" data-parent="#nanostring_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>
<tr>
<td>
<span id="batch id">
batch id
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
A unique ID that separates the different batches of Nanostring.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="raw data csv">
raw data csv
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Information about a comma separated file.
</td>
<td>
<a href="files.csv.html">
csv
</a>
</td>
</tr>
<tr>
<td>
<span id="normalized data csv">
normalized data csv
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Information about a comma separated file.
</td>
<td>
<a href="files.csv.html">
csv
</a>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
<div class="accordion" id="nanostring_body_accordion">
<div class="card">
<div class="card-header" id="nanostring_body">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#nanostring_body_card" aria-expanded="false" aria-controls="nanostring_body_card">
Data Columns
</button>
</h2>
</div>
<div id="nanostring_body_card" class="collapse" aria-labelledby="nanostring_body" data-parent="#nanostring_body_accordion">
<div class="card-body">
<h5 class="text-muted">Runs</h4>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="run id">
run id
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
A unique ID that separates the different runs of the given same sample.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="reference data rcc">
reference data rcc
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Information about a Nanostring output file. XML-formatted comma-separated tables
</td>
<td>
<a href="files.rcc.html">
rcc
</a>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<div class="accordion" id="raw_data_accordion">
<div class="card">
<div class="card-header" id="raw_data">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#raw_data_card" aria-expanded="false" aria-controls="raw_data_card">
Worksheet - raw data
</button>
</h2>
</div>
<div id="raw_data_card" class="collapse" aria-labelledby="raw_data" data-parent="#raw_data_accordion">
<div class="card-body">
<div class="accordion" id="raw_data_preamble_accordion">
<div class="card">
<div class="card-header" id="raw_data_preamble">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#raw_data_preamble_card" aria-expanded="false" aria-controls="raw_data_preamble_card">
Preamble Rows
</button>
</h2>
</div>
<div id="raw_data_preamble_card" class="collapse" aria-labelledby="raw_data_preamble" data-parent="#raw_data_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="batch id">
batch id
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
A unique ID that separates the different batches of Nanostring.
</td>
<td>
<
string
>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
<div class="accordion" id="raw_data_body_accordion">
<div class="card">
<div class="card-header" id="raw_data_body">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#raw_data_body_card" aria-expanded="false" aria-controls="raw_data_body_card">
Data Columns
</button>
</h2>
</div>
<div id="raw_data_body_card" class="collapse" aria-labelledby="raw_data_body" data-parent="#raw_data_body_accordion">
<div class="card-body">
<h5 class="text-muted">raw data</h4>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="run id">
run id
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
A unique ID that separates the different runs of the given same sample.
</td>
<td>
<
string
>
</td>
</tr>
<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="data rcc">
data rcc
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Information about a Nanostring output file. XML-formatted comma-separated tables
</td>
<td>
<a href="files.rcc.html">
rcc
</a>
</td>
</tr>
</table>
</div>
</div>
</div>
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