docs/docs/assays.cytof.cytof_template.html
<!DOCTYPE html>
<html>
<head>
<title>CIDC Schemas</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css" integrity="sha384-ggOyR0iXCbMQv3Xipma34MD+dH/1fQ784/j6cY/iJTQUOhcWr7x9JvoRxT2MZw1T" crossorigin="anonymous">
<style>
.bd-placeholder-img {
font-size: 1.125rem;
text-anchor: middle;
-webkit-user-select: none;
-moz-user-select: none;
-ms-user-select: none;
user-select: none;
}
@media (min-width: 768px) {
.bd-placeholder-img-lg {
font-size: 3.5rem;
}
}
</style>
</head>
<body>
<main role="main">
<div class="container">
<p>
<a href="index.html">CIDC Documentation</a>
</p>
<h1>
CYTOF assay template
</h1>
<p>
<b>Description:</b> Cytometry by Time-Of-Flight (CyTOF) aka mass-cytometry assay submission.
</p>
</div>
<div class="container">
<div class="accordion" id="Acquisition_and_Preprocessing_accordion">
<div class="card">
<div class="card-header" id="Acquisition_and_Preprocessing">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#Acquisition_and_Preprocessing_card" aria-expanded="false" aria-controls="Acquisition_and_Preprocessing_card">
Worksheet - Acquisition and Preprocessing
</button>
</h2>
</div>
<div id="Acquisition_and_Preprocessing_card" class="collapse" aria-labelledby="Acquisition_and_Preprocessing" data-parent="#Acquisition_and_Preprocessing_accordion">
<div class="card-body">
<div class="accordion" id="Acquisition_and_Preprocessing_preamble_accordion">
<div class="card">
<div class="card-header" id="Acquisition_and_Preprocessing_preamble">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#Acquisition_and_Preprocessing_preamble_card" aria-expanded="false" aria-controls="Acquisition_and_Preprocessing_preamble_card">
Preamble Rows
</button>
</h2>
</div>
<div id="Acquisition_and_Preprocessing_preamble_card" class="collapse" aria-labelledby="Acquisition_and_Preprocessing_preamble" data-parent="#Acquisition_and_Preprocessing_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="assay run id">
assay run id
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
User defined unique identifier for this assay run. Not necessarily unique across batches.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="batch id">
batch id
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
CyTOF batch identification number. Unique to every batch.
</td>
<td>
<
string
>
</td>
</tr>
<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="date of acquisition">
date of acquisition
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Date of CyTOF batch acquisition.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="acquisition buffer">
acquisition buffer
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Cell staining buffer used for antibody and cell dilution.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="bead removal">
bead removal
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Boolean to indicate whether beads have been removed after normalization process
</td>
<td>
<
boolean
>
</td>
</tr>
<tr>
<td>
<span id="instrument">
instrument
</span>
</td>
<td width=55%>
Name of CyTOF instrument on which experiment was conducted.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="injector">
injector
</span>
</td>
<td width=55%>
Name of Injector component used as part of the CyTOF software
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="normalization method">
normalization method
</span>
</td>
<td width=55%>
Process used for normalization prior to analysis, if any.
</td>
<td>
<
string
>
<ul>
<li>"Fluidigm"</li>
<li>"Normalizer v0.3"</li>
<li>"Other"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="debarcoding protocol">
debarcoding protocol
</span>
</td>
<td width=55%>
The strategy/kit used to barcode CyTOF samples, if any
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="harware version">
harware version
</span>
</td>
<td width=55%>
Version no. of instrument hardware used.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="concatenated spike in fcs filename">
concatenated spike in fcs filename
</span>
</td>
<td width=55%>
Processed FCS file for the spike-in.
</td>
<td>
<a href="files.fcs.html">
fcs
</a>
</td>
</tr>
<tr>
<td>
<span id="concatenated raw fcs filename(s)">
concatenated raw fcs filename(s)
</span>
</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>
</table>
</div>
</div>
</div>
</div>
<div class="accordion" id="Acquisition_and_Preprocessing_body_accordion">
<div class="card">
<div class="card-header" id="Acquisition_and_Preprocessing_body">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#Acquisition_and_Preprocessing_body_card" aria-expanded="false" aria-controls="Acquisition_and_Preprocessing_body_card">
Data Columns
</button>
</h2>
</div>
<div id="Acquisition_and_Preprocessing_body_card" class="collapse" aria-labelledby="Acquisition_and_Preprocessing_body" data-parent="#Acquisition_and_Preprocessing_body_accordion">
<div class="card-body">
<h5 class="text-muted">Run info</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>
</table>
<h5 class="text-muted">Preprocessing</h4>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="processed fcs filename">
processed fcs filename
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Final FCS files after all processing. Spike-in's should be removed.
