FlowJo software is used for the analysis of flow cytometry data. This tutorial will introduce you to FlowJo using a simple experiment as an example. A FITC anti-CD8 reagent is titrated to determine the most economical concentration for staining in future experiments. Table of Contents Introduction Step 1: Load samples into the workspace Step 2: Analyze the control sample in detail Step 3: Copy gates and statistics to all samples Step 4: Verify gates on all samples Step 5: Generate a graphical report Step 6: Generate a table of statistics FlowJo is a product of Tree Star, Inc. www.FlowJo.com USA: (800) 366-6045 International: 1 011 541-201-0022 FlowJo@treestar.com FlowJo was written by Adam Treister and Mario Roederer, based on concepts developed with David Parks, Martin Bigos and Wayne Moore.

We are indebted to the Herzenberg laboratory at Stanford and our active and enthusiastic users for their ideas, discussions and tireless testing of new versions. FlowJo is Copyright © Trustees of Leland Stanford Jr. University, 1996-97 FlowJo is Copyright © Tree Star, Inc. 1997-2006 FlowJo for Macintosh is Copyright © Tree Star, Inc. 2006 FlowJo for Windows is Copyright © Tree Star, Inc. 2006 FlowJo Tutorial and Web Site are Copyright © Tree Star, Inc. 1997-2006 • FlowJo Basic Tutorial • • © MMVI-iii • Basic Tutorial Introduction FlowJo software is used for the analysis of flow cytometry data. You can use FlowJo to analyze all of your flow cytometry data - regardless of the cytometer used to collect your data files. This tutorial will introduce you to FlowJo and to the 6 steps involved in analyzing a basic immunophenotyping experiment. 1. Load data into the Workspace. 2. Analyze the control tube data in detail (gate subsets and add statistics). 3. Copy gates and statistics to All Samples. 4. Verify gates on All Samples. 5. Generate a graphical report including All Samples. 6. Generate a table of statistics from All Samples. Instructions to guide you through the analysis of a basic immunophenotyping experiment are contained in this tutorial. Follow along with the provided data files to get a feel for how FlowJo works. If you wish to skip steps, we provide pre-made Workspace files that correspond to each analysis step.

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