<?xml version="1.0" encoding="UTF-8"?>
<?xml-stylesheet type="text/xsl" href="isatab-flowcyt0609.xsl"?>
<!-- 
  ********************************************************************
  * FuGEFlow Experiment Annotation Example
  * **************************************
  * 
  * This document represents an example description of a flow cytometry 
  * experiment that is compliant with the Minimum Information about a 
  * Flow Cytometry Experiment (MIFlowCyt).
  * 
  * The purpose of this document is to validate FuGEFlow - a Flow Cytometry
  * specific extension of the FuGE model. Validation is understood in terms of
  * whether the FuGEFlow XML schema defines a language that allows to describe
  * flow cytometry experiments.
  *
  * This XML document is based on 
  * "MIFlowCyt Experiment Annotation Example" from February 20th, 2008
  * by Maura Gasparetto, Josef Spidlen, and Ryan R. Brinkman
  * 
  * License
  * The work may be used under the terms of the 
  * Creative Commons Attribution-ShareAlike 3.0 Unported license. 
  * You are free to share (copy, distribute and transmit), and adapt 
  * the work under the conditions specified at 
  * http://creativecommons.org/licenses/by-sa/3.0/legalcode
  * 
  * Acknowledgement
  * This work has been supported by NIH grant EB005034 from the 
  * National Institute of Biomedical Imaging And Bioengineering.
  * 
  * Disclaimer
  * The content is solely the responsibility of the authors and 
  * does not necessarily represent the official views of the 
  * National Institute of Biomedical Imaging And Bioengineering 
  * or the National Institutes of Health.
  *
  * Josef Spidlen, Ph.D., jspidlen@bccrc.ca, April 11, 2008
  ********************************************************************** 
  -->
<fuge:FuGE
  
  xmlns:fuge="http://fuge.sourceforge.net/fuge/1.0"
  xmlns:fcm="http://flowcyt.sourceforge.net/fugeflow/"
  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
  
  identifier="Donor_HSC_contribution_MGJSRB20080211" 
  name="Donor HSC Contribution"
  
  xsi:schemaLocation="
    http://flowcyt.sourceforge.net/fugeflow/ ../../XSD/FuGEFlow.xsd
    http://fuge.sourceforge.net/fuge/1.0 ../../XSD/FuGEv1.xsd
    "
  >
  <!--
    The xsi:schemaLocation="http://fuge.sourceforge.net/fuge/1.0 ../XSD/FuGEv1.xsd"
    speeds up the validation agains FuGE XSD (locally). The following can be used to
    validate against FuGE XSD online at sourceforge.net: 
    xsi:schemaLocation="http://fuge.sourceforge.net/fuge/1.0 http://fuge.sourceforge.net/dev/V1Final/FuGEv1.xsd"
  -->
  
  
  <!-- 
    ********************************* 
    Materials
    *********************************
  -->
  <fuge:MaterialCollection>

    <!-- Fluorescent Reagents -->
    <fcm:FluorescentReagent identifier="CD4_TxRed_FluorescentReagent" name="CD4 TxRed Reagent">
      <fcm:_make OntologyTerm_ref="BD-CD4-TxRed_Term" />
      <fcm:_analyteDetector AnalyteDetector_ref="ad_H129.19" />
      <fcm:_reporter Material_ref="TxRed_Reporter_Component" />
      <fcm:_catalogNumber DataProperty_ref="catalogNumber_553648" />
      <fcm:_measuredCharacteristics OntologyTerm_ref="T_helper_OntologyTerm" />
    </fcm:FluorescentReagent>
    <fcm:AnalyteDetector identifier="ad_H129.19">
      <fuge:_characteristics OntologyTerm_ref="anti-CD4-OntologyTerm" />
      <fcm:_analyte Material_ref="CD4" />
      <fcm:_detectorCloneNumber DataProperty_ref="dp_H129.19_CloneNumber" />
    </fcm:AnalyteDetector>
    
    <fcm:FluorescentReagent identifier="CD8_TxRed_FluorescentReagent" name="CD8 TxRed Reagent">
      <fcm:_make OntologyTerm_ref="BD-CD8-TxRed_Term" />
      <fcm:_analyteDetector AnalyteDetector_ref="ad_53-6.7" />
      <fcm:_reporter Material_ref="TxRed_Reporter_Component" />
      <fcm:_catalogNumber DataProperty_ref="catalogNumber_553028" />
      <fcm:_measuredCharacteristics OntologyTerm_ref="T_suppresor_OntologyTerm" />
    </fcm:FluorescentReagent>
    <fcm:AnalyteDetector identifier="ad_53-6.7">
      <fuge:_characteristics OntologyTerm_ref="anti-CD8-OntologyTerm" />
      <fcm:_analyte Material_ref="CD8" />
      <fcm:_detectorCloneNumber DataProperty_ref="dp_53-6.7_CloneNumber" />
    </fcm:AnalyteDetector>
    
    <fcm:FluorescentReagent identifier="CD45R_APC_FluorescentReagent" name="CD45R APC Reagent">
      <fcm:_make OntologyTerm_ref="BD-CD45R-APC_Term" />
      <fcm:_analyteDetector AnalyteDetector_ref="ad_RA3-6B2" />
      <fcm:_reporter Material_ref="APC_Reporter_Component" />
      <fcm:_catalogNumber DataProperty_ref="catalogNumber_553092" />
      <fcm:_measuredCharacteristics OntologyTerm_ref="B_cells_OntologyTerm" />
    </fcm:FluorescentReagent>
    <fcm:AnalyteDetector identifier="ad_RA3-6B2">
      <fuge:_characteristics OntologyTerm_ref="anti-CD45R-OntologyTerm" />
      <fcm:_analyte Material_ref="CD45R" />
      <fcm:_detectorCloneNumber DataProperty_ref="dp_RA3-6B2_CloneNumber" />
    </fcm:AnalyteDetector>
    
    <fcm:FluorescentReagent identifier="Gr1_PE_FluorescentReagent" name="Gr1 PE Reagent">
      <fcm:_make OntologyTerm_ref="BD-Gr1-PE_Term" />
      <fcm:_analyteDetector AnalyteDetector_ref="ad_1A8" />
      <fcm:_reporter Material_ref="PE_Reporter_Component" />
      <fcm:_catalogNumber DataProperty_ref="catalogNumber_551461" />
      <fcm:_measuredCharacteristics OntologyTerm_ref="Granulocytes_OntologyTerm" />
    </fcm:FluorescentReagent>
    <fcm:AnalyteDetector identifier="ad_1A8">
      <fuge:_characteristics OntologyTerm_ref="anti-Gr1-OntologyTerm" />
      <fcm:_analyte Material_ref="Gr1" />
      <fcm:_detectorCloneNumber DataProperty_ref="dp_1A8_CloneNumber" />
    </fcm:AnalyteDetector>
    
    <fcm:FluorescentReagent identifier="CD11b_PE_FluorescentReagent" name="CD11b PE Reagent">
      <fcm:_make OntologyTerm_ref="BD-CD11b-PE_Term" />
      <fcm:_analyteDetector AnalyteDetector_ref="ad_M1-70" />
      <fcm:_reporter Material_ref="PE_Reporter_Component" />
      <fcm:_catalogNumber DataProperty_ref="catalogNumber_557397" />
      <fcm:_measuredCharacteristics OntologyTerm_ref="Monocytes_OntologyTerm" />
    </fcm:FluorescentReagent>
    <fcm:AnalyteDetector identifier="ad_M1-70">
      <fuge:_characteristics OntologyTerm_ref="anti-CD11b-OntologyTerm" />
      <fcm:_analyte Material_ref="CD11b" />
      <fcm:_detectorCloneNumber DataProperty_ref="dp_M1-70_CloneNumber" />
    </fcm:AnalyteDetector>
    
    <fcm:FluorescentReagent identifier="CD45.1_FITC_FluorescentReagent" name="CD45.1 FITC Reagent">
      <fcm:_make OntologyTerm_ref="BD-CD45.1-FITC_Term" />
      <fcm:_analyteDetector AnalyteDetector_ref="ad_A20" />
      <fcm:_reporter Material_ref="FITC_Reporter_Component" />
      <fcm:_catalogNumber DataProperty_ref="catalogNumber_553775" />
      <fcm:_measuredCharacteristics OntologyTerm_ref="Donor_leukocytes_OntologyTerm" />
    </fcm:FluorescentReagent>
    <fcm:AnalyteDetector identifier="ad_A20">
      <fuge:_characteristics OntologyTerm_ref="anti-CD45.1-OntologyTerm" />
      <fcm:_analyte Material_ref="CD45.1" />
      <fcm:_detectorCloneNumber DataProperty_ref="dp_A20_CloneNumber" />
    </fcm:AnalyteDetector>
    
    <fcm:FluorescentReagent identifier="CD45.2_PerCP_FluorescentReagent" name="CD45.2 PerCP Reagent">
      <fcm:_make OntologyTerm_ref="BD-CD45.2-PerCP_Term" />
      <fcm:_analyteDetector AnalyteDetector_ref="ad_104" />
      <fcm:_reporter Material_ref="PerCP_Reporter_Component" />
      <fcm:_catalogNumber DataProperty_ref="catalogNumber_552950" />
      <fcm:_measuredCharacteristics OntologyTerm_ref="Recipient_leukocytes_OntologyTerm" />
    </fcm:FluorescentReagent>
    <fcm:AnalyteDetector identifier="ad_104">
      <fuge:_characteristics OntologyTerm_ref="anti-CD45.2-OntologyTerm" />
      <fcm:_analyte Material_ref="CD45.2" />
      <fcm:_detectorCloneNumber DataProperty_ref="dp_104_CloneNumber" />
    </fcm:AnalyteDetector>
    
    <fcm:FluorescentReagent identifier="DAPI_FluorescentReagent" name="DAPI Reagent">
      <fcm:_make OntologyTerm_ref="Exalpha-DAPI_Term" />
      <fcm:_analyteDetector AnalyteDetector_ref="ad_DAPI" />
      <fcm:_reporter Material_ref="DAPI_Reporter_Component" />
      <fcm:_catalogNumber DataProperty_ref="catalogNumber_7034" />
      <fcm:_measuredCharacteristics OntologyTerm_ref="Cell_viability_OntologyTerm" />
    </fcm:FluorescentReagent>
    <fcm:AnalyteDetector identifier="ad_DAPI">
      <fuge:_characteristics OntologyTerm_ref="DAPI_OntologyTerm" />
      <fcm:_analyte Material_ref="DNA_of_Membrane-compromised_Cells" />
    </fcm:AnalyteDetector>
    
    <!-- 4 Donor mice -->
    <fcm:Organism identifier="Doner_Mouse_1">
      <fuge:_descriptions>
        <fuge:Description text="Animal located at the Animal Resource Centre (ARC) 
          of the BC Cancer Research Centre (BCCRC)" />
      </fuge:_descriptions>
      <fcm:_phenotype Phenotype_ref="black_Pep3b_mouse_phenotype" />
      <fcm:_genotype Genotype_ref="Ly-5_Congenic_C57BL-6_mouse_genotype" />
      <fcm:_gender OntologyTerm_ref="male_OntologyTerm" />
      <fcm:_taxnomyNCBI OntologyTerm_ref="MusMusculus_C57BL-6J_Pep3b" />
      <fcm:_age DataProperty_ref="6_months_data_property" />
    </fcm:Organism>
    
    <fcm:Organism identifier="Doner_Mouse_2">
      <fuge:_descriptions>
        <fuge:Description text="Animal located at the Animal Resource Centre (ARC) 
          of the BC Cancer Research Centre (BCCRC)" />
      </fuge:_descriptions>
      <fcm:_phenotype Phenotype_ref="black_Pep3b_mouse_phenotype" />
      <fcm:_genotype Genotype_ref="Ly-5_Congenic_C57BL-6_mouse_genotype" />
      <fcm:_gender OntologyTerm_ref="male_OntologyTerm" />
      <fcm:_taxnomyNCBI OntologyTerm_ref="MusMusculus_C57BL-6J_Pep3b" />
      <fcm:_age DataProperty_ref="6_months_data_property" />
    </fcm:Organism>
    
    <fcm:Organism identifier="Doner_Mouse_3">
      <fuge:_descriptions>
        <fuge:Description text="Animal located at the Animal Resource Centre (ARC) 
          of the BC Cancer Research Centre (BCCRC)" />
      </fuge:_descriptions>
      <fcm:_phenotype Phenotype_ref="black_Pep3b_mouse_phenotype" />
      <fcm:_genotype Genotype_ref="Ly-5_Congenic_C57BL-6_mouse_genotype" />
      <fcm:_gender OntologyTerm_ref="male_OntologyTerm" />
      <fcm:_taxnomyNCBI OntologyTerm_ref="MusMusculus_C57BL-6J_Pep3b" />
      <fcm:_age DataProperty_ref="6_months_data_property" />
    </fcm:Organism>
    
    <fcm:Organism identifier="Doner_Mouse_4">
      <fuge:_descriptions>
        <fuge:Description text="Animal located at the Animal Resource Centre (ARC) 
          of the BC Cancer Research Centre (BCCRC)" />
      </fuge:_descriptions>
      <fcm:_phenotype Phenotype_ref="black_Pep3b_mouse_phenotype" />
      <fcm:_genotype Genotype_ref="Ly-5_Congenic_C57BL-6_mouse_genotype" />
      <fcm:_gender OntologyTerm_ref="male_OntologyTerm" />
      <fcm:_taxnomyNCBI OntologyTerm_ref="MusMusculus_C57BL-6J_Pep3b" />
      <fcm:_age DataProperty_ref="6_months_data_property" />
    </fcm:Organism>
    
    <!-- 12 Recipient Mice -->
    <fcm:Organism identifier="Recipient_Mouse_1">
      <fuge:_descriptions>
        <fuge:Description text="Animal located at the Animal Resource Centre (ARC) 
          of the BC Cancer Research Centre (BCCRC)" />
      </fuge:_descriptions>
      <fcm:_phenotype Phenotype_ref="White_W41_W41_mouse_phenotype" />
      <fcm:_genotype Genotype_ref="C57BL/6J_W41/W41_mouse_genotype" />
      <fcm:_gender OntologyTerm_ref="male_OntologyTerm" />
      <fcm:_taxnomyNCBI OntologyTerm_ref="MusMusculus_C57BL-6J_Pep3b" />
      <fcm:_age DataProperty_ref="6_months_data_property" />
    </fcm:Organism>
    
    <fcm:Organism identifier="Recipient_Mouse_2">
      <fuge:_descriptions>
        <fuge:Description text="Animal located at the Animal Resource Centre (ARC) 
          of the BC Cancer Research Centre (BCCRC)" />
      </fuge:_descriptions>
      <fcm:_phenotype Phenotype_ref="White_W41_W41_mouse_phenotype" />
      <fcm:_genotype Genotype_ref="C57BL/6J_W41/W41_mouse_genotype" />
      <fcm:_gender OntologyTerm_ref="male_OntologyTerm" />
      <fcm:_taxnomyNCBI OntologyTerm_ref="MusMusculus_C57BL-6J_Pep3b" />
      <fcm:_age DataProperty_ref="6_months_data_property" />
    </fcm:Organism>
    
    <fcm:Organism identifier="Recipient_Mouse_3">
      <fuge:_descriptions>
        <fuge:Description text="Animal located at the Animal Resource Centre (ARC) 
          of the BC Cancer Research Centre (BCCRC)" />
      </fuge:_descriptions>
      <fcm:_phenotype Phenotype_ref="White_W41_W41_mouse_phenotype" />
      <fcm:_genotype Genotype_ref="C57BL/6J_W41/W41_mouse_genotype" />
      <fcm:_gender OntologyTerm_ref="male_OntologyTerm" />
      <fcm:_taxnomyNCBI OntologyTerm_ref="MusMusculus_C57BL-6J_Pep3b" />
      <fcm:_age DataProperty_ref="6_months_data_property" />
    </fcm:Organism>
    
    <fcm:Organism identifier="Recipient_Mouse_4">
      <fuge:_descriptions>
        <fuge:Description text="Animal located at the Animal Resource Centre (ARC) 
          of the BC Cancer Research Centre (BCCRC)" />
      </fuge:_descriptions>
      <fcm:_phenotype Phenotype_ref="White_W41_W41_mouse_phenotype" />
      <fcm:_genotype Genotype_ref="C57BL/6J_W41/W41_mouse_genotype" />
      <fcm:_gender OntologyTerm_ref="male_OntologyTerm" />
      <fcm:_taxnomyNCBI OntologyTerm_ref="MusMusculus_C57BL-6J_Pep3b" />
      <fcm:_age DataProperty_ref="6_months_data_property" />
    </fcm:Organism>
    