</td>
<td>
<a href="files.fcs.html">
fcs
</a>
</td>
</tr>
<tr>
<td>
<span id="concatenation version">
concatenation version
</span>
</td>
<td width=55%>
Concatenation of FCS files into a single FCS version number.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="normalization version">
normalization version
</span>
</td>
<td width=55%>
Version of normalization for CyTOF assay batch.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="preprocessing_notes">
preprocessing_notes
</span>
</td>
<td width=55%>
Any notes pertaining to preprocessing of CyTOF data.
</td>
<td>
<
string
>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<div class="accordion" id="Antibody_Information_accordion">
<div class="card">
<div class="card-header" id="Antibody_Information">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#Antibody_Information_card" aria-expanded="false" aria-controls="Antibody_Information_card">
Worksheet - Antibody Information
</button>
</h2>
</div>
<div id="Antibody_Information_card" class="collapse" aria-labelledby="Antibody_Information" data-parent="#Antibody_Information_accordion">
<div class="card-body">
<div class="accordion" id="Antibody_Information_body_accordion">
<div class="card">
<div class="card-header" id="Antibody_Information_body">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#Antibody_Information_body_card" aria-expanded="false" aria-controls="Antibody_Information_body_card">
Data Columns
</button>
</h2>
</div>
<div id="Antibody_Information_body_card" class="collapse" aria-labelledby="Antibody_Information_body" data-parent="#Antibody_Information_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="target">
target
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Antibody type collected for this study.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="clone">
clone
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Resulting type of antibody clone from primary antibody sample.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="antibody company">
antibody company
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Company from which antibody sample was derived.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="catalog number">
catalog number
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Antibody registry catalog number assigned to antibody sample.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="lot number">
lot number
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Identification number assigned to the particular quantity or lot of material from manufacturer.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="isotope">
isotope
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Antibody isotype used to help differentiate antibody signals.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="dilution">
dilution
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Concentration ratio of dilution buffer for primary antibody.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="stain_type">
stain_type
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Type of staining method used for antibody.
</td>
<td>
<
string
>
<ul>
<li>"Surface Stain"</li>
<li>"Intracellular"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="usage">
usage
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
How this antibody should be used in automatic analysis
</td>
<td>
<
string
>
<ul>
<li>"Ignored"</li>
<li>"Used"</li>
<li>"Barcoding"</li>
<li>"Analysis Only"</li>
</ul>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<div class="accordion" id="Controls_and_Spike-Ins_accordion">
<div class="card">
<div class="card-header" id="Controls_and_Spike-Ins">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#Controls_and_Spike-Ins_card" aria-expanded="false" aria-controls="Controls_and_Spike-Ins_card">
Worksheet - Controls and Spike-Ins
</button>
</h2>
</div>
<div id="Controls_and_Spike-Ins_card" class="collapse" aria-labelledby="Controls_and_Spike-Ins" data-parent="#Controls_and_Spike-Ins_accordion">
<div class="card-body">
<div class="accordion" id="Controls_and_Spike-Ins_preamble_accordion">
<div class="card">
<div class="card-header" id="Controls_and_Spike-Ins_preamble">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#Controls_and_Spike-Ins_preamble_card" aria-expanded="false" aria-controls="Controls_and_Spike-Ins_preamble_card">
Preamble Rows
</button>
</h2>
</div>
<div id="Controls_and_Spike-Ins_preamble_card" class="collapse" aria-labelledby="Controls_and_Spike-Ins_preamble" data-parent="#Controls_and_Spike-Ins_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>
</table>
</div>
</div>
</div>
</div>
<div class="accordion" id="Controls_and_Spike-Ins_body_accordion">
<div class="card">
<div class="card-header" id="Controls_and_Spike-Ins_body">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#Controls_and_Spike-Ins_body_card" aria-expanded="false" aria-controls="Controls_and_Spike-Ins_body_card">
Data Columns
</button>
</h2>
</div>
<div id="Controls_and_Spike-Ins_body_card" class="collapse" aria-labelledby="Controls_and_Spike-Ins_body" data-parent="#Controls_and_Spike-Ins_body_accordion">
<div class="card-body">
<h5 class="text-muted">Controls info</h4>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="processed fcs filename">
processed fcs filename
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Final FCS files after all processing. Spike-in's should be removed.
