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)

Josef Spidlen1, Karin Breuer2, Ryan Brinkman1

1 BC Cancer Agency, Terry Fox Laboratory, Vancouver, British Columbia, Canada, 2 Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
Publication Name:  Current Protocols in Cytometry
Unit Number:  Unit 10.18
DOI:  10.1002/0471142956.cy1018s61
Online Posting Date:  July, 2012
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Abstract

FlowRepository.org is a Web‐based flow cytometry data repository provided by the International Society for Advancement of Cytometry (ISAC). It supports storage, annotation, analysis, and sharing of flow cytometry datasets. A fundamental tenet of scientific research is that published results should be open to independent validation and refutation. With FlowRepository, researchers can annotate their datasets in compliance with the Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) standard, thus greatly facilitating third‐party interpretation of their data. In this unit, we will mainly focus on the deposition, sharing, and annotation of flow cytometry data. Curr. Protoc. Cytom. 61:10.18.1‐10.18.26. © 2012 by John Wiley & Sons, Inc.

Keywords: data repository; data sharing; minimum information; annotation; flow cytometry

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: FlowRepository Public Data Retrieval
  • Basic Protocol 2: FlowRepository Data Upload and Annotation
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

Basic Protocol 1: FlowRepository Public Data Retrieval

  Materials
  • A computer with an Internet connection and a supported Web browser: Firefox (http://www.mozilla.org) is recommended; some other major Web browsers, such as Safari, Internet Explorer, or Chrome can also be used; however, their use may result in suboptimal visual appearance or limited functionality of the application
  • Ability to run Java applets in your Web browser: the Java version should be version 1.5.1 or higher (Java version 1.6 or higher is recommended, preferably provided by Sun Microsystems Inc.); navigate your browser to http://javatester.org/version.html to verify your ability to run Java and your Java version. If needed, Mac users should use the Apple software update feature to install Java; Windows users can get the latest Java from a Java download page (http://www.java.com), and Linux users should preferably obtain Java and the Firefox Java plugin directly from their distribution.
  • A Google ID, Yahoo! ID, or another OpenID, optional: the ID is not needed for basic anonymous read‐only access to FlowRepository, but it is required in order to deposit and annotate datasets, analyze data online, and perform additional advanced tasks. You may have an OpenID already if you have an account with certain Web‐based service providers, such as Google, Yahoo!, Flickr, AOL, Orange, Blogger, WordPress, or MySpace. Visit http://openid.net/get‐an‐openid/ for further details.

Basic Protocol 2: FlowRepository Data Upload and Annotation

  Materials
  • Necessary resources are the same as for protocol 1, with the exception of OpenID, which is required for protocol 2, whereas it is optional for most of protocol 1
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Figures