    <fcm:Organism identifier="Recipient_Mouse_5">
      <fuge:_descriptions>
        <fuge:Description text="Animal located at the Animal Resource Centre (ARC) 
          of the BC Cancer Research Centre (BCCRC)" />
      </fuge:_descriptions>
      <fcm:_phenotype Phenotype_ref="White_W41_W41_mouse_phenotype" />
      <fcm:_genotype Genotype_ref="C57BL/6J_W41/W41_mouse_genotype" />
      <fcm:_gender OntologyTerm_ref="male_OntologyTerm" />
      <fcm:_taxnomyNCBI OntologyTerm_ref="MusMusculus_C57BL-6J_Pep3b" />
      <fcm:_age DataProperty_ref="6_months_data_property" />
    </fcm:Organism>
    
    <fcm:Organism identifier="Recipient_Mouse_6">
      <fuge:_descriptions>
        <fuge:Description text="Animal located at the Animal Resource Centre (ARC) 
          of the BC Cancer Research Centre (BCCRC)" />
      </fuge:_descriptions>
      <fcm:_phenotype Phenotype_ref="White_W41_W41_mouse_phenotype" />
      <fcm:_genotype Genotype_ref="C57BL/6J_W41/W41_mouse_genotype" />
      <fcm:_gender OntologyTerm_ref="male_OntologyTerm" />
      <fcm:_taxnomyNCBI OntologyTerm_ref="MusMusculus_C57BL-6J_Pep3b" />
      <fcm:_age DataProperty_ref="6_months_data_property" />
    </fcm:Organism>
    
    <fcm:Organism identifier="Recipient_Mouse_7">
      <fuge:_descriptions>
        <fuge:Description text="Animal located at the Animal Resource Centre (ARC) 
          of the BC Cancer Research Centre (BCCRC)" />
      </fuge:_descriptions>
      <fcm:_phenotype Phenotype_ref="White_W41_W41_mouse_phenotype" />
      <fcm:_genotype Genotype_ref="C57BL/6J_W41/W41_mouse_genotype" />
      <fcm:_gender OntologyTerm_ref="male_OntologyTerm" />
      <fcm:_taxnomyNCBI OntologyTerm_ref="MusMusculus_C57BL-6J_Pep3b" />
      <fcm:_age DataProperty_ref="6_months_data_property" />
    </fcm:Organism>
    
    <fcm:Organism identifier="Recipient_Mouse_8">
      <fuge:_descriptions>
        <fuge:Description text="Animal located at the Animal Resource Centre (ARC) 
          of the BC Cancer Research Centre (BCCRC)" />
      </fuge:_descriptions>
      <fcm:_phenotype Phenotype_ref="White_W41_W41_mouse_phenotype" />
      <fcm:_genotype Genotype_ref="C57BL/6J_W41/W41_mouse_genotype" />
      <fcm:_gender OntologyTerm_ref="male_OntologyTerm" />
      <fcm:_taxnomyNCBI OntologyTerm_ref="MusMusculus_C57BL-6J_Pep3b" />
      <fcm:_age DataProperty_ref="6_months_data_property" />
    </fcm:Organism>
    
    <fcm:Organism identifier="Recipient_Mouse_9">
      <fuge:_descriptions>
        <fuge:Description text="Animal located at the Animal Resource Centre (ARC) 
          of the BC Cancer Research Centre (BCCRC)" />
      </fuge:_descriptions>
      <fcm:_phenotype Phenotype_ref="White_W41_W41_mouse_phenotype" />
      <fcm:_genotype Genotype_ref="C57BL/6J_W41/W41_mouse_genotype" />
      <fcm:_gender OntologyTerm_ref="male_OntologyTerm" />
      <fcm:_taxnomyNCBI OntologyTerm_ref="MusMusculus_C57BL-6J_Pep3b" />
      <fcm:_age DataProperty_ref="6_months_data_property" />
    </fcm:Organism>
    
    <fcm:Organism identifier="Recipient_Mouse_10">
      <fuge:_descriptions>
        <fuge:Description text="Animal located at the Animal Resource Centre (ARC) 
          of the BC Cancer Research Centre (BCCRC)" />
      </fuge:_descriptions>
      <fcm:_phenotype Phenotype_ref="White_W41_W41_mouse_phenotype" />
      <fcm:_genotype Genotype_ref="C57BL/6J_W41/W41_mouse_genotype" />
      <fcm:_gender OntologyTerm_ref="male_OntologyTerm" />
      <fcm:_taxnomyNCBI OntologyTerm_ref="MusMusculus_C57BL-6J_Pep3b" />
      <fcm:_age DataProperty_ref="6_months_data_property" />
    </fcm:Organism>
    
    <fcm:Organism identifier="Recipient_Mouse_11">
      <fuge:_descriptions>
        <fuge:Description text="Animal located at the Animal Resource Centre (ARC) 
          of the BC Cancer Research Centre (BCCRC)" />
      </fuge:_descriptions>
      <fcm:_phenotype Phenotype_ref="White_W41_W41_mouse_phenotype" />
      <fcm:_genotype Genotype_ref="C57BL/6J_W41/W41_mouse_genotype" />
      <fcm:_gender OntologyTerm_ref="male_OntologyTerm" />
      <fcm:_taxnomyNCBI OntologyTerm_ref="MusMusculus_C57BL-6J_Pep3b" />
      <fcm:_age DataProperty_ref="6_months_data_property" />
    </fcm:Organism>
    
    <fcm:Organism identifier="Recipient_Mouse_12">
      <fuge:_descriptions>
        <fuge:Description text="Animal located at the Animal Resource Centre (ARC) 
          of the BC Cancer Research Centre (BCCRC)" />
      </fuge:_descriptions>
      <fcm:_phenotype Phenotype_ref="White_W41_W41_mouse_phenotype" />
      <fcm:_genotype Genotype_ref="C57BL/6J_W41/W41_mouse_genotype" />
      <fcm:_gender OntologyTerm_ref="male_OntologyTerm" />
      <fcm:_taxnomyNCBI OntologyTerm_ref="MusMusculus_C57BL-6J_Pep3b" />
      <fcm:_age DataProperty_ref="6_months_data_property" />
    </fcm:Organism>
    
    <!-- 12 Equally stained samples -->
    <fcm:Sample name="Sample 1" identifier="Sample_1">
      <fcm:_subType OntologyTerm_ref="Biological_Sample_OntologyTerm"/>
      <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_1" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD4_TxRed_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD8_TxRed_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45R_APC_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="Gr1_PE_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD11b_PE_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45.1_FITC_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45.2_PerCP_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="DAPI_FluorescentReagent" />
      <fcm:_otherInfo OntologyTerm_ref="SampleCharacteristicDescription_OntologyTerm" />
    </fcm:Sample>
    
    <fcm:Sample name="Sample 2" identifier="Sample_2">
      <fcm:_subType OntologyTerm_ref="Biological_Sample_OntologyTerm"/>
      <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_2" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD4_TxRed_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD8_TxRed_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45R_APC_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="Gr1_PE_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD11b_PE_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45.1_FITC_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45.2_PerCP_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="DAPI_FluorescentReagent" />
      <fcm:_otherInfo OntologyTerm_ref="SampleCharacteristicDescription_OntologyTerm" />
    </fcm:Sample>
    
    <fcm:Sample name="Sample 3" identifier="Sample_3">
      <fcm:_subType OntologyTerm_ref="Biological_Sample_OntologyTerm"/>
      <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_3" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD4_TxRed_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD8_TxRed_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45R_APC_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="Gr1_PE_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD11b_PE_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45.1_FITC_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45.2_PerCP_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="DAPI_FluorescentReagent" />
      <fcm:_otherInfo OntologyTerm_ref="SampleCharacteristicDescription_OntologyTerm" />
    </fcm:Sample>
    
    <fcm:Sample name="Sample 4" identifier="Sample_4">
      <fcm:_subType OntologyTerm_ref="Biological_Sample_OntologyTerm"/>
      <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_4" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD4_TxRed_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD8_TxRed_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45R_APC_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="Gr1_PE_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD11b_PE_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45.1_FITC_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45.2_PerCP_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="DAPI_FluorescentReagent" />
      <fcm:_otherInfo OntologyTerm_ref="SampleCharacteristicDescription_OntologyTerm" />
    </fcm:Sample>
    
    <fcm:Sample name="Sample 5" identifier="Sample_5">
      <fcm:_subType OntologyTerm_ref="Biological_Sample_OntologyTerm"/>
      <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_5" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD4_TxRed_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD8_TxRed_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45R_APC_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="Gr1_PE_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD11b_PE_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45.1_FITC_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45.2_PerCP_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="DAPI_FluorescentReagent" />
      <fcm:_otherInfo OntologyTerm_ref="SampleCharacteristicDescription_OntologyTerm" />
    </fcm:Sample>
    
    <fcm:Sample name="Sample 6" identifier="Sample_6">
      <fcm:_subType OntologyTerm_ref="Biological_Sample_OntologyTerm"/>
      <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_6" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD4_TxRed_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD8_TxRed_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45R_APC_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="Gr1_PE_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD11b_PE_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45.1_FITC_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45.2_PerCP_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="DAPI_FluorescentReagent" />
      <fcm:_otherInfo OntologyTerm_ref="SampleCharacteristicDescription_OntologyTerm" />
    </fcm:Sample>
    
    <fcm:Sample name="Sample 7" identifier="Sample_7">
      <fcm:_subType OntologyTerm_ref="Biological_Sample_OntologyTerm"/>
      <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_7" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD4_TxRed_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD8_TxRed_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45R_APC_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="Gr1_PE_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD11b_PE_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45.1_FITC_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45.2_PerCP_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="DAPI_FluorescentReagent" />
      <fcm:_otherInfo OntologyTerm_ref="SampleCharacteristicDescription_OntologyTerm" />
    </fcm:Sample>
    
    <fcm:Sample name="Sample 8" identifier="Sample_8">
      <fcm:_subType OntologyTerm_ref="Biological_Sample_OntologyTerm"/>
      <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_8" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD4_TxRed_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD8_TxRed_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45R_APC_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="Gr1_PE_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD11b_PE_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45.1_FITC_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45.2_PerCP_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="DAPI_FluorescentReagent" />
      <fcm:_otherInfo OntologyTerm_ref="SampleCharacteristicDescription_OntologyTerm" />
    </fcm:Sample>
    
    <fcm:Sample name="Sample 9" identifier="Sample_9">
      <fcm:_subType OntologyTerm_ref="Biological_Sample_OntologyTerm"/>
      <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_9" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD4_TxRed_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD8_TxRed_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45R_APC_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="Gr1_PE_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD11b_PE_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45.1_FITC_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45.2_PerCP_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="DAPI_FluorescentReagent" />
      <fcm:_otherInfo OntologyTerm_ref="SampleCharacteristicDescription_OntologyTerm" />
    </fcm:Sample>
    
    <fcm:Sample name="Sample 10" identifier="Sample_10">
      <fcm:_subType OntologyTerm_ref="Biological_Sample_OntologyTerm"/>
      <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_10" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD4_TxRed_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD8_TxRed_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45R_APC_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="Gr1_PE_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD11b_PE_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45.1_FITC_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45.2_PerCP_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="DAPI_FluorescentReagent" />
      <fcm:_otherInfo OntologyTerm_ref="SampleCharacteristicDescription_OntologyTerm" />
    </fcm:Sample>
    
    <fcm:Sample name="Sample 11" identifier="Sample_11">
      <fcm:_subType OntologyTerm_ref="Biological_Sample_OntologyTerm"/>
      <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_11" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD4_TxRed_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD8_TxRed_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45R_APC_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="Gr1_PE_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD11b_PE_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45.1_FITC_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45.2_PerCP_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="DAPI_FluorescentReagent" />
      <fcm:_otherInfo OntologyTerm_ref="SampleCharacteristicDescription_OntologyTerm" />
    </fcm:Sample>
    
    <fcm:Sample name="Sample 12" identifier="Sample_12">
      <fcm:_subType OntologyTerm_ref="Biological_Sample_OntologyTerm"/>
      <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_12" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD4_TxRed_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD8_TxRed_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45R_APC_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="Gr1_PE_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD11b_PE_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45.1_FITC_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="CD45.2_PerCP_FluorescentReagent" />
      <fcm:_stainingReagent FluorescentReagent_ref="DAPI_FluorescentReagent" />
      <fcm:_otherInfo OntologyTerm_ref="SampleCharacteristicDescription_OntologyTerm" />
    </fcm:Sample>
    
    <!-- HSC from doners (to be transplanted to a recipient) -->
    <fuge:GenericMaterial identifier="HSC_from_donor_1">
      <fuge:_characteristics OntologyTerm_ref="HSC_OntologyTerm" />
    </fuge:GenericMaterial>
    <fuge:GenericMaterial identifier="HSC_from_donor_2">
      <fuge:_characteristics OntologyTerm_ref="HSC_OntologyTerm" />
    </fuge:GenericMaterial>
    <fuge:GenericMaterial identifier="HSC_from_donor_3">
      <fuge:_characteristics OntologyTerm_ref="HSC_OntologyTerm" />
    </fuge:GenericMaterial>
    <fuge:GenericMaterial identifier="KSL_HSC_from_donor_4">
      <fuge:_characteristics OntologyTerm_ref="KSL_HSC_OntologyTerm" />
    </fuge:GenericMaterial>
    
    <!-- Staining components / Analyte reporters -->
    <fuge:GenericMaterial name="TxRed" identifier="TxRed_Reporter_Component">
      <fuge:_characteristics OntologyTerm_ref="TexasRed_OntologyTerm" />
    </fuge:GenericMaterial>
    <fuge:GenericMaterial name="APC" identifier="APC_Reporter_Component">
      <fuge:_characteristics OntologyTerm_ref="APC_OntologyTerm" />
    </fuge:GenericMaterial>
    <fuge:GenericMaterial name="PE" identifier="PE_Reporter_Component">
      <fuge:_characteristics OntologyTerm_ref="PE_OntologyTerm" />
    </fuge:GenericMaterial>
    <fuge:GenericMaterial name="FITC" identifier="FITC_Reporter_Component">
      <fuge:_characteristics OntologyTerm_ref="FITC_OntologyTerm" />
    </fuge:GenericMaterial>
    <fuge:GenericMaterial name="PerCP" identifier="PerCP_Reporter_Component">
      <fuge:_characteristics OntologyTerm_ref="PerCP_OntologyTerm" />
    </fuge:GenericMaterial>
    <fuge:GenericMaterial name="DAPI" identifier="DAPI_Reporter_Component">
      <fuge:_characteristics OntologyTerm_ref="DAPI_OntologyTerm" />
    </fuge:GenericMaterial>
    
    <!-- Analytes -->
    <fuge:GenericMaterial identifier="CD4">
      <fuge:_characteristics OntologyTerm_ref="CD4-OntologyTerm" />
    </fuge:GenericMaterial>
    <fuge:GenericMaterial identifier="CD8">
      <fuge:_characteristics OntologyTerm_ref="CD8-OntologyTerm" />
    </fuge:GenericMaterial>
    <fuge:GenericMaterial identifier="CD45R">
      <fuge:_characteristics OntologyTerm_ref="CD45R-OntologyTerm" />
    </fuge:GenericMaterial>
    <fuge:GenericMaterial identifier="Gr1">
      <fuge:_characteristics OntologyTerm_ref="Gr1-OntologyTerm" />
    </fuge:GenericMaterial>
    <fuge:GenericMaterial identifier="CD11b">
      <fuge:_characteristics OntologyTerm_ref="CD11b-OntologyTerm" />
    </fuge:GenericMaterial>
    <fuge:GenericMaterial identifier="CD45.1">
      <fuge:_characteristics OntologyTerm_ref="CD45.1-OntologyTerm" />
    </fuge:GenericMaterial>
    <fuge:GenericMaterial identifier="CD45.2">
      <fuge:_characteristics OntologyTerm_ref="CD45.2-OntologyTerm" />
    </fuge:GenericMaterial>
    <fuge:GenericMaterial identifier="CD45.2">
      <fuge:_characteristics OntologyTerm_ref="CD45.2-OntologyTerm" />
    </fuge:GenericMaterial>
    <fuge:GenericMaterial identifier="DNA_of_Membrane-compromised_Cells">
      <fuge:_characteristics OntologyTerm_ref="DNA_of_Membrane-compromised_Cells-OntologyTerm" />
    </fuge:GenericMaterial>
    
