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UNIT 10.18 Preparing a Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) Compliant Manuscript Using the International Society for Advancement of Cytometry (ISAC) FCS File Repository (FlowRepository.org)

  1. Josef Spidlen1,
  2. Karin Breuer2,
  3. Ryan Brinkman1

Published Online: 1 JUL 2012

DOI: 10.1002/0471142956.cy1018s61

Current Protocols in Cytometry

Current Protocols in Cytometry

How to Cite

Spidlen, J., Breuer, K. and Brinkman, R. 2012. Preparing a Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) Compliant Manuscript Using the International Society for Advancement of Cytometry (ISAC) FCS File Repository (FlowRepository.org). Current Protocols in Cytometry. 61:10.18:10.18.1–10.18.26.

Author Information

  1. 1

    BC Cancer Agency, Terry Fox Laboratory, Vancouver, British Columbia, Canada

  2. 2

    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada

Publication History

  1. Published Online: 1 JUL 2012
  2. Published Print: JUL 2012
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Figure 10.18.1. FlowRepository—landing page. The landing page of FlowRepository allows users to quickly browse or query public datasets.

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Figure 10.18.2. Result of a query. Repository queries return a list of matching datasets.

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Figure 10.18.3. Dataset download. The download box includes links for downloading FCS files, illustrations, attachment, and gating. Downloading FCS files starts a Java applet where users select the download location (i.e., a folder locally on their computer) and which data files to download.

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Figure 10.18.4. List of experiment FCS files. The advanced experiment view lists FCS files including details, such as staining panel assignment, experiment variables, tube identification, number of events, and size of the data file. Additional details may be displayed by clicking on the details link near each of the FCS file name.

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Figure 10.18.5. MIFlowCyt compliance details. Provided and missing information are summarized for each section of MIFlowCyt; additional details may be expanded by clicking on the check mark symbols. Mousing over the “i” in the top right corner displays more information about MIFlowCyt score calculation.

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Figure 10.18.6. New experiment form. Basic experimental metadata should be provided for each new dataset as required by MIFlowCyt.

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Figure 10.18.7. FCS file categorization. FlowRepository will automatically assign FCS files into experimental files, compensation controls, and other controls. Users may adjust the categorization if needed.

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Figure 10.18.8. FCS panel assignment. FlowRepository will assign FCS files to staining panels based on distinct groups of markers detected in the data. Users may adjust these assignments and rename, add, or delete panels if needed.

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Figure 10.18.9. Reagents available for annotation. Users describe available reagents in the annotation data section. Later on, samples can be annotated with these reagents.

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Figure 10.18.10. New reagent form. Reagent details should be provided as required by MIFlowCyt.

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Figure 10.18.11. Adding an organism from the NCBI taxonomy. Suggestions will be displayed after three or more characters are typed.

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Figure 10.18.12. Creation of a biological sample source template. Required fields will change dynamically based on the type of sample source specified. Values provided in a template may be adjusted when the template is used to annotate specific samples.

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Figure 10.18.13. Application of a reagent. The characteristic being measured should be specified when samples (or templates) are annotated with reagents, since the same reagent could be used for slightly different purposes in different experiments.

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Figure 10.18.14. Setting up experimental variables. Experimental variables are defined and assigned in the illustration creation section.

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Figure 10.18.15. Conditions assignment. Experimental variables (e.g., sample stimulation conditions) can be assigned to FCS files by dragging and dropping the file labels to appropriate boxes.

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Figure 10.18.16. Description of instrumentation settings. The dialog window is asking for details as required by MIFlowCyt. Consequently, it will be significantly simplified if default instrumentation settings are used.

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Figure 10.18.17. Definition of optical path. An optical path can be defined by dragging and dropping its components into an ordered list in the yellow box. Details about each component need to be provided prior saving the optical path.

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Figure 10.18.18. MIFlowCyt compliance review of own experiments. An additional column with references to improve the annotation is provided if applicable.