docs/docs/assays.cytof.html
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<div class="container">
<p>
<a href="index.html">CIDC Documentation</a>
</p>
<h1>
CYTOF Assay
</h1>
<p>
<b>Description:</b> Information about the acquisition and analysis CyTOF data.
</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="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="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="acquisition_buffer">
acquisition_buffer
</span>
</td>
<td width=55%>
Cell staining buffer used for antibody and cell dilution.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="barcoding_key_csv">
barcoding_key_csv
</span>
</td>
<td width=55%>
The master debarcoding key in a CSV file
</td>
<td>
<a href="files.csv.html">
csv
</a>
</td>
</tr>
<tr>
<td>
<span id="bead_removal">
bead_removal
</span>
</td>
<td width=55%>
Boolean to indicate whether beads have been removed after normalization process
</td>
<td>
<
boolean
>
</td>
</tr>
<tr>
<td>
<span id="date_of_acquisition">
date_of_acquisition
</span>
</td>
<td width=55%>
Date of CyTOF batch acquisition.
</td>
<td>
<
string
>
</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="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="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="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="source_fcs">
source_fcs
</span>
</td>
<td width=55%>
The raw FCS file(s) generated running this batch.
</td>
<td>
<
array
>
<br>
<a href="files.fcs.html">
fcs
</a>
</td>
</tr>
<tr>
<td>
<span id="spike_in_fcs">
spike_in_fcs
</span>
</td>
<td width=55%>
Processed FCS file for the spike-in.
</td>
<td>
<a href="files.fcs.html">
fcs
</a>
</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="cytof_antibodies_accordion">
<div class="card">
<div class="card-header" id="cytof_antibodies">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#cytof_antibodies_card" aria-expanded="false" aria-controls="cytof_antibodies_card">
cytof_antibodies
</button>
<sup><mark>required</mark></sup>
<div style="float: right;">
<
array
>
</div>
</div>
<div id="cytof_antibodies_card" class="collapse" aria-labelledby="cytof_antibodies">
<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="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="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="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>
<tr>
<td>
<span id="antibody">
antibody
</span>
</td>
<td width=55%>
Antibody type collected for this study.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="cat_num">
cat_num
</span>
</td>
<td width=55%>
Antibody registry catalog number assigned to antibody sample.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="clone">
clone
</span>
</td>
<td width=55%>
Resulting type of antibody clone from primary antibody sample.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="company">
company
</span>
</td>
<td width=55%>
Company from which antibody sample was derived.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="lot_num">
lot_num
</span>
</td>
<td width=55%>
Identification number assigned to the particular quantity or lot of material from manufacturer.
</td>
<td>
<
string
>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</td>
</tr>
<tr>
<td colspan=3 class="container">
<div class="accordion" id="barcodes_accordion">
<div class="card">
<div class="card-header" id="barcodes">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#barcodes_card" aria-expanded="false" aria-controls="barcodes_card">
barcodes
</button>
<div style="float: right;">
<
array
>
</div>
</div>
<div id="barcodes_card" class="collapse" aria-labelledby="barcodes">
<div class="card-body">
A data record for the barcoding strategy of a CyTOF assay batch.
<br>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="barcode_id">
barcode_id
</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_num">
barcode_num
</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>
</td>
</tr>
<tr>
<td colspan=3 class="container">
<div class="accordion" id="records_accordion">
<div class="card">
<div class="card-header" id="records">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#records_card" aria-expanded="false" aria-controls="records_card">
records
</button>
<sup><mark>required</mark></sup>
<div style="float: right;">
<
array
>
</div>
</div>
<div id="records_card" class="collapse" aria-labelledby="records">
<div class="card-body">
A single sample-level data record from CyTOF a assay batch.
<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="preprocessing_notes">
preprocessing_notes
</span>
</td>
<td width=55%>
Any notes pertaining to preprocessing of CyTOF data.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td colspan=3 class="container">
<div class="accordion" id="input_files_accordion">
<div class="card">
<div class="card-header" id="input_files">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#input_files_card" aria-expanded="false" aria-controls="input_files_card">
input_files
</button>
<sup><mark>required</mark></sup>
<div style="float: right;">
<
object
>
</div>
</div>
<div id="input_files_card" class="collapse" aria-labelledby="input_files">
<div class="card-body">
CyTOF Assay Input Files
<br>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<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="processed_fcs">
processed_fcs
</span>
</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>
</table>
</div>
</div>
</div>
</div>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</td>
</tr>
<tr>
<td colspan=3 class="container">
<div class="accordion" id="controls_accordion">
<div class="card">
<div class="card-header" id="controls">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#controls_card" aria-expanded="false" aria-controls="controls_card">
controls
</button>
<div style="float: right;">
<
array
>
</div>
</div>
<div id="controls_card" class="collapse" aria-labelledby="controls">
<div class="card-body">
A data record for the control files in a CyTOF assay batch.