  </fuge:MaterialCollection>
  

  <!-- 
    ********************************* 
    References
    *********************************
  -->
  <fuge:ReferenceableCollection>
    <fuge:BibliographicReference identifier="bibRef_1_Szilvassy_1990" 
      name="Szilvassy et al., 1990"
      authors="Szilvassy, S.J.; Humphries, R.K.; Lansdorp, P.M.; Eaves, A.C.; Eaves, C.J."
      title="Quantitative Assay for Totipotent Reconstituting Hematopoietic Stem Cells by a Competitive Repopulation Strategy"
      publication="Proceedings of the National Academy of Sciences"
      year="1990" volume="87" pages="8736-8740" />
  </fuge:ReferenceableCollection>


  <!-- 
    ********************************* 
    Investigations and its components
    *********************************
  -->
  <fuge:InvestigationCollection>
    
    <!-- A single investigation having multiple components (a component # of transplanted cells) -->
    <fuge:Investigation 
      identifier="DonHSCC2LMC 2006-07-28 MGCS" 
      start="2006-07-08T00:00:00" end="2006-11-30T00:00:00" 
      name="Donor hematopoietic stem cells contribution to lymphocytes and myeloid cells">
      
      <fuge:_descriptions>
        <fuge:Description 
          text="The Competitive Repopulation Assay is used for the experiment. It is a quantitative 
          assay for long-term repopulating stem cells with the potential for reconstituting all 
          hematopoietic lineages. This assay has two key features. The first is the use of competitive 
          repopulation conditions that ensure not only the detection of a very primitive class of 
          hematopoietic stem cells but also the survival of lethally irradiated mice transplanted with 
          very low numbers of such cells. The second is the use of a limiting-dilution experimental 
          design to allow stem cell quantitation." />
      </fuge:_descriptions>
      
      <fuge:_bibliographicReferences BibliographicReference_ref="bibRef_1_Szilvassy_1990" />
      
      <!-- Investigation components based on the number of transplanted HSC cells -->
      <fuge:InvestigationComponent identifier="IC_5HSC">
        <fuge:_factors Factor_ref="fact_5HSC" />
        <fuge:_factors Factor_ref="fact_0KSLHSC" />
        <fuge:_qualityControlDescription>
          <fuge:Description text="This investigation component is a negative control." />
        </fuge:_qualityControlDescription>
        <fuge:_allProtocolApplications ProtocolApplication_ref="Collect_cells_from_doner_1" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Collect_cells_from_doner_2" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Collect_cells_from_doner_3" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Inject_cells_into_recipient_1" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Inject_cells_into_recipient_4" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Inject_cells_into_recipient_7" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Create_Sample_1" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Create_Sample_4" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Create_Sample_7" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Create_data01.fcs" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Create_data04.fcs" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Create_data07.fcs" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Compensate_and_gate_data01.fsc" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Compensate_and_gate_data04.fsc" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Compensate_and_gate_data07.fsc" />
      </fuge:InvestigationComponent>
      
      <fuge:InvestigationComponent identifier="IC_20HSC">
        <fuge:_factors Factor_ref="fact_20HSC" />
        <fuge:_factors Factor_ref="fact_0KSLHSC" />
        <fuge:_qualityControlDescription>
          <fuge:Description text="This investigation component is a negative control." />
        </fuge:_qualityControlDescription>
        <fuge:_allProtocolApplications ProtocolApplication_ref="Collect_cells_from_doner_1" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Collect_cells_from_doner_2" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Collect_cells_from_doner_3" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Inject_cells_into_recipient_2" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Inject_cells_into_recipient_5" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Inject_cells_into_recipient_8" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Create_Sample_2" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Create_Sample_5" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Create_Sample_8" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Create_data02.fcs" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Create_data05.fcs" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Create_data08.fcs" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Compensate_and_gate_data02.fsc" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Compensate_and_gate_data05.fsc" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Compensate_and_gate_data08.fsc" />
      </fuge:InvestigationComponent>
      
      <fuge:InvestigationComponent identifier="IC_100HSC">
        <fuge:_factors Factor_ref="fact_100HSC" />
        <fuge:_factors Factor_ref="fact_0KSLHSC" />
        <fuge:_qualityControlDescription>
          <fuge:Description 
            text="PB has been collected from positive as well as negative mice in order to provide a 
            staining control. Mice from the 500 KSL group were consider as the positive controls; mice 
            that are not reconstituted as the negative controls." />
        </fuge:_qualityControlDescription>
        <fuge:_allProtocolApplications ProtocolApplication_ref="Collect_cells_from_doner_1" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Collect_cells_from_doner_2" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Collect_cells_from_doner_3" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Inject_cells_into_recipient_3" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Inject_cells_into_recipient_6" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Inject_cells_into_recipient_9" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Create_Sample_3" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Create_Sample_6" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Create_Sample_9" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Create_data03.fcs" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Create_data06.fcs" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Create_data09.fcs" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Compensate_and_gate_data03.fsc" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Compensate_and_gate_data06.fsc" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Compensate_and_gate_data09.fsc" />
      </fuge:InvestigationComponent>
      
      <fuge:InvestigationComponent identifier="IC_500KSLHSC">
        <fuge:_factors Factor_ref="fact_0HSC" />
        <fuge:_factors Factor_ref="fact_500KSLHSC" />
        <fuge:_qualityControlDescription>
          <fuge:Description text="This investigation component is a positive control." />
        </fuge:_qualityControlDescription>
        <fuge:_allProtocolApplications ProtocolApplication_ref="Collect_cells_from_doner_4" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Inject_cells_into_recipient_10" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Inject_cells_into_recipient_11" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Inject_cells_into_recipient_12" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Create_Sample_10" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Create_Sample_11" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Create_Sample_12" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Create_data10.fcs" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Create_data11.fcs" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Create_data12.fcs" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Compensate_and_gate_data10.fsc" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Compensate_and_gate_data11.fsc" />
        <fuge:_allProtocolApplications ProtocolApplication_ref="Compensate_and_gate_data12.fsc" />
      </fuge:InvestigationComponent>
      
      <fuge:ContactRole Contact_ref="Clayton_Smith">
        <fuge:_role OntologyTerm_ref="OBI_0000103" />
      </fuge:ContactRole>
      
      <fuge:ContactRole Contact_ref="Maura_Gasparetto">
        <fuge:_role OntologyTerm_ref="OBI_0000357" />
      </fuge:ContactRole>
      
      <fuge:ContactRole Contact_ref="TFL_BCCRC">
        <fuge:_role OntologyTerm_ref="OBI_0000184" />
      </fuge:ContactRole>
      
      <fuge:_sourceMaterials Material_ref="Doner_Mouse_1" />
      <fuge:_sourceMaterials Material_ref="Doner_Mouse_2" />
      <fuge:_sourceMaterials Material_ref="Doner_Mouse_3" />
      <fuge:_sourceMaterials Material_ref="Doner_Mouse_4" />
      <fuge:_sourceMaterials Material_ref="Recipient_Mouse_1" />
      <fuge:_sourceMaterials Material_ref="Recipient_Mouse_2" />
      <fuge:_sourceMaterials Material_ref="Recipient_Mouse_3" />
      <fuge:_sourceMaterials Material_ref="Recipient_Mouse_4" />
      <fuge:_sourceMaterials Material_ref="Recipient_Mouse_5" />
      <fuge:_sourceMaterials Material_ref="Recipient_Mouse_6" />
      <fuge:_sourceMaterials Material_ref="Recipient_Mouse_7" />
      <fuge:_sourceMaterials Material_ref="Recipient_Mouse_8" />
      <fuge:_sourceMaterials Material_ref="Recipient_Mouse_9" />
      <fuge:_sourceMaterials Material_ref="Recipient_Mouse_10" />
      <fuge:_sourceMaterials Material_ref="Recipient_Mouse_11" />
      <fuge:_sourceMaterials Material_ref="Recipient_Mouse_12" />
      <fuge:_sourceMaterials Material_ref="CD4_TxRed_FluorescentReagent" />
      <fuge:_sourceMaterials Material_ref="CD8_TxRed_FluorescentReagent" />
      <fuge:_sourceMaterials Material_ref="CD45R_APC_FluorescentReagent" />
      <fuge:_sourceMaterials Material_ref="Gr1_PE_FluorescentReagent" />
      <fuge:_sourceMaterials Material_ref="CD11b_PE_FluorescentReagent" />
      <fuge:_sourceMaterials Material_ref="CD45.1_FITC_FluorescentReagent" />
      <fuge:_sourceMaterials Material_ref="CD45.2_PerCP_FluorescentReagent" />
      <fuge:_sourceMaterials Material_ref="DAPI_FluorescentReagent" />
      
      <fuge:_hypothesis>
        <fuge:Description 
          text="The purpose of the experiment is to quantify donor hematopoietic stem cells (HSC) contribution 
          to lymphocytes and myeloid cells by flow cytometric analysis of peripheral blood (PB) cells stained 
          with appropriate combinations of donor specific marker and lineage specific antibodies. The hypothesis 
          is that donor HSC contribute significantly to recipient’s lymphocytes and myeloid cells." />
      </fuge:_hypothesis>
      
      <fuge:_conclusion>
        <fuge:Description 
          text="Mice are considered reconstituted (positive) if their PB contains at least one percent of donor derived 
          myeloid and lymphoid cells at 4 months or later post transplantation. In this sense, 1 mouse out of 3 in the 
          5 cell group was considered positive, 1 mouse out of 3 in the 20 cell group was considered positive, all 3 
          mice in the 100 cell group were considered positive and all 3 mice in the 500 cell control group were 
          considered positive. This indicates that higher number of transplanted HSC cells invokes donor derived 
          myeloid and lymphoid cells in the recipient." />
      </fuge:_conclusion>
      
      <fuge:_investigationSummary OntologyTerm_ref="keyword_1_blood" />
      <fuge:_investigationSummary OntologyTerm_ref="keyword_2_transplant" />
      <fuge:_investigationSummary OntologyTerm_ref="keyword_3_donor" />
      <fuge:_investigationSummary OntologyTerm_ref="keyword_4_recipient" />
      <fuge:_investigationSummary OntologyTerm_ref="keyword_5_leukocyte" />
      <fuge:_investigationSummary OntologyTerm_ref="keyword_6_lymphocyte" />
      <fuge:_investigationSummary OntologyTerm_ref="keyword_7_monocyte" />
      <fuge:_investigationSummary OntologyTerm_ref="keyword_8_granulocyte" />
      
    </fuge:Investigation>

    <fuge:Factor identifier="fact_0HSC">
      <fuge:FactorValue>
        <fuge:AtomicValue value="0" />
      </fuge:FactorValue>
      <fuge:_factorType OntologyTerm_ref="injected_donor_HSC_no" />
    </fuge:Factor>
    <fuge:Factor identifier="fact_5HSC">
      <fuge:FactorValue>
        <fuge:AtomicValue value="5" />
      </fuge:FactorValue>
      <fuge:_factorType OntologyTerm_ref="injected_donor_HSC_no" />
    </fuge:Factor>
    <fuge:Factor identifier="fact_20HSC">
      <fuge:FactorValue>
        <fuge:AtomicValue value="20" />
      </fuge:FactorValue>
      <fuge:_factorType OntologyTerm_ref="injected_donor_HSC_no" />
    </fuge:Factor>
    <fuge:Factor identifier="fact_100HSC">
      <fuge:FactorValue>
        <fuge:AtomicValue value="100" />
      </fuge:FactorValue>
      <fuge:_factorType OntologyTerm_ref="injected_donor_HSC_no" />
    </fuge:Factor>
    <fuge:Factor identifier="fact_0KSLHSC">
      <fuge:FactorValue>
        <fuge:AtomicValue value="0" />
      </fuge:FactorValue>
      <fuge:_factorType OntologyTerm_ref="injected_control_HSC_no" />
    </fuge:Factor>
    <fuge:Factor identifier="fact_500KSLHSC">
      <fuge:FactorValue>
        <fuge:AtomicValue value="0" />
      </fuge:FactorValue>
      <fuge:_factorType OntologyTerm_ref="injected_control_HSC_no" />
    </fuge:Factor>
  
  </fuge:InvestigationCollection>
  
  <!-- 
    ********************************* 
    Data
    *********************************
  -->
  <fuge:DataCollection>
    
    <!-- 12 list mode data files (FCS files), one file per recipient-->
    <fcm:ListModeDataFile location="file://data01.fcs" identifier="data01.fcs" name="data01.fcs">
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        <fuge:NameValueType name="Leukocytes" value="58.8" />
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        Leukocytes (FSC-SSC):                       58.8% of the total number of cells
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        <fuge:NameValueType name="Leukocytes" value="57.1" />
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        Leukocytes (FSC-SSC):                       57.1% of the total number of cells
        Viable Leukocytes (FSC-FL8):                94.5% of Leukocytes
        Donor-derived Viable Leukocytes (FL1-FL4):   0.8% of Viable Leukocytes
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        <fuge:NameValueType name="Leukocytes" value="55.6" />
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        Leukocytes (FSC-SSC):                       55.6% of the total number of cells
        Viable Leukocytes (FSC-FL8):                93.1% of Leukocytes
        Donor-derived Viable Leukocytes (FL1-FL4):  43.1% of Viable Leukocytes
        Doner-derived B cells (FL2-FL6):            30.9% of Donor-derived Viable Leukocytes
        Doner-derived T cells (FL3-FL6):            30.4% of Donor-derived Viable Leukocytes
        Doner-derived Myeloid cells (FL2-FL6):      38.8% of Donor-derived Viable Leukocytes
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        <fuge:NameValueType name="Leukocytes" value="54.8" />
        <fuge:NameValueType name="Viable Leukocytes" value="97.2" />
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        Leukocytes (FSC-SSC):                       54.8% of the total number of cells
        Viable Leukocytes (FSC-FL8):                97.2% of Leukocytes
        Donor-derived Viable Leukocytes (FL1-FL4):   0.1% of Viable Leukocytes
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        <fuge:NameValueType name="Leukocytes" value="53.6" />
        <fuge:NameValueType name="Viable Leukocytes" value="92.5" />
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        Leukocytes (FSC-SSC):                       53.6% of the total number of cells
        Viable Leukocytes (FSC-FL8):                92.5% of Leukocytes
        Donor-derived Viable Leukocytes (FL1-FL4):  10.8% of Viable Leukocytes
        Doner-derived B cells (FL2-FL6):            29.0% of Donor-derived Viable Leukocytes
        Doner-derived T cells (FL3-FL6):            31.5% of Donor-derived Viable Leukocytes
        Doner-derived Myeloid cells (FL2-FL6):      39.5% of Donor-derived Viable Leukocytes
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        <fuge:NameValueType name="Sample" value="6" />
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        <fuge:NameValueType name="Leukocytes" value="56.6" />
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        Leukocytes (FSC-SSC):                       56.6% of the total number of cells
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        Leukocytes (FSC-SSC):                       48.8% of the total number of cells
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        Leukocytes (FSC-SSC):                       55.8% of the total number of cells
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        <fuge:NameValueType name="Sample" value="9" />
        <fuge:NameValueType name="Cells" value="100" />
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        <fuge:NameValueType name="Leukocytes" value="48.7" />
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        Leukocytes (FSC-SSC):                       48.7% of the total number of cells
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        Doner-derived T cells (FL3-FL6):            28.0% of Donor-derived Viable Leukocytes
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        <fuge:NameValueType name="Leukocytes" value="55.8" />
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        Leukocytes (FSC-SSC):                       55.8% of the total number of cells
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        Doner-derived T cells (FL3-FL6):            32.1% of Donor-derived Viable Leukocytes
        Doner-derived Myeloid cells (FL2-FL6):      66.8% of Donor-derived Viable Leukocytes
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        <fuge:NameValueType name="Leukocytes" value="56.8" />
        <fuge:NameValueType name="Viable Leukocytes" value="93.7" />
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        Leukocytes (FSC-SSC):                       56.8% of the total number of cells
        Viable Leukocytes (FSC-FL8):                93.7% of Leukocytes
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        Doner-derived B cells (FL2-FL6):            32.5% of Donor-derived Viable Leukocytes
        Doner-derived T cells (FL3-FL6):            32.0% of Donor-derived Viable Leukocytes
        Doner-derived Myeloid cells (FL2-FL6):      66.5% of Donor-derived Viable Leukocytes
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    <fuge:GenericInternalData identifier="Results_for_Sample_12">
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        <fuge:NameValueType name="Sample" value="12" />
        <fuge:NameValueType name="Cells" value="500" />
        <fuge:NameValueType name="Doner" value="4" />
        <fuge:NameValueType name="Result" value="Positive" />
        
