Web‐Based Analysis and Publication of Flow Cytometry Experiments

Nikesh Kotecha1, Peter O. Krutzik2, Jonathan M. Irish3

1 Stanford University Biomedical Informatics Program, Stanford, California, 2 Stanford University Department of Microbiology and Immunology, Stanford, California, 3 Stanford University School of Medicine, Stanford, California
Publication Name:  Current Protocols in Cytometry
Unit Number:  Unit 10.17
DOI:  10.1002/0471142956.cy1017s53
Online Posting Date:  July, 2010
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Abstract

Cytobank is a Web‐based application for storage, analysis, and sharing of flow cytometry experiments. Researchers use a Web browser to log in and use a wide range of tools developed for basic and advanced flow cytometry. In addition to providing access to standard cytometry tools from any computer, Cytobank creates a platform and community for developing new analysis and publication tools. Figure layouts created on Cytobank are designed to allow transparent access to the underlying experiment annotation and data processing steps. Since all flow cytometry files and analysis data are stored on a central server, experiments and figures can be viewed or edited by anyone with the proper permission, from any computer with Internet access. Once a primary researcher has performed the initial analysis of the data, collaborators can engage in experiment analysis and make their own figure layouts using the gated, compensated experiment files. Cytobank is available to the scientific community at http://www.cytobank.org. Curr. Protoc. Cytom. 53:10.17.1‐10.17.24. © 2010 by John Wiley & Sons, Inc.

Keywords: Cytobank; database; storage platform; analysis; flow cytometry

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Online Storage of Flow Cytometry Data
  • Basic Protocol 2: Analysis of Phospho‐Flow Signaling Experiments
  • Basic Protocol 3: Annotating and Gating Experiments
  • Basic Protocol 4: Sharing Illustrations and Data with Collaborators
  • Basic Protocol 5: Publishing Experimental Data and Figures
  • Basic Protocol 6: Initiating New Analysis of a Published Dataset
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

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Figures

Videos

Literature Cited

   Barrett, T., Troup, D.B., Wilhite, S.E., Ledoux, P., Rudnev, D., Evangelista, C., Kim, I.F., Soboleva, A., Tomashevsky, M., Marshall, K.A., Phillippy, K.H., Sherman, P.M., Muertter, R.N., and Edgar, R. 2009. NCBI GEO: Archive for high‐throughput functional genomic data. Nucleic Acids Res. 37:885‐890.
   Demeter, J., Beauheim, C., Gollub, J., Hernandez‐Boussard, T., Jin, H., Maier, D., Matese, J.C., Nitzberg, M., Wymore, F., Zachariah, Z.K., Brown, P.O., Sherlock, G., and Ball, C.A. 2007. The Stanford Microarray Database: Implementation of new analysis tools and open source release of software. Nucleic Acids Res. 35:766‐770.
   Frelinger, J., Kepler, T.B., and Chan, C. 2008. Flow: Statistics, visualization and informatics for flow cytometry. Biol. Med. 3:10.
   Hahne, F., LeMeur, N., Brinkman, R.R., Ellis, B., Haaland, P., Sarkar, D., Spidlen, J., Strain, E., and Gentleman, R. 2009. FlowCore: A bioconductor package for high throughput flow cytometry. BMC Bioinformatics 10:106.
   Irish, J.M., Hovland, R., Krutzik, P.O., Perez, O.D., Bruserud, Ø., Gjertsen, B.T., and Nolan, G.P. 2004. Single cell profiling of potentiated phospho‐protein networks in cancer cells. Cell 118:217‐228.
   Irish, J.M., Kotecha, N., and Nolan, G.P. 2006. Mapping normal and cancer cell signaling networks: Towards single‐cell proteomics. Nat. Rev. Cancer 6:146‐155.
   Krutzik, P.O. and Nolan, G.P. 2003. Intracellular phospho‐protein staining techniques for flow cytometry: Monitoring single cell signaling events. Cytometry A 55:61‐70.
   Krutzik, P.O. and Nolan, G.P. 2006. Fluorescent cell barcoding in flow cytometry allows high‐throughput drug screening and signaling profiling. Nat. Methods 3:361‐368.
   Sachs, K., Perez, O., Pe'er, D., Lauffenburger, D.A., and Nolan, G.P. 2005. Causal protein‐signaling networks derived from multiparameter single‐cell data. Science 308:523‐529.
Internet Resources
  http://www.cytobank.org
  This is the home page for Cytobank with links for logging in and registration, getting started, and to the latest documentation.
  http://docs.cytobank.org
  This is the documentation site for Cytobank with links to the latest tutorials and frequently asked questions.
  http://www.mozilla.org
  This is the homepage for Mozilla, creators of the FireFox Web browser. Cytobank works best with FireFox.
  http://www.java.com
  This is the homepage for Java, with links and information about installing Java on your computer. Cytobank requires that your Web browser be configured to run java applets.
  http://www.javatester.org/version.html
  This site can test whether your browser can run Java applets.
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