<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_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="control_name">
control_name
</span>
</td>
<td width=55%>
Name or identifier of a control sample.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td colspan=3 class="container">
<div class="accordion" id="input_files_accordion">
<div class="card">
<div class="card-header" id="input_files">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#input_files_card" aria-expanded="false" aria-controls="input_files_card">
input_files
</button>
<sup><mark>required</mark></sup>
<div style="float: right;">
<
object
>
</div>
</div>
<div id="input_files_card" class="collapse" aria-labelledby="input_files">
<div class="card-body">
CyTOF Assay Input Files
<br>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<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="processed_fcs">
processed_fcs
</span>
</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="spike_in_fcs">
spike_in_fcs
</span>
</td>
<td width=55%>
Processed FCS file for the spike-in.
</td>
<td>
<a href="files.fcs.html">
fcs
</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="analysis_metadata">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#analysis_metadata_card" aria-expanded="false" aria-controls="analysis_metadata_card">
Analysis Metadata
</button>
</h2>
</div>
<div id="analysis_metadata_card" class="collapse" aria-labelledby="analysis_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="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="astrolabe_analysis">
astrolabe_analysis
</span>
</td>
<td width=55%>
Information about a ZIP file.
</td>
<td>
<a href="files.zip.html">
zip
</a>
</td>
</tr>
<tr>
<td>
<span id="astrolabe_reports">
astrolabe_reports
</span>
</td>
<td width=55%>
Information about a ZIP file.
</td>
<td>
<a href="files.zip.html">
zip
</a>
</td>
</tr>
<tr>
<td>
<span id="control_files_analysis">
control_files_analysis
</span>
</td>
<td width=55%>
Information about a ZIP file.
</td>
<td>
<a href="files.zip.html">
zip
</a>
</td>
</tr>
</table>
</div>
</div>
</div>
<div class="card">
<div class="card-header" id="analysis_data">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#analysis_data_card" aria-expanded="false" aria-controls="analysis_data_card">
Analysis Data
</button>
</h2>
</div>
<div id="analysis_data_card" class="collapse" aria-labelledby="analysis_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="records_accordion">
<div class="card">
<div class="card-header" id="records">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#records_card" aria-expanded="false" aria-controls="records_card">
records
</button>
<sup><mark>required</mark></sup>
<div style="float: right;">
<
array
>
</div>
</div>
<div id="records_card" class="collapse" aria-labelledby="records">
<div class="card-body">
A single sample-level data record from CyTOF a assay batch.
<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 colspan=3 class="container">
<div class="accordion" id="output_files_accordion">
<div class="card">
<div class="card-header" id="output_files">
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<
object
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Output files generated from the CyTOF assay: FCS file with enumerations for compartment, assignment and profiling cell labels; 3 CSV keys for mapping from respective enumeration indices to the cell labels; 3 CSV files providing cell count information for each of the cell labels
<br>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="assignment">
assignment
</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="cell_counts_assignment">
cell_counts_assignment
</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="cell_counts_compartment">
cell_counts_compartment
</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="cell_counts_profiling">
cell_counts_profiling
</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="compartment">
compartment
</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="fcs_file">
fcs_file
</span>
</td>
<td width=55%>
Information about a FCS file.
</td>
<td>
<a href="files.fcs.html">
fcs
</a>
</td>
</tr>
<tr>
<td>
<span id="profiling">
profiling
</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>
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</td>
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<tr>
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<
array
>
</div>
</div>
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<div class="card-body">
A list of samples excluded from analysis, along with the reasons why.
<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="reason_excluded">
reason_excluded
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
A comment describing why this sample is missing from the pipeline output.
</td>
<td>
<
string
>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</td>
</tr>
</table>
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Assay Uploads
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<th>Entity</th>
<th>Description</th>
</tr>
</thead>
<tr>
<td width=25%>
<a href='assays.cytof.cytof_template.html'>
CYTOF assay template
</a>
</td>
<td>
Cytometry by Time-Of-Flight (CyTOF) aka mass-cytometry assay submission.
</td>
</tr>
</table>
</div>
</div>
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Analysis Uploads
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<table class="table table-striped">
<thead>
<tr>
<th>Entity</th>
<th>Description</th>
</tr>
</thead>
<tr>
<td width=25%>
<a href='assays.cytof.cytof_analysis_template.html'>
CyTOF analysis template
</a>
</td>
<td>
Cytometry by Time-Of-Flight (CyTOF) analysis submission.
</td>
</tr>
</table>
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