        <fuge:NameValueType name="Leukocytes" value="52.9" />
        <fuge:NameValueType name="Viable Leukocytes" value="91.7" />
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        <fuge:NameValueType name="Doner-derived B-cells" value="30.1" />
        <fuge:NameValueType name="Doner-derived T-cells" value="31.3" />
        <fuge:NameValueType name="Doner-derived Myeloid cells" value="68.6" />
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        Leukocytes (FSC-SSC):                       52.9% of the total number of cells
        Viable Leukocytes (FSC-FL8):                91.7% of Leukocytes
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        Doner-derived B cells (FL2-FL6):            30.1% of Donor-derived Viable Leukocytes
        Doner-derived T cells (FL3-FL6):            31.3% of Donor-derived Viable Leukocytes
        Doner-derived Myeloid cells (FL2-FL6):      68.6% of Donor-derived Viable Leukocytes
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  </fuge:DataCollection>
  
  <!-- 
    ********************************* 
    Contact Details
    *********************************
  -->
  <fuge:AuditCollection>
    <fuge:Person identifier="Clayton_Smith"
      name="Clayton Smith" address="BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada"
      email="clsmith@bccancer.bc.ca" phone="+1-813-903-6870" fax="+1-604-877-0712" 
      lastName="Smith" firstName="Clayton" midInitials="A" />
    <fuge:Person identifier="Maura_Gasparetto"
      name="Maura Gasparetto" address="Terry Fox Laboratory, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada"
      email="mgaspare@bccrc.ca" lastName="Gasparetto" firstName="Maura" />
    <fuge:Organization identifier="TFL_BCCRC"
      name="Terry Fox Laboratory, BC Cancer Research Centre" address="675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada" />
  </fuge:AuditCollection>
  
  <!-- 
    ********************************* 
    Protocols
    *********************************
  -->
  <fuge:ProtocolCollection>
    
    <!-- Protocols for collection and injection of donor HSC -->
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    <fuge:GenericProtocol identifier="Inject_Cells_Protocol" protocolText="Inject cells into recipient mouse" >
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    <!-- Staining and treatment protocol -->
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        FcGamaI/III (Mouse BD FcBlock™, CD16/CD32, catalogue no. 553141 and 553142) have been used to block nonspecific 
        staining due to FcR. To block FcR with BD FcBlock reagents, the cells are preincubated with 10 µg/ml of BD FcBlock 
        antibody per 2x107 cells for 15–20 min at 4°C. The cells are not washed before the first staining step." />
      <fuge:GenericAction identifier="Staining_Action" actionOrdinal="3"
        actionText="Cells have been incubated for 40 minutes at 4°C in a staining buffer (approx. 106 cells in 100µl of 
        staining buffer). The staining buffer contained a pre-titrated, optimal concentration (≤ 1µg) of a fluorescent 
        monoclonal antibody specific for a receptor or with an immunoglobulin (Ig) isotype-matched control respectively." />
      <fuge:GenericAction identifier="Washing_Action" actionOrdinal="4"
        actionText="After the incubation, cells have been washed 1x with 2ml of staining buffer and pelleted by 
        centrifugation (250 X g for 5 min); supernatant has been removed." />
      <fuge:GenericAction identifier="Resuspend_in_PBSFCS_Action" actionOrdinal="5"
        actionText="Finally, cells have been resuspended in PBS/2%FCS (Phosphate Buffered Solution, Fetal Calf Serum) 
        for flow cytometric analysis." />
    </fuge:GenericProtocol>
    
    <!-- Data acquisition protocol -->
    <fuge:GenericProtocol identifier="Data_Acquisition_Protocol" protocolText="Run samples through the cytometer and collect FCS data files.">
      <fuge:GenericAction identifier="Setup_Instrument" actionOrdinal="1"
         actionText="Calibrate the instrument and set detector voltages">
        <fuge:GenericParameter identifier="FSC_Voltage" isInputParam="true" />
        <fuge:GenericParameter identifier="SSC_Voltage" isInputParam="true" />
        <fuge:GenericParameter identifier="FL1_Voltage" isInputParam="true" />
        <fuge:GenericParameter identifier="FL2_Voltage" isInputParam="true" />
        <fuge:GenericParameter identifier="FL3_Voltage" isInputParam="true" />
        <fuge:GenericParameter identifier="FL4_Voltage" isInputParam="true" />
        <fuge:GenericParameter identifier="FL6_Voltage" isInputParam="true" />
        <fuge:GenericParameter identifier="FL8_Voltage" isInputParam="true" />
      </fuge:GenericAction>
      <fuge:GenericAction identifier="Run_Instrument" actionOrdinal="2"
      actionText="Run the sample through the cytometer and get list mode data file" />
    </fuge:GenericProtocol>

    <!-- Data analysis protocol - created as a combination of compensation and gating -->
    <fuge:GenericProtocol identifier="CompensateAndGateProtocol">
      <fuge:GenericAction identifier="compensationAction" Protocol_ref="CompPr" actionOrdinal="1" actionText="Compensate the data file" />
      <fuge:GenericAction identifier="gatingAction" Protocol_ref="GatingPr" actionOrdinal="2" actionText="Gate the data file" />
    </fuge:GenericProtocol>

    <!-- Compensation Protocol - appears as the first action in the CompensateAndGateProtocol -->
    <fcm:CompensationProtocol identifier="CompPr" name="Compensation Protocol">
      <fcm:_compensationType OntologyTerm_ref="SW_compensation" />
      <fcm:_spilloverMatrix ExternalData_ref="spillover_01" />
    </fcm:CompensationProtocol>
    
    <!--  - appears as the second action in the CompensateAndGateProtocol -->
    <fcm:DataFilteringProtocol identifier="GatingPr" name="" >
      <fcm:_gate ExternalData_ref="gating_file" />
    </fcm:DataFilteringProtocol>
    
    <!-- Software used for compensation and gating -->
    <fcm:Software identifier="FlowJo_6_4_7_on_MacOSX_10_2_3" name="FlowJo" version="6.4.7">
      <fuge:_uri>
        <fuge:URI location="http://www.flowjo.com/" />
      </fuge:_uri>
      <fuge:_types OntologyTerm_ref="FCM_Analysis_SW_OntologyTerm" />
      <fcm:_operatingSystem OntologyTerm_ref="Mackintosh_OSX_10_2_3_OntologyTerm" />
    </fcm:Software>
    
    <!-- Software used to create this XML file -->
    <fuge:GenericSoftware identifier="oXygen" version="8.1" name="oXygen XML Editor">
      <fuge:_uri>
        <fuge:URI location="http://www.oxygenxml.com/" />
      </fuge:_uri>
      <fuge:_types OntologyTerm_ref="XML_Editor" />
    </fuge:GenericSoftware>
    
    <!-- ProtocolApplication - get HSC from doners -->
    <fuge:GenericProtocolApplication Protocol_ref="Donor_Cells_Collection_Protocol" identifier="Collect_cells_from_doner_1" 
      activityDate="2006-07-28T12:00:00-08:00">
      <fuge:_outputMaterials Material_ref="HSC_from_donor_1" />
      <fuge:_inputCompleteMaterials Material_ref="Doner_Mouse_1" />
    </fuge:GenericProtocolApplication>
    <fuge:GenericProtocolApplication Protocol_ref="Donor_Cells_Collection_Protocol" identifier="Collect_cells_from_doner_2"
      activityDate="2006-07-28T12:00:00-08:00">
      <fuge:_outputMaterials Material_ref="HSC_from_donor_2" />
      <fuge:_inputCompleteMaterials Material_ref="Doner_Mouse_2" />
    </fuge:GenericProtocolApplication>
    <fuge:GenericProtocolApplication Protocol_ref="Donor_Cells_Collection_Protocol" identifier="Collect_cells_from_doner_3"
      activityDate="2006-07-28T12:00:00-08:00">
      <fuge:_outputMaterials Material_ref="HSC_from_donor_3" />
      <fuge:_inputCompleteMaterials Material_ref="Doner_Mouse_3" />
    </fuge:GenericProtocolApplication>
    <fuge:GenericProtocolApplication Protocol_ref="Donor_Cells_Collection_Protocol" identifier="Collect_cells_from_doner_4"
      activityDate="2006-07-28T12:00:00-08:00">
      <fuge:_outputMaterials Material_ref="KSL_HSC_from_donor_4" />
      <fuge:_inputCompleteMaterials Material_ref="Doner_Mouse_4" />
    </fuge:GenericProtocolApplication>

    <!-- ProtocolApplication - inject HSC into recipients -->
    <fuge:GenericProtocolApplication Protocol_ref="Inject_Cells_Protocol" identifier="Inject_cells_into_recipient_1"
      activityDate="2006-07-28T15:00:00-08:00">
      <fuge:ActionApplication Action_ref="Irradiation" identifier="Irradiation_of_recipient_1">
        <fuge:ParameterValue Parameter_ref="dose">
          <fuge:AtomicValue value="360"><fuge:_unit OntologyTerm_ref="rad_irradiation_unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
      </fuge:ActionApplication>
      <fuge:ActionApplication Action_ref="Injection" identifier="Injection_into_recipient_1" />
      <fuge:GenericMaterialMeasurement Material_ref="HSC_from_donor_1">
        <fuge:AtomicValue value="5"><fuge:_unit OntologyTerm_ref="Cell_Unit_OntologyTerm" /></fuge:AtomicValue>
      </fuge:GenericMaterialMeasurement>
      <fuge:_outputMaterials Material_ref="Recipient_Mouse_1" />
    </fuge:GenericProtocolApplication>

    <fuge:GenericProtocolApplication Protocol_ref="Inject_Cells_Protocol" identifier="Inject_cells_into_recipient_2"
      activityDate="2006-07-28T15:00:00-08:00">
      <fuge:ActionApplication Action_ref="Irradiation" identifier="Irradiation_of_recipient_2">
        <fuge:ParameterValue Parameter_ref="dose">
          <fuge:AtomicValue value="360"><fuge:_unit OntologyTerm_ref="rad_irradiation_unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
      </fuge:ActionApplication>
      <fuge:ActionApplication Action_ref="Injection" identifier="Injection_into_recipient_2" />
      <fuge:GenericMaterialMeasurement Material_ref="HSC_from_donor_1">
        <fuge:AtomicValue value="20"><fuge:_unit OntologyTerm_ref="Cell_Unit_OntologyTerm" /></fuge:AtomicValue>
      </fuge:GenericMaterialMeasurement>
      <fuge:_outputMaterials Material_ref="Recipient_Mouse_2" />
    </fuge:GenericProtocolApplication>

    <fuge:GenericProtocolApplication Protocol_ref="Inject_Cells_Protocol" identifier="Inject_cells_into_recipient_3"
      activityDate="2006-07-28T15:00:00-08:00">
      <fuge:ActionApplication Action_ref="Irradiation" identifier="Irradiation_of_recipient_3">
        <fuge:ParameterValue Parameter_ref="dose">
          <fuge:AtomicValue value="360"><fuge:_unit OntologyTerm_ref="rad_irradiation_unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
      </fuge:ActionApplication>
      <fuge:ActionApplication Action_ref="Injection" identifier="Injection_into_recipient_3" />
      <fuge:GenericMaterialMeasurement Material_ref="HSC_from_donor_1">
        <fuge:AtomicValue value="100"><fuge:_unit OntologyTerm_ref="Cell_Unit_OntologyTerm" /></fuge:AtomicValue>
      </fuge:GenericMaterialMeasurement>
      <fuge:_outputMaterials Material_ref="Recipient_Mouse_3" />
    </fuge:GenericProtocolApplication>
    
    <fuge:GenericProtocolApplication Protocol_ref="Inject_Cells_Protocol" identifier="Inject_cells_into_recipient_4"
      activityDate="2006-07-28T15:00:00-08:00">
      <fuge:ActionApplication Action_ref="Irradiation" identifier="Irradiation_of_recipient_4">
        <fuge:ParameterValue Parameter_ref="dose">
          <fuge:AtomicValue value="360"><fuge:_unit OntologyTerm_ref="rad_irradiation_unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
      </fuge:ActionApplication>
      <fuge:ActionApplication Action_ref="Injection" identifier="Injection_into_recipient_4" />
      <fuge:GenericMaterialMeasurement Material_ref="HSC_from_donor_2">
        <fuge:AtomicValue value="5"><fuge:_unit OntologyTerm_ref="Cell_Unit_OntologyTerm" /></fuge:AtomicValue>
      </fuge:GenericMaterialMeasurement>
      <fuge:_outputMaterials Material_ref="Recipient_Mouse_4" />
    </fuge:GenericProtocolApplication>

    <fuge:GenericProtocolApplication Protocol_ref="Inject_Cells_Protocol" identifier="Inject_cells_into_recipient_5"
      activityDate="2006-07-28T15:00:00-08:00">
      <fuge:ActionApplication Action_ref="Irradiation" identifier="Irradiation_of_recipient_5">
        <fuge:ParameterValue Parameter_ref="dose">
          <fuge:AtomicValue value="360"><fuge:_unit OntologyTerm_ref="rad_irradiation_unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
      </fuge:ActionApplication>
      <fuge:ActionApplication Action_ref="Injection" identifier="Injection_into_recipient_5" />
      <fuge:GenericMaterialMeasurement Material_ref="HSC_from_donor_2">
        <fuge:AtomicValue value="20"><fuge:_unit OntologyTerm_ref="Cell_Unit_OntologyTerm" /></fuge:AtomicValue>
      </fuge:GenericMaterialMeasurement>
      <fuge:_outputMaterials Material_ref="Recipient_Mouse_5" />
    </fuge:GenericProtocolApplication>

    <fuge:GenericProtocolApplication Protocol_ref="Inject_Cells_Protocol" identifier="Inject_cells_into_recipient_6"
      activityDate="2006-07-28T15:00:00-08:00">
      <fuge:ActionApplication Action_ref="Irradiation" identifier="Irradiation_of_recipient_6">
        <fuge:ParameterValue Parameter_ref="dose">
          <fuge:AtomicValue value="360"><fuge:_unit OntologyTerm_ref="rad_irradiation_unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
      </fuge:ActionApplication>
      <fuge:ActionApplication Action_ref="Injection" identifier="Injection_into_recipient_6" />
      <fuge:GenericMaterialMeasurement Material_ref="HSC_from_donor_2">
        <fuge:AtomicValue value="100"><fuge:_unit OntologyTerm_ref="Cell_Unit_OntologyTerm" /></fuge:AtomicValue>
      </fuge:GenericMaterialMeasurement>
      <fuge:_outputMaterials Material_ref="Recipient_Mouse_6" />
    </fuge:GenericProtocolApplication>

    <fuge:GenericProtocolApplication Protocol_ref="Inject_Cells_Protocol" identifier="Inject_cells_into_recipient_7"
      activityDate="2006-07-28T15:00:00-08:00">
      <fuge:ActionApplication Action_ref="Irradiation" identifier="Irradiation_of_recipient_7">
        <fuge:ParameterValue Parameter_ref="dose">
          <fuge:AtomicValue value="360"><fuge:_unit OntologyTerm_ref="rad_irradiation_unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
      </fuge:ActionApplication>
      <fuge:ActionApplication Action_ref="Injection" identifier="Injection_into_recipient_7" />
      <fuge:GenericMaterialMeasurement Material_ref="HSC_from_donor_3">
        <fuge:AtomicValue value="5"><fuge:_unit OntologyTerm_ref="Cell_Unit_OntologyTerm" /></fuge:AtomicValue>
      </fuge:GenericMaterialMeasurement>
      <fuge:_outputMaterials Material_ref="Recipient_Mouse_7" />
    </fuge:GenericProtocolApplication>

    <fuge:GenericProtocolApplication Protocol_ref="Inject_Cells_Protocol" identifier="Inject_cells_into_recipient_8"
      activityDate="2006-07-28T15:00:00-08:00">
      <fuge:ActionApplication Action_ref="Irradiation" identifier="Irradiation_of_recipient_8">
        <fuge:ParameterValue Parameter_ref="dose">
          <fuge:AtomicValue value="360"><fuge:_unit OntologyTerm_ref="rad_irradiation_unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
      </fuge:ActionApplication>
      <fuge:ActionApplication Action_ref="Injection" identifier="Injection_into_recipient_8" />
      <fuge:GenericMaterialMeasurement Material_ref="HSC_from_donor_3">
        <fuge:AtomicValue value="20"><fuge:_unit OntologyTerm_ref="Cell_Unit_OntologyTerm" /></fuge:AtomicValue>
      </fuge:GenericMaterialMeasurement>
      <fuge:_outputMaterials Material_ref="Recipient_Mouse_8" />
    </fuge:GenericProtocolApplication>

