MIFlowCyt
Categories
1. Experiment Overview
1.1. What should be reported:
A brief description of the goal of the experiment. This should include the rationale and hypothesis.
Reported:
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1.2. What should be reported:
The keywords should include terms from an appropriate vocabulary (e.g., MeSH) to describe the experiment.
Reported:
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1.3. What should be reported:
Variables are attribute(s) that differ between samples within an experiment due to pre-existing differences in sample states or due to experimental manipulation of the samples. For additional information, consult the supplementary information of the references [1].
Reported:
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1.4. What should be reported:
List the experimental primary contact name and email.
Reported:
National Institutes of Health
1.5. What should be reported:
The description may include information for additional individuals involved in the experiment, including their contact details and their role.
Reported:
Joshua Welsh joshua.welsh@nih.gov
1.6. What should be reported:
The date or time period during which the investigation was performed (i.e., from collecting and treating samples to performing data analysis) shall be stated.
Reported:
07-Aug-2019
1.7. What should be reported:
A brief summary of the interpretation of the results or outcome of the experiment shall be provided if available.
Reported:
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1.8. What should be reported:
A description of the quality control measures used such as replicates, calibrations, control assays, etc. shall be provided. If another experiment was performed for the purposes of establishing quality control standards, that experiment may be referenced.
Reported:
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2. Flow Sample/Specimen details
2.1.1.1. What should be reported:
Sample materials shall be described according to 2.1.1, 2.1.2, or 2.1.3, based on the type of the sample material. Each sample shall be distinguished from other samples within the same experiment. For additional information, consult the supplementary information of the references [1].
Reported:
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2.1.1.2. What should be reported:
The source of the biological sample shall be described (e.g., wildtype mouse, C57BL/6 spleen, C57BL/6 splenocytes). If the source is a cell line the description shall include its name, ATCC [17] (or equivalent) number, and cell type.
Reported:
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2.1.1.3. What should be reported:
See supplementary information of reference and consult sections 1-2.1.1.3.7 for detailed descriptions of expected information [1].
Reported:
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2.1.2.2. What should be reported:
The location of the sample origin shall be specified. This should include longitude and latitude if relevant.
Reported:
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2.3. What should be reported:
The description shall include details about treatment agents, which play the role of experiment variables, or shall specify that samples were untreated.
Reported:
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2.4. What should be reported:
The expected and possible types of cells or other particles in the sample material, and their expected and possible measurable characteristics should be noted as these represent the key information for choosing appropriate reagents with respect to the experimental goal. The following information shall be provided about each fluorescence reagent used. Information about the characteristic(s) being measured, as well as details about what plays the role of analyte, analyte detector, and analyte reporter should be descriptive enough to allow for accurate interpretation of the experiment data.
Reported:
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3. Instrument Details
3.1. What should be reported:
The instrument manufacturer shall be specified by stating its name (e.g., MIFlowCyt Cytometry Systems, Inc.). A URL pointing to manufacturer web pages may also be provided.
Reported:
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3.2. What should be reported:
The instrument model shall be specified (e.g., CytMeter Elite-2000). It may include the instrument serial number.
Reported:
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3.3. What should be reported:
The system and its configurations have significant impact on experimental results and as such the following shall be provided. Please consult the supplementary information of the reference for additional information [1].
Reported:
Refer to Sample Acq Info and Instr Settings sheets for a list of data files.
4. Data Analysis Details
4.1. What should be reported:
The list-mode data files (e.g., FCS files) shall be provided directly or details on how they may be requested shall be stated.
Reported:
Refer to MIFlowCytEV section 7.1
4.2. What should be reported:
A description of the type of compensation used shall be included (e.g., no compensation, hardware compensation, computed compensation) and the spillover or compensation matrix shall be provided when possible (i.e., it may not be available for old data but shall be provided when available). While the spillover matrix is preferred, the compensation matrix is also acceptable. The type of the matrix (i.e., spillover vs. compensation) shall be explicitly stated.
Reported:
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4.3. What should be reported:
Describe each data/parameter transformation performed during analysis when the transformation does not qualify as compensation.
Reported:
Refer to MIFlowCytEV sections 4 and 5 for detailed description of data transformation.
4.4.1. What should be reported:
The subpopulation identified by the gate shall be briefly described and the gating strategy or a reference to where it is described in detail should be provided
Reported:
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4.4.2. What should be reported:
Percentage of events within the gate shall be provided specifically stating the denominator. The denominator shall be either the total population of events or another gate. When the denominator is another gate, this shall also be exactly specified in recursive fashion so that the gating strategy can be followed up to the original data set.
Reported:
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4.4.3. What should be reported:
Either the exact mathematical descriptions of each gate boundary shall be provided using an open and freely available specification, or this information shall be provided in the form of images.
Reported:
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