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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

Literature Cited

  1. Literature Cited
  2. Key References
  3. Internet Resources
  • 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

  1. Literature Cited
  2. Key References
  3. Internet Resources
  • 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

  1. Literature Cited
  2. Key References
  3. Internet Resources

This is the home page of FlowRepository, with links for browsing and querying public datasets, logging in, registration, user's guides and recent documentation.

This is the home page of Mozilla with links to obtain the latest version of Firefox. Firefox is the recommended Web browser for FlowRepository.

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.

Java download page; Windows users should use this page to obtain or update Java if needed.

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.

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.