    <fuge:GenericProtocolApplication Protocol_ref="Inject_Cells_Protocol" identifier="Inject_cells_into_recipient_9"
      activityDate="2006-07-28T15:00:00-08:00">
      <fuge:ActionApplication Action_ref="Irradiation" identifier="Irradiation_of_recipient_9">
        <fuge:ParameterValue Parameter_ref="dose">
          <fuge:AtomicValue value="360"><fuge:_unit OntologyTerm_ref="rad_irradiation_unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
      </fuge:ActionApplication>
      <fuge:ActionApplication Action_ref="Injection" identifier="Injection_into_recipient_9" />
      <fuge:GenericMaterialMeasurement Material_ref="HSC_from_donor_3">
        <fuge:AtomicValue value="100"><fuge:_unit OntologyTerm_ref="Cell_Unit_OntologyTerm" /></fuge:AtomicValue>
      </fuge:GenericMaterialMeasurement>
      <fuge:_outputMaterials Material_ref="Recipient_Mouse_9" />
    </fuge:GenericProtocolApplication>

    <fuge:GenericProtocolApplication Protocol_ref="Inject_Cells_Protocol" identifier="Inject_cells_into_recipient_10"
      activityDate="2006-07-28T15:00:00-08:00">
      <fuge:ActionApplication Action_ref="Irradiation" identifier="Irradiation_of_recipient_10">
        <fuge:ParameterValue Parameter_ref="dose">
          <fuge:AtomicValue value="360"><fuge:_unit OntologyTerm_ref="rad_irradiation_unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
      </fuge:ActionApplication>
      <fuge:ActionApplication Action_ref="Injection" identifier="Injection_into_recipient_10" />
      <fuge:GenericMaterialMeasurement Material_ref="KSL_HSC_from_donor_4">
        <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="Cell_Unit_OntologyTerm" /></fuge:AtomicValue>
      </fuge:GenericMaterialMeasurement>
      <fuge:_outputMaterials Material_ref="Recipient_Mouse_10" />
    </fuge:GenericProtocolApplication>

    <fuge:GenericProtocolApplication Protocol_ref="Inject_Cells_Protocol" identifier="Inject_cells_into_recipient_11"
      activityDate="2006-07-28T15:00:00-08:00">
      <fuge:ActionApplication Action_ref="Irradiation" identifier="Irradiation_of_recipient_11">
        <fuge:ParameterValue Parameter_ref="dose">
          <fuge:AtomicValue value="360"><fuge:_unit OntologyTerm_ref="rad_irradiation_unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
      </fuge:ActionApplication>
      <fuge:ActionApplication Action_ref="Injection" identifier="Injection_into_recipient_11" />
      <fuge:GenericMaterialMeasurement Material_ref="KSL_HSC_from_donor_4">
        <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="Cell_Unit_OntologyTerm" /></fuge:AtomicValue>
      </fuge:GenericMaterialMeasurement>
      <fuge:_outputMaterials Material_ref="Recipient_Mouse_11" />
    </fuge:GenericProtocolApplication>

    <fuge:GenericProtocolApplication Protocol_ref="Inject_Cells_Protocol" identifier="Inject_cells_into_recipient_12"
      activityDate="2006-07-28T15:00:00-08:00">
      <fuge:ActionApplication Action_ref="Irradiation" identifier="Irradiation_of_recipient_12">
        <fuge:ParameterValue Parameter_ref="dose">
          <fuge:AtomicValue value="360"><fuge:_unit OntologyTerm_ref="rad_irradiation_unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
      </fuge:ActionApplication>
      <fuge:ActionApplication Action_ref="Injection" identifier="Injection_into_recipient_12" />
      <fuge:GenericMaterialMeasurement Material_ref="KSL_HSC_from_donor_4">
        <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="Cell_Unit_OntologyTerm" /></fuge:AtomicValue>
      </fuge:GenericMaterialMeasurement>
      <fuge:_outputMaterials Material_ref="Recipient_Mouse_12" />
    </fuge:GenericProtocolApplication>
    
    <!-- ProtocolApplication - Threatment and staining (creating samples) -->
    <fuge:GenericProtocolApplication Protocol_ref="Staining_Protocol" identifier="Create_Sample_1"
      activityDate="2006-11-20T14:00:00-08:00">
      <fuge:ActionApplication Action_ref="Adjust_Concentration_Action" identifier="CS1_1" />
      <fuge:ActionApplication Action_ref="Block_Immunoglobulin_Fc_Receptors_Action" identifier="CS1_2" />
      <fuge:ActionApplication Action_ref="Staining_Action" identifier="CS1_3" />
      <fuge:ActionApplication Action_ref="Washing_Action" identifier="CS1_4" />
      <fuge:ActionApplication Action_ref="Resuspend_in_PBSFCS_Action" identifier="CS1_5" />
      <fuge:GenericMaterialMeasurement Material_ref="Recipient_Mouse_1">
        <fuge:AtomicValue value="60"><fuge:_unit OntologyTerm_ref="micro_liter_unit_OntologyTerm" /></fuge:AtomicValue>
      </fuge:GenericMaterialMeasurement>
      <fuge:_outputMaterials Material_ref="Sample_1" />
    </fuge:GenericProtocolApplication>
    
    <fuge:GenericProtocolApplication Protocol_ref="Staining_Protocol" identifier="Create_Sample_2"
      activityDate="2006-11-20T14:00:00-08:00">
      <fuge:ActionApplication Action_ref="Adjust_Concentration_Action" identifier="CS2_1" />
      <fuge:ActionApplication Action_ref="Block_Immunoglobulin_Fc_Receptors_Action" identifier="CS2_2" />
      <fuge:ActionApplication Action_ref="Staining_Action" identifier="CS2_3" />
      <fuge:ActionApplication Action_ref="Washing_Action" identifier="CS2_4" />
      <fuge:ActionApplication Action_ref="Resuspend_in_PBSFCS_Action" identifier="CS2_5" />
      <fuge:GenericMaterialMeasurement Material_ref="Recipient_Mouse_2">
        <fuge:AtomicValue value="60"><fuge:_unit OntologyTerm_ref="micro_liter_unit_OntologyTerm" /></fuge:AtomicValue>
      </fuge:GenericMaterialMeasurement>
      <fuge:_outputMaterials Material_ref="Sample_2" />
    </fuge:GenericProtocolApplication>
    
    <fuge:GenericProtocolApplication Protocol_ref="Staining_Protocol" identifier="Create_Sample_3"
      activityDate="2006-11-20T14:00:00-08:00">
      <fuge:ActionApplication Action_ref="Adjust_Concentration_Action" identifier="CS3_1" />
      <fuge:ActionApplication Action_ref="Block_Immunoglobulin_Fc_Receptors_Action" identifier="CS3_2" />
      <fuge:ActionApplication Action_ref="Staining_Action" identifier="CS3_3" />
      <fuge:ActionApplication Action_ref="Washing_Action" identifier="CS3_4" />
      <fuge:ActionApplication Action_ref="Resuspend_in_PBSFCS_Action" identifier="CS3_5" />
      <fuge:GenericMaterialMeasurement Material_ref="Recipient_Mouse_3">
        <fuge:AtomicValue value="60"><fuge:_unit OntologyTerm_ref="micro_liter_unit_OntologyTerm" /></fuge:AtomicValue>
      </fuge:GenericMaterialMeasurement>
      <fuge:_outputMaterials Material_ref="Sample_3" />
    </fuge:GenericProtocolApplication>
    
    <fuge:GenericProtocolApplication Protocol_ref="Staining_Protocol" identifier="Create_Sample_4"
      activityDate="2006-11-20T14:00:00-08:00">
      <fuge:ActionApplication Action_ref="Adjust_Concentration_Action" identifier="CS4_1" />
      <fuge:ActionApplication Action_ref="Block_Immunoglobulin_Fc_Receptors_Action" identifier="CS4_2" />
      <fuge:ActionApplication Action_ref="Staining_Action" identifier="CS4_3" />
      <fuge:ActionApplication Action_ref="Washing_Action" identifier="CS4_4" />
      <fuge:ActionApplication Action_ref="Resuspend_in_PBSFCS_Action" identifier="CS4_5" />
      <fuge:GenericMaterialMeasurement Material_ref="Recipient_Mouse_4">
        <fuge:AtomicValue value="60"><fuge:_unit OntologyTerm_ref="micro_liter_unit_OntologyTerm" /></fuge:AtomicValue>
      </fuge:GenericMaterialMeasurement>
      <fuge:_outputMaterials Material_ref="Sample_4" />
    </fuge:GenericProtocolApplication>
    
    <fuge:GenericProtocolApplication Protocol_ref="Staining_Protocol" identifier="Create_Sample_5"
      activityDate="2006-11-20T14:00:00-08:00">
      <fuge:ActionApplication Action_ref="Adjust_Concentration_Action" identifier="CS5_1" />
      <fuge:ActionApplication Action_ref="Block_Immunoglobulin_Fc_Receptors_Action" identifier="CS5_2" />
      <fuge:ActionApplication Action_ref="Staining_Action" identifier="CS5_3" />
      <fuge:ActionApplication Action_ref="Washing_Action" identifier="CS5_4" />
      <fuge:ActionApplication Action_ref="Resuspend_in_PBSFCS_Action" identifier="CS5_5" />
      <fuge:GenericMaterialMeasurement Material_ref="Recipient_Mouse_5">
        <fuge:AtomicValue value="60"><fuge:_unit OntologyTerm_ref="micro_liter_unit_OntologyTerm" /></fuge:AtomicValue>
      </fuge:GenericMaterialMeasurement>
      <fuge:_outputMaterials Material_ref="Sample_5" />
    </fuge:GenericProtocolApplication>

    <fuge:GenericProtocolApplication Protocol_ref="Staining_Protocol" identifier="Create_Sample_6"
      activityDate="2006-11-20T14:00:00-08:00">
      <fuge:ActionApplication Action_ref="Adjust_Concentration_Action" identifier="CS6_1" />
      <fuge:ActionApplication Action_ref="Block_Immunoglobulin_Fc_Receptors_Action" identifier="CS6_2" />
      <fuge:ActionApplication Action_ref="Staining_Action" identifier="CS6_3" />
      <fuge:ActionApplication Action_ref="Washing_Action" identifier="CS6_4" />
      <fuge:ActionApplication Action_ref="Resuspend_in_PBSFCS_Action" identifier="CS6_5" />
      <fuge:GenericMaterialMeasurement Material_ref="Recipient_Mouse_6">
        <fuge:AtomicValue value="60"><fuge:_unit OntologyTerm_ref="micro_liter_unit_OntologyTerm" /></fuge:AtomicValue>
      </fuge:GenericMaterialMeasurement>
      <fuge:_outputMaterials Material_ref="Sample_6" />
    </fuge:GenericProtocolApplication>
    
    <fuge:GenericProtocolApplication Protocol_ref="Staining_Protocol" identifier="Create_Sample_7"
      activityDate="2006-11-20T14:00:00-08:00">
      <fuge:ActionApplication Action_ref="Adjust_Concentration_Action" identifier="CS7_1" />
      <fuge:ActionApplication Action_ref="Block_Immunoglobulin_Fc_Receptors_Action" identifier="CS7_2" />
      <fuge:ActionApplication Action_ref="Staining_Action" identifier="CS7_3" />
      <fuge:ActionApplication Action_ref="Washing_Action" identifier="CS7_4" />
      <fuge:ActionApplication Action_ref="Resuspend_in_PBSFCS_Action" identifier="CS7_5" />
      <fuge:GenericMaterialMeasurement Material_ref="Recipient_Mouse_7">
        <fuge:AtomicValue value="60"><fuge:_unit OntologyTerm_ref="micro_liter_unit_OntologyTerm" /></fuge:AtomicValue>
      </fuge:GenericMaterialMeasurement>
      <fuge:_outputMaterials Material_ref="Sample_7" />
    </fuge:GenericProtocolApplication>
    
    <fuge:GenericProtocolApplication Protocol_ref="Staining_Protocol" identifier="Create_Sample_8"
      activityDate="2006-11-20T14:00:00-08:00">
      <fuge:ActionApplication Action_ref="Adjust_Concentration_Action" identifier="CS8_1" />
      <fuge:ActionApplication Action_ref="Block_Immunoglobulin_Fc_Receptors_Action" identifier="CS8_2" />
      <fuge:ActionApplication Action_ref="Staining_Action" identifier="CS8_3" />
      <fuge:ActionApplication Action_ref="Washing_Action" identifier="CS8_4" />
      <fuge:ActionApplication Action_ref="Resuspend_in_PBSFCS_Action" identifier="CS8_5" />
      <fuge:GenericMaterialMeasurement Material_ref="Recipient_Mouse_8">
        <fuge:AtomicValue value="60"><fuge:_unit OntologyTerm_ref="micro_liter_unit_OntologyTerm" /></fuge:AtomicValue>
      </fuge:GenericMaterialMeasurement>
      <fuge:_outputMaterials Material_ref="Sample_8" />
    </fuge:GenericProtocolApplication>
    
    <fuge:GenericProtocolApplication Protocol_ref="Staining_Protocol" identifier="Create_Sample_9"
      activityDate="2006-11-20T14:00:00-08:00">
      <fuge:ActionApplication Action_ref="Adjust_Concentration_Action" identifier="CS9_1" >
        <fuge:ParameterValue Parameter_ref="cell concentration">
          <fuge:AtomicValue value="106"><fuge:_unit OntologyTerm_ref="CellsPerML_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
      </fuge:ActionApplication>
      <fuge:ActionApplication Action_ref="Block_Immunoglobulin_Fc_Receptors_Action" identifier="CS9_2" />
      <fuge:ActionApplication Action_ref="Staining_Action" identifier="CS9_3" />
      <fuge:ActionApplication Action_ref="Washing_Action" identifier="CS9_4" />
      <fuge:ActionApplication Action_ref="Resuspend_in_PBSFCS_Action" identifier="CS9_5" />
      <fuge:GenericMaterialMeasurement Material_ref="Recipient_Mouse_9">
        <fuge:AtomicValue value="65"><fuge:_unit OntologyTerm_ref="micro_liter_unit_OntologyTerm" /></fuge:AtomicValue>
      </fuge:GenericMaterialMeasurement>
      <fuge:_outputMaterials Material_ref="Sample_9" />
    </fuge:GenericProtocolApplication>

    <fuge:GenericProtocolApplication Protocol_ref="Staining_Protocol" identifier="Create_Sample_10"
      activityDate="2006-11-20T14:00:00-08:00">
      <fuge:ActionApplication Action_ref="Adjust_Concentration_Action" identifier="CS10_1" />
      <fuge:ActionApplication Action_ref="Block_Immunoglobulin_Fc_Receptors_Action" identifier="CS10_2" />
      <fuge:ActionApplication Action_ref="Staining_Action" identifier="CS10_3" />
      <fuge:ActionApplication Action_ref="Washing_Action" identifier="CS10_4" />
      <fuge:ActionApplication Action_ref="Resuspend_in_PBSFCS_Action" identifier="CS10_5" />
      <fuge:GenericMaterialMeasurement Material_ref="Recipient_Mouse_10">
        <fuge:AtomicValue value="60"><fuge:_unit OntologyTerm_ref="micro_liter_unit_OntologyTerm" /></fuge:AtomicValue>
      </fuge:GenericMaterialMeasurement>
      <fuge:_outputMaterials Material_ref="Sample_10" />
    </fuge:GenericProtocolApplication>
    
    <fuge:GenericProtocolApplication Protocol_ref="Staining_Protocol" identifier="Create_Sample_11"
      activityDate="2006-11-20T14:00:00-08:00">
      <fuge:ActionApplication Action_ref="Adjust_Concentration_Action" identifier="CS11_1" />
      <fuge:ActionApplication Action_ref="Block_Immunoglobulin_Fc_Receptors_Action" identifier="CS11_2" />
      <fuge:ActionApplication Action_ref="Staining_Action" identifier="CS11_3" />
      <fuge:ActionApplication Action_ref="Washing_Action" identifier="CS11_4" />
      <fuge:ActionApplication Action_ref="Resuspend_in_PBSFCS_Action" identifier="CS11_5" />
      <fuge:GenericMaterialMeasurement Material_ref="Recipient_Mouse_11">
        <fuge:AtomicValue value="60"><fuge:_unit OntologyTerm_ref="micro_liter_unit_OntologyTerm" /></fuge:AtomicValue>
      </fuge:GenericMaterialMeasurement>
      <fuge:_outputMaterials Material_ref="Sample_11" />
    </fuge:GenericProtocolApplication>
    
