docs/docs/assays.nanostring.html
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<p>
<a href="index.html">CIDC Documentation</a>
</p>
<h1>
Nanostring Assay
</h1>
<p>
<b>Description:</b> A microarray assay for expression levels, suitable for smaller samples than RNA-seq
</p>
</div>
<div class="container">
<div class="accordion" id="assay_accordion">
<div class="card">
<div class="card-header" id="assay_metadata">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#assay_metadata_card" aria-expanded="false" aria-controls="assay_metadata_card">
Assay Metadata
</button>
</h2>
</div>
<div id="assay_metadata_card" class="collapse" aria-labelledby="assay_metadata" data-parent="#assay_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>
</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>
</td>
<td width=55%>
A unique ID that separates the different batches of Nanostring.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td colspan=3 class="container">
<div class="accordion" id="data_accordion">
<div class="card">
<div class="card-header" id="data">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#data_card" aria-expanded="false" aria-controls="data_card">
data
</button>
<sup><mark>required</mark></sup>
<div style="float: right;">
<
object
>
</div>
</div>
<div id="data_card" class="collapse" aria-labelledby="data">
<div class="card-body">
<br>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="normalized">
normalized
</span>
</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="raw">
raw
</span>
</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>
</td>
</tr>
</table>
</div>
</div>
</div>
<div class="card">
<div class="card-header" id="assay_data">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#assay_data_card" aria-expanded="false" aria-controls="assay_data_card">
Assay Data
</button>
</h2>
</div>
<div id="assay_data_card" class="collapse" aria-labelledby="assay_data" data-parent="#assay_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 colspan=3 class="container">
<div class="accordion" id="runs_accordion">
<div class="card">
<div class="card-header" id="runs">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#runs_card" aria-expanded="false" aria-controls="runs_card">
runs
</button>
<sup><mark>required</mark></sup>
<div style="float: right;">
<
array
>
</div>
</div>
<div id="runs_card" class="collapse" aria-labelledby="runs">
<div class="card-body">
A single Nanostring run.
<br>
<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="control_raw_rcc">
control_raw_rcc
</span>
</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>
<tr>
<td colspan=3 class="container">
<div class="accordion" id="samples_accordion">
<div class="card">
<div class="card-header" id="samples">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#samples_card" aria-expanded="false" aria-controls="samples_card">
samples
</button>
<sup><mark>required</mark></sup>
<div style="float: right;">
<
array
>
</div>
</div>
<div id="samples_card" class="collapse" aria-labelledby="samples">
<div class="card-body">
A data record for a single sample from a single Nanostring run.
<br>
<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="raw_rcc">
raw_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>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</td>
</tr>
</table>
</div>
</div>
</div>
<div class="card">
<div class="card-header" id="assay_uploads">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#assay_uploads_card" aria-expanded="false" aria-controls="assay_uploads_card">
Assay Uploads
</button>
</h2>
</div>
<div id="assay_uploads_card" class="collapse" aria-labelledby="assay_uploads" data-parent="#assay_accordion">
<div class="card-body">
<table class="table table-striped">
<thead>
<tr>
<th>Entity</th>
<th>Description</th>
</tr>
</thead>
<tr>
<td width=25%>
<a href='assays.nanostring.nanostring_template.html'>
Nanostring assay template
</a>
</td>
<td>
Nanostring sequencing submission.
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
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