Videos

Literature Cited

   Bashashati, A. and Brinkman, R.R. 2009. A survey of flow cytometry data analysis methods. Adv. Bioinformatics 584603.
   Blimkie, D., Fortuno, E.S. 3rd, Thommai, F., Xu, L., Fernandes, E., Crabtree, J., Rein‐Weston, A., Jansen, K., Brinkman, R.R., and Kollmann, T.R. 2010. Identification of B cells through negative gating: An example of the MIFlowCyt standard applied. Cytometry A 77:546‐551.
   Bocsi, J. and Tárnok, A. 2008. Toward automation of flow data analysis. Cytometry A 73:679‐680.
   Burgoon, L.D. 2006. The need for standards, not guidelines, in biological data reporting and sharing. Nat. Biotechnol. 24:1369‐1373.
   Field, D., Sansone, S., Collis, A., Booth, T., Dukes, P., Gregurick, S.K., Kennedy, K., Kolar, P., Kolker, E., Maxon, M., Millard, S., Mugabushaka, A., Perrin, N., Remacle, J.E., Remington, K., Rocca‐Serra, P., Taylor, C.F., Thorley, M., Tiwari, B., and Wilbanks, J. 2009. 'omics data sharing. Science 326:234‐236.
   Harrelson, J.M. and Falletta, J.M. 2007. The privacy rule (HIPAA) as it relates to clinical research. Cancer Treat. Res. 132:199‐207.
   Ioannidis, J.P., Allison, D.B., Ball, C.A., Coulibaly, I., Cui., X., Culhane, A.C., Falchi., M., Furlanello, C., Game, L., Jurman, G., Mangion, J., Mehta, T., Nitzberg, M., Page, G.P., Petretto, E., and van Noort, V. 2009. Repeatability of published microarray gene expression analyses. Nat. Genet. 41:149‐55.
   Lee, J.A., Spidlen, J., Boyce, K., Cai, J., Crosbie, N., Dalphin, M., Furlong, J., Gasparetto, M., Goldberg, M., Goralczyk, E.M., Hyun, B., Jansen, K., Kollmann, T., Kong, M., Leif, R., McWeeney, S., Moloshok, T.D., Moore, W., Nolan, G., Nolan, J., Nikolich‐Zugich, J., Parrish, D., Purcell, B., Qian, Y., Selvaraj, B., Smith, C., Tchuvatkina, O., Wertheimer, A., Wilkinson, P., Wilson, C., Wood, J., Zigon, R., Scheuermann, R.H., and Brinkman, R.R. 2008. MIFlowCyt: The Minimum Information about a Flow Cytometry Experiment. Cytometry A 73:926‐930.
   Lugli, E., Roederer, M., and Cossarizza, A. 2010. Data analysis in flow cytometry: The future just started. Cytometry A 77:705‐713.
   Spidlen, J., Leif, R.C., Moore, W., Roederer, M., and Brinkman, R.R. 2008. Gating‐ML: XML‐based gating descriptions in flow cytometry. Cytometry A 73:1151‐1157.
   Spidlen, J., Moore, W., Parks, D., Goldberg, M., Bray, C., Bierre, P., Gorombey, P., Hyun, B., Hubbard, M., Lange, S., Lefebvre, R., Leif, R., Novo, D., Ostruszka, L., Treister, A., Wood, J., Murphy, R.F., Roederer, M., Sudar, D., Zigon, R., and Brinkman, R.R. 2010. Data File Standard for Flow Cytometry, version FCS 3.1. Cytometry A 77:97‐100.
   Taylor, C.F., Field, D., Sansone, S.A., Aerts, J., Apweiler, R., Ashburner, M., Ball, C.A., Binz, P.A., Bogue, M., Booth, T., Brazma, A., Brinkman, R.R., Michael Clark, A., Deutsch, E.W., Fiehn, O., Fostel, J., Ghazal, P., Gibson, F., Gray, T., Grimes, G., Hancock, J.M., Hardy, N.W., Hermjakob, H., Julian, R.K. Jr., Kane, M., Kettner, C., Kinsinger, C., Kolker, E., Kuiper, M., Le Novère, N., Leebens‐Mack, J., Lewis, S.E., Lord, P., Mallon, A.M., Marthandan, N., Masuya, H., McNally, R., Mehrle, A., Morrison, N., Orchard, S., Quackenbush, J., Reecy, J.M., Robertson, D.G., Rocca‐Serra, P., Rodriguez, H., Rosenfelder, H., Santoyo‐Lopez, J., Scheuermann, R.H., Schober, D., Smith, B., Snape, J., Stoeckert, C.J. Jr, Tipton, K., Sterk, P., Untergasser, A., Vandesompele, J., and Wiemann, S. 2008. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: The MIBBI project. Nat. Biotechnol. 26:889‐896.
Key References
   Lee et al., 2008.
  This reference contains the full normative text of the MIFlowCyt specification, which specifies the required minimal annotation for publishing flow cytometry experiments. Reviewing MIFlowCyt will provide readers with additional clarification of what metadata to provide when describing their datasets.
   Kotecha, N., Krutzik, P.O., and Irish, J.M. 2010. Web‐based analysis and publication of flow cytometry experiments. Curr. Protoc. Cytom. 53:10.17.1‐10.17.24.
  This reference describes several protocols to publish, analyze, and share flow cytometry data using Cytobank. Since FlowRepository is built on top of the Cytobank platform, most of the procedures described in these protocols are also applicable for FlowRepository. Therefore, this reference provides additional resources and guidelines for FlowRepository users.
Internet Resources
   https://flowrepository.org/
  This is the home page of FlowRepository, with links for browsing and querying public datasets, logging in, registration, user's guides and recent documentation.
   http://www.mozilla.org/
  This is the home page of Mozilla with links to obtain the latest version of Firefox. Firefox is the recommended Web browser for FlowRepository.
   http://javatester.org/version.html
  Java Tester is a Web page that helps you verify your ability to run Java applets in your Web browser, as well as the version of Java that your Web browser is using. The ability to run Java version 1.5.1 or higher is a requirement for accessing FlowRepository. Java version 1.6 or higher is recommended.
   http://www.java.com/
  Java download page; Windows users should use this page to obtain or update Java if needed.
   http://openid.net/get‐an‐openid/
  An OpenID Web site helps to determine whether you have an OpenID already and suggests options in case you need to obtain one. FlowRepository requires an OpenID in order to deposit and annotate datasets, analyze data online, and perform additional advanced tasks.
   http://docs.cytobank.org/
  The documentation site for Cytobank; most of the Cytobank documentation is also applicable for FlowRepository since FlowRepository is built on top of the Cytobank platform.
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