    <fuge:GenericProtocolApplication Protocol_ref="Staining_Protocol" identifier="Create_Sample_12"
      activityDate="2006-11-20T14:00:00-08:00">
      <fuge:ActionApplication Action_ref="Adjust_Concentration_Action" identifier="CS12_1" />
      <fuge:ActionApplication Action_ref="Block_Immunoglobulin_Fc_Receptors_Action" identifier="CS12_2" />
      <fuge:ActionApplication Action_ref="Staining_Action" identifier="CS12_3" />
      <fuge:ActionApplication Action_ref="Washing_Action" identifier="CS12_4" />
      <fuge:ActionApplication Action_ref="Resuspend_in_PBSFCS_Action" identifier="CS12_5" />
      <fuge:GenericMaterialMeasurement Material_ref="Recipient_Mouse_12">
        <fuge:AtomicValue value="60"><fuge:_unit OntologyTerm_ref="micro_liter_unit_OntologyTerm" /></fuge:AtomicValue>
      </fuge:GenericMaterialMeasurement>
      <fuge:_outputMaterials Material_ref="Sample_12" />
    </fuge:GenericProtocolApplication>
    
    <!-- Data acquisition protocol applications -->
    <fuge:GenericProtocolApplication Protocol_ref="Data_Acquisition_Protocol" identifier="Create_data01.fcs"
      activityDate="2006-11-21T15:00:00-08:00">
      <fuge:ActionApplication Action_ref="Setup_Instrument" identifier="Setup_Instrument_for_data01.fcs">
        <fuge:ParameterValue Parameter_ref="FSC_Voltage">
          <fuge:AtomicValue value="220"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="SSC_Voltage">
          <fuge:AtomicValue value="330"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL1_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL2_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL3_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL4_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL6_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL8_Voltage">
          <fuge:AtomicValue value="550"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
      </fuge:ActionApplication>
      <fuge:ActionApplication Action_ref="Run_Instrument" identifier="Run_Instrument_for_data01.fcs" />
      <fuge:EquipmentApplication Equipment_ref="BD_FACSAria_Flow_Cytometer_SN_P0143" identifier="EqPrApp_for_data01.fcs" />
      <fuge:_outputData Data_ref="data01.fcs" />
      <fuge:_inputCompleteMaterials Material_ref="Sample_1" />
    </fuge:GenericProtocolApplication>
    
    <fuge:GenericProtocolApplication Protocol_ref="Data_Acquisition_Protocol" identifier="Create_data02.fcs"
      activityDate="2006-11-21T15:10:00-08:00">
      <fuge:ActionApplication Action_ref="Setup_Instrument" identifier="Setup_Instrument_for_data02.fcs">
        <fuge:ParameterValue Parameter_ref="FSC_Voltage">
          <fuge:AtomicValue value="220"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="SSC_Voltage">
          <fuge:AtomicValue value="330"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL1_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL2_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL3_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL4_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL6_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL8_Voltage">
          <fuge:AtomicValue value="550"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
      </fuge:ActionApplication>
      <fuge:ActionApplication Action_ref="Run_Instrument" identifier="Run_Instrument_for_data02.fcs" />
      <fuge:EquipmentApplication Equipment_ref="BD_FACSAria_Flow_Cytometer_SN_P0143" identifier="EqPrApp_for_data02.fcs" />
      <fuge:_outputData Data_ref="data02.fcs" />
      <fuge:_inputCompleteMaterials Material_ref="Sample_2" />
    </fuge:GenericProtocolApplication>
    
    <fuge:GenericProtocolApplication Protocol_ref="Data_Acquisition_Protocol" identifier="Create_data03.fcs"
      activityDate="2006-11-21T15:20:00-08:00">
      <fuge:ActionApplication Action_ref="Setup_Instrument" identifier="Setup_Instrument_for_data03.fcs">
        <fuge:ParameterValue Parameter_ref="FSC_Voltage">
          <fuge:AtomicValue value="220"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="SSC_Voltage">
          <fuge:AtomicValue value="330"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL1_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL2_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL3_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL4_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL6_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL8_Voltage">
          <fuge:AtomicValue value="550"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
      </fuge:ActionApplication>
      <fuge:ActionApplication Action_ref="Run_Instrument" identifier="Run_Instrument_for_data03.fcs" />
      <fuge:EquipmentApplication Equipment_ref="BD_FACSAria_Flow_Cytometer_SN_P0143" identifier="EqPrApp_for_data03.fcs" />
      <fuge:_outputData Data_ref="data03.fcs" />
      <fuge:_inputCompleteMaterials Material_ref="Sample_3" />
    </fuge:GenericProtocolApplication>
    
    <fuge:GenericProtocolApplication Protocol_ref="Data_Acquisition_Protocol" identifier="Create_data04.fcs"
      activityDate="2006-11-21T15:30:00-08:00">
      <fuge:ActionApplication Action_ref="Setup_Instrument" identifier="Setup_Instrument_for_data04.fcs">
        <fuge:ParameterValue Parameter_ref="FSC_Voltage">
          <fuge:AtomicValue value="220"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="SSC_Voltage">
          <fuge:AtomicValue value="330"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL1_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL2_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL3_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL4_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL6_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL8_Voltage">
          <fuge:AtomicValue value="550"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
      </fuge:ActionApplication>
      <fuge:ActionApplication Action_ref="Run_Instrument" identifier="Run_Instrument_for_data04.fcs" />
      <fuge:EquipmentApplication Equipment_ref="BD_FACSAria_Flow_Cytometer_SN_P0143" identifier="EqPrApp_for_data04.fcs" />
      <fuge:_outputData Data_ref="data04.fcs" />
      <fuge:_inputCompleteMaterials Material_ref="Sample_4" />
    </fuge:GenericProtocolApplication>
    
    <fuge:GenericProtocolApplication Protocol_ref="Data_Acquisition_Protocol" identifier="Create_data05.fcs"
      activityDate="2006-11-21T15:40:00-08:00">
      <fuge:ActionApplication Action_ref="Setup_Instrument" identifier="Setup_Instrument_for_data05.fcs">
        <fuge:ParameterValue Parameter_ref="FSC_Voltage">
          <fuge:AtomicValue value="220"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="SSC_Voltage">
          <fuge:AtomicValue value="330"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL1_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL2_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL3_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL4_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL6_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL8_Voltage">
          <fuge:AtomicValue value="550"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
      </fuge:ActionApplication>
      <fuge:ActionApplication Action_ref="Run_Instrument" identifier="Run_Instrument_for_data05.fcs" />
      <fuge:EquipmentApplication Equipment_ref="BD_FACSAria_Flow_Cytometer_SN_P0143" identifier="EqPrApp_for_data05.fcs" />
      <fuge:_outputData Data_ref="data05.fcs" />
      <fuge:_inputCompleteMaterials Material_ref="Sample_5" />
    </fuge:GenericProtocolApplication>
    
    <fuge:GenericProtocolApplication Protocol_ref="Data_Acquisition_Protocol" identifier="Create_data06.fcs"
      activityDate="2006-11-21T15:50:00-08:00">
      <fuge:ActionApplication Action_ref="Setup_Instrument" identifier="Setup_Instrument_for_data06.fcs">
        <fuge:ParameterValue Parameter_ref="FSC_Voltage">
          <fuge:AtomicValue value="220"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="SSC_Voltage">
          <fuge:AtomicValue value="330"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL1_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL2_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL3_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL4_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL6_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL8_Voltage">
          <fuge:AtomicValue value="550"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
      </fuge:ActionApplication>
      <fuge:ActionApplication Action_ref="Run_Instrument" identifier="Run_Instrument_for_data06.fcs" />
      <fuge:EquipmentApplication Equipment_ref="BD_FACSAria_Flow_Cytometer_SN_P0143" identifier="EqPrApp_for_data06.fcs" />
      <fuge:_outputData Data_ref="data06.fcs" />
      <fuge:_inputCompleteMaterials Material_ref="Sample_6" />
    </fuge:GenericProtocolApplication>
    
    <fuge:GenericProtocolApplication Protocol_ref="Data_Acquisition_Protocol" identifier="Create_data07.fcs"
      activityDate="2006-11-21T16:00:00-08:00">
      <fuge:ActionApplication Action_ref="Setup_Instrument" identifier="Setup_Instrument_for_data07.fcs">
        <fuge:ParameterValue Parameter_ref="FSC_Voltage">
          <fuge:AtomicValue value="220"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="SSC_Voltage">
          <fuge:AtomicValue value="330"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL1_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL2_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL3_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL4_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL6_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL8_Voltage">
          <fuge:AtomicValue value="550"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
      </fuge:ActionApplication>
      <fuge:ActionApplication Action_ref="Run_Instrument" identifier="Run_Instrument_for_data07.fcs" />
      <fuge:EquipmentApplication Equipment_ref="BD_FACSAria_Flow_Cytometer_SN_P0143" identifier="EqPrApp_for_data07.fcs" />
      <fuge:_outputData Data_ref="data07.fcs" />
      <fuge:_inputCompleteMaterials Material_ref="Sample_7" />
    </fuge:GenericProtocolApplication>
    
    <fuge:GenericProtocolApplication Protocol_ref="Data_Acquisition_Protocol" identifier="Create_data08.fcs"
      activityDate="2006-11-21T16:10:00-08:00">
      <fuge:ActionApplication Action_ref="Setup_Instrument" identifier="Setup_Instrument_for_data08.fcs">
        <fuge:ParameterValue Parameter_ref="FSC_Voltage">
          <fuge:AtomicValue value="220"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="SSC_Voltage">
          <fuge:AtomicValue value="330"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL1_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL2_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL3_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL4_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL6_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL8_Voltage">
          <fuge:AtomicValue value="550"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
      </fuge:ActionApplication>
      <fuge:ActionApplication Action_ref="Run_Instrument" identifier="Run_Instrument_for_data08.fcs" />
      <fuge:EquipmentApplication Equipment_ref="BD_FACSAria_Flow_Cytometer_SN_P0143" identifier="EqPrApp_for_data08.fcs" />
      <fuge:_outputData Data_ref="data08.fcs" />
      <fuge:_inputCompleteMaterials Material_ref="Sample_8" />
    </fuge:GenericProtocolApplication>
    
    <fuge:GenericProtocolApplication Protocol_ref="Data_Acquisition_Protocol" identifier="Create_data09.fcs"
      activityDate="2006-11-21T16:20:00-08:00">
      <fuge:ActionApplication Action_ref="Setup_Instrument" identifier="Setup_Instrument_for_data09.fcs">
        <fuge:ParameterValue Parameter_ref="FSC_Voltage">
          <fuge:AtomicValue value="220"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="SSC_Voltage">
          <fuge:AtomicValue value="330"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL1_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL2_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL3_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL4_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL6_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL8_Voltage">
          <fuge:AtomicValue value="550"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
      </fuge:ActionApplication>
      <fuge:ActionApplication Action_ref="Run_Instrument" identifier="Run_Instrument_for_data09.fcs" />
      <fuge:EquipmentApplication Equipment_ref="BD_FACSAria_Flow_Cytometer_SN_P0143" identifier="EqPrApp_for_data09.fcs" />
      <fuge:_outputData Data_ref="data09.fcs" />
      <fuge:_inputCompleteMaterials Material_ref="Sample_9" />
    </fuge:GenericProtocolApplication>
    
    <fuge:GenericProtocolApplication Protocol_ref="Data_Acquisition_Protocol" identifier="Create_data10.fcs"
      activityDate="2006-11-21T16:30:00-08:00">
      <fuge:ActionApplication Action_ref="Setup_Instrument" identifier="Setup_Instrument_for_data10.fcs">
        <fuge:ParameterValue Parameter_ref="FSC_Voltage">
          <fuge:AtomicValue value="220"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="SSC_Voltage">
          <fuge:AtomicValue value="330"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL1_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL2_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL3_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL4_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL6_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL8_Voltage">
          <fuge:AtomicValue value="550"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
      </fuge:ActionApplication>
      <fuge:ActionApplication Action_ref="Run_Instrument" identifier="Run_Instrument_for_data10.fcs" />
      <fuge:EquipmentApplication Equipment_ref="BD_FACSAria_Flow_Cytometer_SN_P0143" identifier="EqPrApp_for_data10.fcs" />
      <fuge:_outputData Data_ref="data10.fcs" />
      <fuge:_inputCompleteMaterials Material_ref="Sample_10" />
    </fuge:GenericProtocolApplication>
    
    <fuge:GenericProtocolApplication Protocol_ref="Data_Acquisition_Protocol" identifier="Create_data11.fcs"
      activityDate="2006-11-21T16:40:00-08:00">
      <fuge:ActionApplication Action_ref="Setup_Instrument" identifier="Setup_Instrument_for_data11.fcs">
        <fuge:ParameterValue Parameter_ref="FSC_Voltage">
          <fuge:AtomicValue value="220"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="SSC_Voltage">
          <fuge:AtomicValue value="330"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL1_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL2_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL3_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL4_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL6_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL8_Voltage">
          <fuge:AtomicValue value="550"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
      </fuge:ActionApplication>
      <fuge:ActionApplication Action_ref="Run_Instrument" identifier="Run_Instrument_for_data11.fcs" />
      <fuge:EquipmentApplication Equipment_ref="BD_FACSAria_Flow_Cytometer_SN_P0143" identifier="EqPrApp_for_data11.fcs" />
      <fuge:_outputData Data_ref="data11.fcs" />
      <fuge:_inputCompleteMaterials Material_ref="Sample_11" />
    </fuge:GenericProtocolApplication>
    
    <fuge:GenericProtocolApplication Protocol_ref="Data_Acquisition_Protocol" identifier="Create_data12.fcs"
      activityDate="2006-11-21T16:50:00-08:00">
      <fuge:ActionApplication Action_ref="Setup_Instrument" identifier="Setup_Instrument_for_data12.fcs">
        <fuge:ParameterValue Parameter_ref="FSC_Voltage">
          <fuge:AtomicValue value="220"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="SSC_Voltage">
          <fuge:AtomicValue value="330"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL1_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL2_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL3_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL4_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL6_Voltage">
          <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
        <fuge:ParameterValue Parameter_ref="FL8_Voltage">
          <fuge:AtomicValue value="550"><fuge:_unit OntologyTerm_ref="V_Unit_OntologyTerm" /></fuge:AtomicValue>
        </fuge:ParameterValue>
      </fuge:ActionApplication>
      <fuge:ActionApplication Action_ref="Run_Instrument" identifier="Run_Instrument_for_data12.fcs" />
      <fuge:EquipmentApplication Equipment_ref="BD_FACSAria_Flow_Cytometer_SN_P0143" identifier="EqPrApp_for_data12.fcs" />
      <fuge:_outputData Data_ref="data12.fcs" />
      <fuge:_inputCompleteMaterials Material_ref="Sample_12" />
    </fuge:GenericProtocolApplication>
    
    <!-- Compensation and  Application -->
    <fuge:GenericProtocolApplication Protocol_ref="CompensateAndGateProtocol" identifier="Compensate_and_gate_data01.fsc" 
      activityDate="2006-11-22T13:00:00-08:00" >
      <fuge:ActionApplication Action_ref="compensationAction" identifier="Compensate_data01.fsc" name="Compensate data01.fsc" />
      <fuge:ActionApplication Action_ref="gatingAction" identifier="Gate_data01.fsc" name="Gate data01.fsc" />
      <fuge:SoftwareApplication Software_ref="FlowJo_6_4_7_on_MacOSX_10_2_3" identifier="FlowJoSample01" />
      <fuge:_inputData Data_ref="data01.fcs" />
      <fuge:_outputData Data_ref="Results_for_Sample_1" />
    </fuge:GenericProtocolApplication>

    <fuge:GenericProtocolApplication Protocol_ref="CompensateAndGateProtocol" identifier="Compensate_and_gate_data02.fsc" 
      activityDate="2006-11-22T13:10:00-08:00" >
      <fuge:ActionApplication Action_ref="compensationAction" identifier="Compensate_data02.fsc" name="Compensate data02.fsc" />
      <fuge:ActionApplication Action_ref="gatingAction" identifier="Gate_data02.fsc" name="Gate data02.fsc" />
      <fuge:SoftwareApplication Software_ref="FlowJo_6_4_7_on_MacOSX_10_2_3" identifier="FlowJoSample02" />
      <fuge:_inputData Data_ref="data02.fcs" />
      <fuge:_outputData Data_ref="Results_for_Sample_2" />
    </fuge:GenericProtocolApplication>
    
    <fuge:GenericProtocolApplication Protocol_ref="CompensateAndGateProtocol" identifier="Compensate_and_gate_data03.fsc" 
      activityDate="2006-11-22T13:20:00-08:00" >
      <fuge:ActionApplication Action_ref="compensationAction" identifier="Compensate_data03.fsc" name="Compensate data03.fsc" />
      <fuge:ActionApplication Action_ref="gatingAction" identifier="Gate_data03.fsc" name="Gate data03.fsc" />
      <fuge:SoftwareApplication Software_ref="FlowJo_6_4_7_on_MacOSX_10_2_3" identifier="FlowJoSample03" />
      <fuge:_inputData Data_ref="data03.fcs" />
      <fuge:_outputData Data_ref="Results_for_Sample_3" />
    </fuge:GenericProtocolApplication>
    