</td>
<td>
<a href="files.fcs.html">
fcs
</a>
</td>
</tr>
<tr>
<td>
<span id="control name">
control name
</span>
</td>
<td width=55%>
Name or identifier of a control sample.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="cimac participant id">
cimac participant id
</span>
</td>
<td width=55%>
Participant identifier assigned by the CIMAC-CIDC Network. Formated as: CTTTPPP for trial code TTT and participant PPP (first 7 characters of CIMAC ID).
</td>
<td>
<
string
>
as regex <br> <code>^C[A-Z0-9]{3}[A-Z0-9]{3}$</code>
</td>
</tr>
<tr>
<td>
<span id="spike-in fcs filename">
spike-in fcs filename
</span>
</td>
<td width=55%>
Processed FCS file for the spike-in.
</td>
<td>
<a href="files.fcs.html">
fcs
</a>
</td>
</tr>
<tr>
<td>
<span id="concatenation version">
concatenation version
</span>
</td>
<td width=55%>
Concatenation of FCS files into a single FCS version number.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="normalization version">
normalization version
</span>
</td>
<td width=55%>
Version of normalization for CyTOF assay batch.
</td>
<td>
<
string
>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<div class="accordion" id="Barcoding_accordion">
<div class="card">
<div class="card-header" id="Barcoding">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#Barcoding_card" aria-expanded="false" aria-controls="Barcoding_card">
Worksheet - Barcoding
</button>
</h2>
</div>
<div id="Barcoding_card" class="collapse" aria-labelledby="Barcoding" data-parent="#Barcoding_accordion">
<div class="card-body">
<div class="accordion" id="Barcoding_preamble_accordion">
<div class="card">
<div class="card-header" id="Barcoding_preamble">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#Barcoding_preamble_card" aria-expanded="false" aria-controls="Barcoding_preamble_card">
Preamble Rows
</button>
</h2>
</div>
<div id="Barcoding_preamble_card" class="collapse" aria-labelledby="Barcoding_preamble" data-parent="#Barcoding_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%>
CyTOF batch identification number. Unique to every batch.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="Debarcoding key file">
Debarcoding key file
</span>
</td>
<td width=55%>
The master debarcoding key in a CSV file
</td>
<td>
<a href="files.csv.html">
csv
</a>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
<div class="accordion" id="Barcoding_body_accordion">
<div class="card">
<div class="card-header" id="Barcoding_body">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#Barcoding_body_card" aria-expanded="false" aria-controls="Barcoding_body_card">
Data Columns
</button>
</h2>
</div>
<div id="Barcoding_body_card" class="collapse" aria-labelledby="Barcoding_body" data-parent="#Barcoding_body_accordion">
<div class="card-body">
<h5 class="text-muted">Barcodes</h4>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="id (cimac id/participant id/control name)">
id (cimac id/participant id/control name)
</span>
</td>
<td width=55%>
CIMAC ID, Participant ID or Control sample for which barcode is assigned.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="barcode number">
barcode number
</span>
</td>
<td width=55%>
Barcode number
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="debarcoding key">
debarcoding key
</span>
</td>
<td width=55%>
Debarcoding key assigned
</td>
<td>
<
string
>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</main>
<script src="https://code.jquery.com/jquery-3.3.1.slim.min.js" integrity="sha384-q8i/X+965DzO0rT7abK41JStQIAqVgRVzpbzo5smXKp4YfRvH+8abtTE1Pi6jizo" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.14.7/umd/popper.min.js" integrity="sha384-UO2eT0CpHqdSJQ6hJty5KVphtPhzWj9WO1clHTMGa3JDZwrnQq4sF86dIHNDz0W1" crossorigin="anonymous"></script>
<script src="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/js/bootstrap.min.js" integrity="sha384-JjSmVgyd0p3pXB1rRibZUAYoIIy6OrQ6VrjIEaFf/nJGzIxFDsf4x0xIM+B07jRM" crossorigin="anonymous"></script>
</body>
</html>