    <fuge:GenericProtocolApplication Protocol_ref="CompensateAndGateProtocol" identifier="Compensate_and_gate_data04.fsc" 
      activityDate="2006-11-22T13:30:00-08:00" >
      <fuge:ActionApplication Action_ref="compensationAction" identifier="Compensate_data04.fsc" name="Compensate data04.fsc" />
      <fuge:ActionApplication Action_ref="gatingAction" identifier="Gate_data04.fsc" name="Gate data04.fsc" />
      <fuge:SoftwareApplication Software_ref="FlowJo_6_4_7_on_MacOSX_10_2_3" identifier="FlowJoSample04" />
      <fuge:_inputData Data_ref="data04.fcs" />
      <fuge:_outputData Data_ref="Results_for_Sample_4" />
    </fuge:GenericProtocolApplication>
    
    <fuge:GenericProtocolApplication Protocol_ref="CompensateAndGateProtocol" identifier="Compensate_and_gate_data05.fsc" 
      activityDate="2006-11-22T13:40:00-08:00" >
      <fuge:ActionApplication Action_ref="compensationAction" identifier="Compensate_data05.fsc" name="Compensate data05.fsc" />
      <fuge:ActionApplication Action_ref="gatingAction" identifier="Gate_data05.fsc" name="Gate data05.fsc" />
      <fuge:SoftwareApplication Software_ref="FlowJo_6_4_7_on_MacOSX_10_2_3" identifier="FlowJoSample05" />
      <fuge:_inputData Data_ref="data05.fcs" />
      <fuge:_outputData Data_ref="Results_for_Sample_5" />
    </fuge:GenericProtocolApplication>
    
    <fuge:GenericProtocolApplication Protocol_ref="CompensateAndGateProtocol" identifier="Compensate_and_gate_data06.fsc" 
      activityDate="2006-11-22T13:50:00-08:00" >
      <fuge:ActionApplication Action_ref="compensationAction" identifier="Compensate_data06.fsc" name="Compensate data06.fsc" />
      <fuge:ActionApplication Action_ref="gatingAction" identifier="Gate_data06.fsc" name="Gate data06.fsc" />
      <fuge:SoftwareApplication Software_ref="FlowJo_6_4_7_on_MacOSX_10_2_3" identifier="FlowJoSample06" />
      <fuge:_inputData Data_ref="data06.fcs" />
      <fuge:_outputData Data_ref="Results_for_Sample_6" />
    </fuge:GenericProtocolApplication>
    
    <fuge:GenericProtocolApplication Protocol_ref="CompensateAndGateProtocol" identifier="Compensate_and_gate_data07.fsc" 
      activityDate="2006-11-22T14:00:00-08:00" >
      <fuge:ActionApplication Action_ref="compensationAction" identifier="Compensate_data07.fsc" name="Compensate data07.fsc" />
      <fuge:ActionApplication Action_ref="gatingAction" identifier="Gate_data07.fsc" name="Gate data07.fsc" />
      <fuge:SoftwareApplication Software_ref="FlowJo_6_4_7_on_MacOSX_10_2_3" identifier="FlowJoSample07" />
      <fuge:_inputData Data_ref="data07.fcs" />
      <fuge:_outputData Data_ref="Results_for_Sample_7" />
    </fuge:GenericProtocolApplication>
    
    <fuge:GenericProtocolApplication Protocol_ref="CompensateAndGateProtocol" identifier="Compensate_and_gate_data08.fsc" 
      activityDate="2006-11-22T14:10:00-08:00" >
      <fuge:ActionApplication Action_ref="compensationAction" identifier="Compensate_data08.fsc" name="Compensate data08.fsc" />
      <fuge:ActionApplication Action_ref="gatingAction" identifier="Gate_data02.fsc" name="Gate data08.fsc" />
      <fuge:SoftwareApplication Software_ref="FlowJo_6_4_7_on_MacOSX_10_2_3" identifier="FlowJoSample08" />
      <fuge:_inputData Data_ref="data08.fcs" />
      <fuge:_outputData Data_ref="Results_for_Sample_8" />
    </fuge:GenericProtocolApplication>
    
    <fuge:GenericProtocolApplication Protocol_ref="CompensateAndGateProtocol" identifier="Compensate_and_gate_data09.fsc" 
      activityDate="2006-11-22T14:20:00-08:00" >
      <fuge:ActionApplication Action_ref="compensationAction" identifier="Compensate_data09.fsc" name="Compensate data09.fsc" />
      <fuge:ActionApplication Action_ref="gatingAction" identifier="Gate_data09.fsc" name="Gate data09.fsc" />
      <fuge:SoftwareApplication Software_ref="FlowJo_6_4_7_on_MacOSX_10_2_3" identifier="FlowJoSample09" />
      <fuge:_inputData Data_ref="data09.fcs" />
      <fuge:_outputData Data_ref="Results_for_Sample_9" />
    </fuge:GenericProtocolApplication>
    
    <fuge:GenericProtocolApplication Protocol_ref="CompensateAndGateProtocol" identifier="Compensate_and_gate_data10.fsc" 
      activityDate="2006-11-22T14:30:00-08:00" >
      <fuge:ActionApplication Action_ref="compensationAction" identifier="Compensate_data10.fsc" name="Compensate data10.fsc" />
      <fuge:ActionApplication Action_ref="gatingAction" identifier="Gate_data10.fsc" name="Gate data10.fsc" />
      <fuge:SoftwareApplication Software_ref="FlowJo_6_4_7_on_MacOSX_10_2_3" identifier="FlowJoSample10" />
      <fuge:_inputData Data_ref="data10.fcs" />
      <fuge:_outputData Data_ref="Results_for_Sample_10" />
    </fuge:GenericProtocolApplication>
    
    <fuge:GenericProtocolApplication Protocol_ref="CompensateAndGateProtocol" identifier="Compensate_and_gate_data11.fsc" 
      activityDate="2006-11-22T14:40:00-08:00" >
      <fuge:ActionApplication Action_ref="compensationAction" identifier="Compensate_data11.fsc" name="Compensate data11.fsc" />
      <fuge:ActionApplication Action_ref="gatingAction" identifier="Gate_data11.fsc" name="Gate data11.fsc" />
      <fuge:SoftwareApplication Software_ref="FlowJo_6_4_7_on_MacOSX_10_2_3" identifier="FlowJoSample11" />
      <fuge:_inputData Data_ref="data11.fcs" />
      <fuge:_outputData Data_ref="Results_for_Sample_11" />
    </fuge:GenericProtocolApplication>
    
    <fuge:GenericProtocolApplication Protocol_ref="CompensateAndGateProtocol" identifier="Compensate_and_gate_data12.fsc" 
      activityDate="2006-11-22T14:50:00-08:00" >
      <fuge:ActionApplication Action_ref="compensationAction" identifier="Compensate_data12.fsc" name="Compensate data12.fsc" />
      <fuge:ActionApplication Action_ref="gatingAction" identifier="Gate_data12.fsc" name="Gate data12.fsc" />
      <fuge:SoftwareApplication Software_ref="FlowJo_6_4_7_on_MacOSX_10_2_3" identifier="FlowJoSample12" />
      <fuge:_inputData Data_ref="data12.fcs" />
      <fuge:_outputData Data_ref="Results_for_Sample_12" />
    </fuge:GenericProtocolApplication>
    
    <!-- Instrumentation description -->
    <fcm:Cytometer identifier="BD_FACSAria_Flow_Cytometer_SN_P0143">
      <!--
        *************************************************************************************************** 
        Please note that MIFlowCyt only requires the make, model# and user-altered and configured parts.
        Here, we are trying to describe the whole instrument just to test that the model and the XSD allows
        for such a description!
        ***************************************************************************************************
      -->
      <fuge:_make OntologyTerm_ref="BD_OntologyTerm" />
      <fuge:_model OntologyTerm_ref="OBI_0400040" />
      <fcm:FlowCell identifier="Cuvette_flow_cell">
        <fcm:_flowCellType OntologyTerm_ref="Cuvette_OntologyTerm" />
        <fcm:_flowCellOtherInfo>
          <fuge:Description text="Quartz Cuvette Flow Cell, 160-um x 250-um, 15-mm long" />
        </fcm:_flowCellOtherInfo>
      </fcm:FlowCell>
      <fcm:OpticalFilter identifier="LP735o" instalationDate="2006-02-15T00:00:00">
        <fuge:_make OntologyTerm_ref="BD_OntologyTerm" />
        <fuge:_model OntologyTerm_ref="BD_LP735_OntologyTerm" />
        <fcm:_minTransmittedWavelength DataProperty_ref="dp_735nm" />
        <fcm:_opticalFilterType OntologyTerm_ref="OBI_0400067"/>
        <fcm:_opticalFilterOtherInfo>
          <fuge:Description text="Before PMT-A; Octagon (488nm laser), intended dye: PECy-7" />
        </fcm:_opticalFilterOtherInfo>
      </fcm:OpticalFilter>
      <fcm:OpticalFilter identifier="BP780_60o" instalationDate="2006-02-15T00:00:00">
        <fuge:_make OntologyTerm_ref="BD_OntologyTerm" />
        <fuge:_model OntologyTerm_ref="BD_BP780_60_OntologyTerm" />
        <fcm:_minTransmittedWavelength DataProperty_ref="dp_750nm" />
        <fcm:_maxTransmittedWavelength DataProperty_ref="dp_810nm" />
        <fcm:_opticalFilterType OntologyTerm_ref="OBI_0400013"/>
        <fcm:_opticalFilterOtherInfo>
          <fuge:Description text="Before PMT-A; Octagon (488nm laser), intended dye: PECy-7" />
        </fcm:_opticalFilterOtherInfo>
      </fcm:OpticalFilter>
      <fcm:OpticalFilter identifier="LP655o" instalationDate="2006-02-15T00:00:00">
        <fuge:_make OntologyTerm_ref="BD_OntologyTerm" />
        <fuge:_model OntologyTerm_ref="BD_LP655_OntologyTerm" />
        <fcm:_minTransmittedWavelength DataProperty_ref="dp_655nm" />
        <fcm:_opticalFilterType OntologyTerm_ref="OBI_0400067"/>
        <fcm:_opticalFilterOtherInfo>
          <fuge:Description text="Before PMT-B (FL4); Octagon (488nm laser), intended dye: PerCP" />
        </fcm:_opticalFilterOtherInfo>
      </fcm:OpticalFilter>
      <fcm:OpticalFilter identifier="BP675_20o" instalationDate="2006-02-15T00:00:00">
        <fuge:_make OntologyTerm_ref="BD_OntologyTerm" />
        <fuge:_model OntologyTerm_ref="BD_BP675_20_OntologyTerm" />
        <fcm:_minTransmittedWavelength DataProperty_ref="dp_665nm" />
        <fcm:_maxTransmittedWavelength DataProperty_ref="dp_685nm" />
        <fcm:_opticalFilterType OntologyTerm_ref="OBI_0400013"/>
        <fcm:_opticalFilterOtherInfo>
          <fuge:Description text="Before PMT-B (FL4); Octagon (488nm laser), intended dye: PerCP" />
        </fcm:_opticalFilterOtherInfo>
      </fcm:OpticalFilter>
      <fcm:OpticalFilter identifier="LP595o" instalationDate="2006-02-15T00:00:00">
        <fuge:_make OntologyTerm_ref="BD_OntologyTerm" />
        <fuge:_model OntologyTerm_ref="BD_LP595_OntologyTerm" />
        <fcm:_minTransmittedWavelength DataProperty_ref="dp_595nm" />
        <fcm:_opticalFilterType OntologyTerm_ref="OBI_0400067"/>
        <fcm:_opticalFilterOtherInfo>
          <fuge:Description text="Before PMT-C (FL3); Octagon (488nm laser), intended dye: PE-TxRed" />
        </fcm:_opticalFilterOtherInfo>
      </fcm:OpticalFilter>
      <fcm:OpticalFilter identifier="BP610_20o" instalationDate="2006-02-15T00:00:00">
        <fuge:_make OntologyTerm_ref="BD_OntologyTerm" />
        <fuge:_model OntologyTerm_ref="BD_BP610_20_OntologyTerm" />
        <fcm:_minTransmittedWavelength DataProperty_ref="dp_600nm" />
        <fcm:_maxTransmittedWavelength DataProperty_ref="dp_620nm" />
        <fcm:_opticalFilterType OntologyTerm_ref="OBI_0400013"/>
        <fcm:_opticalFilterOtherInfo>
          <fuge:Description text="Before PMT-C (FL3); Octagon (488nm laser), intended dye: PE-TxRed" />
        </fcm:_opticalFilterOtherInfo>
      </fcm:OpticalFilter>
      <fcm:OpticalFilter identifier="LP556o" instalationDate="2006-02-15T00:00:00">
        <fuge:_make OntologyTerm_ref="BD_OntologyTerm" />
        <fuge:_model OntologyTerm_ref="BD_LP556_OntologyTerm" />
        <fcm:_minTransmittedWavelength DataProperty_ref="dp_556nm" />
        <fcm:_opticalFilterType OntologyTerm_ref="OBI_0400067"/>
        <fcm:_opticalFilterOtherInfo>
          <fuge:Description text="Before PMT-D (FL2); Octagon (488nm laser), intended dye: PE or PI" />
        </fcm:_opticalFilterOtherInfo>
      </fcm:OpticalFilter>
      <fcm:OpticalFilter identifier="BP575_26o" instalationDate="2006-02-15T00:00:00">
        <fuge:_make OntologyTerm_ref="BD_OntologyTerm" />
        <fuge:_model OntologyTerm_ref="BD_BP575_26_OntologyTerm" />
        <fcm:_minTransmittedWavelength DataProperty_ref="dp_562nm" />
        <fcm:_maxTransmittedWavelength DataProperty_ref="dp_588nm" />
        <fcm:_opticalFilterType OntologyTerm_ref="OBI_0400013"/>
        <fcm:_opticalFilterOtherInfo>
          <fuge:Description text="Before PMT-D (FL2); Octagon (488nm laser), intended dye: PE or PI" />
        </fcm:_opticalFilterOtherInfo>
      </fcm:OpticalFilter>
      <fcm:OpticalFilter identifier="LP502o" instalationDate="2006-02-15T00:00:00">
        <fuge:_make OntologyTerm_ref="BD_OntologyTerm" />
        <fuge:_model OntologyTerm_ref="BD_LP502_OntologyTerm" />
        <fcm:_minTransmittedWavelength DataProperty_ref="dp_502nm" />
        <fcm:_opticalFilterType OntologyTerm_ref="OBI_0400067"/>
        <fcm:_opticalFilterOtherInfo>
          <fuge:Description text="Before PMT-E (FL1); Octagon (488nm laser), intended dye: FITC" />
        </fcm:_opticalFilterOtherInfo>
      </fcm:OpticalFilter>
      <fcm:OpticalFilter identifier="BP530_30o" instalationDate="2006-02-15T00:00:00">
        <fuge:_make OntologyTerm_ref="BD_OntologyTerm" />
        <fuge:_model OntologyTerm_ref="BD_BP530_30_OntologyTerm" />
        <fcm:_minTransmittedWavelength DataProperty_ref="dp_515nm" />
        <fcm:_maxTransmittedWavelength DataProperty_ref="dp_545nm" />
        <fcm:_opticalFilterType OntologyTerm_ref="OBI_0400013"/>
        <fcm:_opticalFilterOtherInfo>
          <fuge:Description text="Before PMT-E (FL1); Octagon (488nm laser), intended dye: FITC" />
        </fcm:_opticalFilterOtherInfo>
      </fcm:OpticalFilter>
      <fcm:OpticalFilter identifier="BP488_10o" instalationDate="2006-02-15T00:00:00">
        <fuge:_make OntologyTerm_ref="BD_OntologyTerm" />
        <fuge:_model OntologyTerm_ref="BD_BP488_10_OntologyTerm" />
        <fcm:_minTransmittedWavelength DataProperty_ref="dp_483nm" />
        <fcm:_maxTransmittedWavelength DataProperty_ref="dp_493nm" />
        <fcm:_opticalFilterType OntologyTerm_ref="OBI_0400013"/>
        <fcm:_opticalFilterOtherInfo>
          <fuge:Description text="Before PMT-F; Octagon (488nm laser), SSC" />
        </fcm:_opticalFilterOtherInfo>
      </fcm:OpticalFilter>
      <fcm:OpticalFilter identifier="LP735t1" instalationDate="2006-02-15T00:00:00">
        <fuge:_make OntologyTerm_ref="BD_OntologyTerm" />
        <fuge:_model OntologyTerm_ref="BD_LP735_OntologyTerm" />
        <fcm:_minTransmittedWavelength DataProperty_ref="dp_735nm" />
        <fcm:_opticalFilterType OntologyTerm_ref="OBI_0400067"/>
        <fcm:_opticalFilterOtherInfo>
          <fuge:Description text="Before PMT-A; Trigon 1 (633nm laser), intended dye: APC-Cy7" />
        </fcm:_opticalFilterOtherInfo>
      </fcm:OpticalFilter>
      <fcm:OpticalFilter identifier="BP780_60t1" instalationDate="2006-02-15T00:00:00">
        <fuge:_make OntologyTerm_ref="BD_OntologyTerm" />
        <fuge:_model OntologyTerm_ref="BD_BP780_60_OntologyTerm" />
        <fcm:_minTransmittedWavelength DataProperty_ref="dp_750nm" />
        <fcm:_maxTransmittedWavelength DataProperty_ref="dp_810nm" />
        <fcm:_opticalFilterType OntologyTerm_ref="OBI_0400013"/>
        <fcm:_opticalFilterOtherInfo>
          <fuge:Description text="Before PMT-A; Trigon 1 (633nm laser), intended dye: APC-Cy7" />
        </fcm:_opticalFilterOtherInfo>
      </fcm:OpticalFilter>
      <fcm:OpticalFilter identifier="BP660_20t1" instalationDate="2006-02-15T00:00:00">
        <fuge:_make OntologyTerm_ref="BD_OntologyTerm" />
        <fuge:_model OntologyTerm_ref="BD_BP660_20_OntologyTerm" />
        <fcm:_minTransmittedWavelength DataProperty_ref="dp_650nm" />
        <fcm:_maxTransmittedWavelength DataProperty_ref="dp_670nm" />
        <fcm:_opticalFilterType OntologyTerm_ref="OBI_0400013"/>
        <fcm:_opticalFilterOtherInfo>
          <fuge:Description text="Before PMT-B (FL6); Trigon 1 (633nm laser), intended dye: APC" />
        </fcm:_opticalFilterOtherInfo>
      </fcm:OpticalFilter>
      <fcm:OpticalFilter identifier="LP502t2" instalationDate="2006-02-15T00:00:00">
        <fuge:_make OntologyTerm_ref="BD_OntologyTerm" />
        <fuge:_model OntologyTerm_ref="BD_LP502_OntologyTerm" />
        <fcm:_minTransmittedWavelength DataProperty_ref="dp_502nm" />
        <fcm:_opticalFilterType OntologyTerm_ref="OBI_0400067"/>
        <fcm:_opticalFilterOtherInfo>
          <fuge:Description text="Before PMT-A (FL8); Trigon 2 (407nm laser), intended dye: DAPI" />
        </fcm:_opticalFilterOtherInfo>
      </fcm:OpticalFilter>
      <fcm:OpticalFilter identifier="BP530_30t2" instalationDate="2006-02-15T00:00:00">
        <fuge:_make OntologyTerm_ref="BD_OntologyTerm" />
        <fuge:_model OntologyTerm_ref="BD_BP530_30_OntologyTerm" />
        <fcm:_minTransmittedWavelength DataProperty_ref="dp_515nm" />
        <fcm:_maxTransmittedWavelength DataProperty_ref="dp_545nm" />
        <fcm:_opticalFilterType OntologyTerm_ref="OBI_0400013"/>
        <fcm:_opticalFilterOtherInfo>
          <fuge:Description text="Before PMT-A (FL8); Trigon 2 (407nm laser), intended dye: DAPI" />
        </fcm:_opticalFilterOtherInfo>
      </fcm:OpticalFilter>
      <fcm:OpticalFilter identifier="BP450_40t2" instalationDate="2006-02-15T00:00:00">
        <fuge:_make OntologyTerm_ref="BD_OntologyTerm" />
        <fuge:_model OntologyTerm_ref="BD_BP450_40_OntologyTerm" />
        <fcm:_minTransmittedWavelength DataProperty_ref="dp_430nm" />
        <fcm:_maxTransmittedWavelength DataProperty_ref="dp_470nm" />
        <fcm:_opticalFilterType OntologyTerm_ref="OBI_0400013"/>
        <fcm:_opticalFilterOtherInfo>
          <fuge:Description text="Before PMT-B; Trigon 2 (407nm laser), intended dye: Pacific Blue, Cascade Blue, Alexa Fluor 405" />
        </fcm:_opticalFilterOtherInfo>
      </fcm:OpticalFilter>
      <fcm:OpticalDetector identifier="FSC" name="Forward Scatter">
        <fcm:_opticalDetectorType OntologyTerm_ref="OBI_0400083" />
        <fcm:_opticalDetectorAmplificationType><fuge:Description text="linear" /></fcm:_opticalDetectorAmplificationType>
        <fcm:_opticalDetectorVoltage DataProperty_ref="dp_220V" />
      </fcm:OpticalDetector>
      <fcm:OpticalDetector identifier="SSC" name="Side Scatter">
        <fcm:_opticalDetectorType OntologyTerm_ref="OBI_0400084" />
        <fcm:_opticalDetectorAmplificationType><fuge:Description text="linear" /></fcm:_opticalDetectorAmplificationType>
        <fcm:_opticalDetectorVoltage DataProperty_ref="dp_330V" />
        <fcm:_opticalDetectorOtherInfo>
          <fuge:Description text="PMT-F; Octagon (488nm laser)" />
        </fcm:_opticalDetectorOtherInfo>
      </fcm:OpticalDetector>
      <fcm:OpticalDetector identifier="FL1" name="FL1">
        <fcm:_opticalDetectorType OntologyTerm_ref="OBI_0400084" />
        <fcm:_opticalDetectorAmplificationType><fuge:Description text="log" /></fcm:_opticalDetectorAmplificationType>
        <fcm:_opticalDetectorVoltage DataProperty_ref="dp_500V" />
        <fcm:_opticalDetectorOtherInfo>
          <fuge:Description text="PMT-E; Octagon (488nm laser)" />
        </fcm:_opticalDetectorOtherInfo>
      </fcm:OpticalDetector>
      <fcm:OpticalDetector identifier="FL2" name="FL2">
        <fcm:_opticalDetectorType OntologyTerm_ref="OBI_0400084" />
        <fcm:_opticalDetectorAmplificationType><fuge:Description text="log" /></fcm:_opticalDetectorAmplificationType>
        <fcm:_opticalDetectorVoltage DataProperty_ref="dp_500V" />
        <fcm:_opticalDetectorOtherInfo>
          <fuge:Description text="PMT-D; Octagon (488nm laser)" />
        </fcm:_opticalDetectorOtherInfo>
      </fcm:OpticalDetector>
      <fcm:OpticalDetector identifier="FL3" name="FL3">
        <fcm:_opticalDetectorType OntologyTerm_ref="OBI_0400084" />
        <fcm:_opticalDetectorAmplificationType><fuge:Description text="log" /></fcm:_opticalDetectorAmplificationType>
        <fcm:_opticalDetectorVoltage DataProperty_ref="dp_500V" />
        <fcm:_opticalDetectorOtherInfo>
          <fuge:Description text="PMT-C; Octagon (488nm laser)" />
        </fcm:_opticalDetectorOtherInfo>
      </fcm:OpticalDetector>
      <fcm:OpticalDetector identifier="FL4" name="FL4">
        <fcm:_opticalDetectorType OntologyTerm_ref="OBI_0400084" />
        <fcm:_opticalDetectorAmplificationType><fuge:Description text="log" /></fcm:_opticalDetectorAmplificationType>
        <fcm:_opticalDetectorVoltage DataProperty_ref="dp_500V" />
        <fcm:_opticalDetectorOtherInfo>
          <fuge:Description text="PMT-B; Octagon (488nm laser)" />
        </fcm:_opticalDetectorOtherInfo>
      </fcm:OpticalDetector>
      <fcm:OpticalDetector identifier="FL6" name="FL6">
        <fcm:_opticalDetectorType OntologyTerm_ref="OBI_0400084" />
        <fcm:_opticalDetectorAmplificationType><fuge:Description text="log" /></fcm:_opticalDetectorAmplificationType>
        <fcm:_opticalDetectorVoltage DataProperty_ref="dp_500V" />
        <fcm:_opticalDetectorOtherInfo>
          <fuge:Description text="PMT-B; Trigon 1 (633nm laser)" />
        </fcm:_opticalDetectorOtherInfo>
      </fcm:OpticalDetector>
      <fcm:OpticalDetector identifier="FL8" name="FL8">
        <fcm:_opticalDetectorType OntologyTerm_ref="OBI_0400084" />
        <fcm:_opticalDetectorAmplificationType><fuge:Description text="log" /></fcm:_opticalDetectorAmplificationType>
        <fcm:_opticalDetectorVoltage DataProperty_ref="dp_550V" />
        <fcm:_opticalDetectorOtherInfo>
          <fuge:Description text="PMT-A; Trigon 2 (407nm laser)" />
        </fcm:_opticalDetectorOtherInfo>
      </fcm:OpticalDetector>
      <fcm:LightSource identifier="Laser_488nm" name="Laser 488nm">
        <fcm:_lightSourceType OntologyTerm_ref="OBI_0400096" />
        <fcm:_lightSourceExcitatoryWavelength DataProperty_ref="dp_488nm" />
        <fcm:_lightSourcePower DataProperty_ref="dp_15mW" />
        <fcm:_lightSourcePolarization>
          <fuge:Description text="N/A" />
        </fcm:_lightSourcePolarization>
        <fcm:_lightSourceBeam>
          <fuge:Description text="Elliptical Shape, Beam height is 9 +/- 3um and beam width is 65 +/- 7um" />
        </fcm:_lightSourceBeam>
        <fcm:_lightSourceOtherInfo>
          <fuge:Description text="Coherent Sapphire, Class IIIb." />
        </fcm:_lightSourceOtherInfo>
      </fcm:LightSource>
      <fcm:LightSource identifier="Laser_633nm" name="Laser 633nm">
        <fcm:_lightSourceType OntologyTerm_ref="OBI_0400053" />
        <fcm:_lightSourceExcitatoryWavelength DataProperty_ref="dp_633nm" />
        <fcm:_lightSourcePower DataProperty_ref="dp_15mW" />
        <fcm:_lightSourceBeam>
          <fuge:Description text="Elliptical Shape, Beam height is 9 +/- 3um and beam width is 65 +/- 7um" />
        </fcm:_lightSourceBeam>
        <fcm:_lightSourceOtherInfo>
          <fuge:Description text="JDS UniphaseTM HeNe air-cooled, Class IIIb." />
        </fcm:_lightSourceOtherInfo>
      </fcm:LightSource>
      <fcm:LightSource identifier="Laser_407nm" name="Laser 407nm">
        <fcm:_lightSourceType OntologyTerm_ref="OBI_0400096" />
        <fcm:_lightSourceExcitatoryWavelength DataProperty_ref="dp_407nm" />
        <fcm:_lightSourcePower DataProperty_ref="dp_15mW" />
        <fcm:_lightSourceBeam>
          <fuge:Description text="Elliptical Shape, Beam height is 9 +/- 3um and beam width is 65 +/- 7um" />
        </fcm:_lightSourceBeam>
        <fcm:_lightSourceOtherInfo>
          <fuge:Description text="Point Source Violet solid state, Class IIIb." />
        </fcm:_lightSourceOtherInfo>
      </fcm:LightSource>
      <fcm:OpticalPathDesctiption identifier="FSC-OpticalPath" name="FSC Optical Path">
        <fcm:OpticalPathComponent LightSource_ref="Laser_488nm" />
        <fcm:OpticalPathComponent OpticalDetector_ref="FSC" />
      </fcm:OpticalPathDesctiption>
      <fcm:OpticalPathDesctiption identifier="SSC-OpticalPath" name="SSC Optical Path">
        <fcm:OpticalPathComponent LightSource_ref="Laser_488nm" />
        <fcm:OpticalPathComponent OpticalFilter_ref="BP488_10o" />
        <fcm:OpticalPathComponent OpticalDetector_ref="SSC" />
      </fcm:OpticalPathDesctiption>
      <fcm:OpticalPathDesctiption identifier="FL1-OpticalPath" name="FL1 Optical Path">
        <fcm:OpticalPathComponent LightSource_ref="Laser_488nm" />
        <fcm:OpticalPathComponent OpticalFilter_ref="LP502o" />
        <fcm:OpticalPathComponent OpticalFilter_ref="BP530_30o" />
        <fcm:OpticalPathComponent OpticalDetector_ref="FL1" />
      </fcm:OpticalPathDesctiption>
      <fcm:OpticalPathDesctiption identifier="FL2-OpticalPath" name="FL2 Optical Path">
        <fcm:OpticalPathComponent LightSource_ref="Laser_488nm" />
        <fcm:OpticalPathComponent OpticalFilter_ref="LP556o" />
        <fcm:OpticalPathComponent OpticalFilter_ref="BP575_26o" />
        <fcm:OpticalPathComponent OpticalDetector_ref="FL2" />
      </fcm:OpticalPathDesctiption>
      <fcm:OpticalPathDesctiption identifier="FL3-OpticalPath" name="FL3 Optical Path">
        <fcm:OpticalPathComponent LightSource_ref="Laser_488nm" />
        <fcm:OpticalPathComponent OpticalFilter_ref="LP595o" />
        <fcm:OpticalPathComponent OpticalFilter_ref="BP610_20o" />
        <fcm:OpticalPathComponent OpticalDetector_ref="FL3" />
      </fcm:OpticalPathDesctiption>
      <fcm:OpticalPathDesctiption identifier="FL4-OpticalPath" name="FL4 Optical Path">
        <fcm:OpticalPathComponent LightSource_ref="Laser_488nm" />
        <fcm:OpticalPathComponent OpticalFilter_ref="LP655o" />
        <fcm:OpticalPathComponent OpticalFilter_ref="BP675_20o" />
        <fcm:OpticalPathComponent OpticalDetector_ref="FL4" />
      </fcm:OpticalPathDesctiption>
      <fcm:OpticalPathDesctiption identifier="FL6-OpticalPath" name="FL6 Optical Path">
        <fcm:OpticalPathComponent LightSource_ref="Laser_633nm" />
        <fcm:OpticalPathComponent OpticalFilter_ref="BP660_20t1" />
        <fcm:OpticalPathComponent OpticalDetector_ref="FL6" />
      </fcm:OpticalPathDesctiption>
      <fcm:OpticalPathDesctiption identifier="FL8-OpticalPath" name="FL8 Optical Path">
        <fcm:OpticalPathComponent LightSource_ref="Laser_407nm" />
        <fcm:OpticalPathComponent OpticalFilter_ref="LP502t2" />
        <fcm:OpticalPathComponent OpticalFilter_ref="BP530_30t2" />
        <fcm:OpticalPathComponent OpticalDetector_ref="FL8" />
      </fcm:OpticalPathDesctiption>
    </fcm:Cytometer>

  </fuge:ProtocolCollection>
  
  <!-- 
    ********************************* 
    Ontological Terms
    *********************************
  -->
  <fuge:OntologyCollection>
    
    <!-- Keywords, trying MeSH -->
    <fuge:OntologyIndividual 
      term="Blood" OntologySource_ref="http://www.nlm.nih.gov/mesh/meshhome.html"  
      termAccession="MeSH:Q000097" identifier="keyword_1_blood" />
    <fuge:OntologyIndividual 
      term="Transplants" OntologySource_ref="http://www.nlm.nih.gov/mesh/meshhome.html" 
      termAccession="MeSH:D019737" identifier="keyword_2_transplant" />
    <fuge:OntologyIndividual 
      term="Donor" termAccession="N/A" identifier="keyword_3_donor" />
    <fuge:OntologyIndividual 
      term="Recipient" termAccession="N/A" identifier="keyword_4_recipient" />
    <fuge:OntologyIndividual 
      term="Leukocytes" OntologySource_ref="http://www.nlm.nih.gov/mesh/meshhome.html" 
      termAccession="MeSH:D007962" identifier="keyword_5_leukocyte" />
    <fuge:OntologyIndividual 
      term="Lymphocytes" OntologySource_ref="http://www.nlm.nih.gov/mesh/meshhome.html" 
      termAccession="MeSH:D008214" identifier="keyword_6_lymphocyte" />
    <fuge:OntologyIndividual 
      term="Monocytes" OntologySource_ref="http://www.nlm.nih.gov/mesh/meshhome.html" 
      termAccession="MeSH:D009000" identifier="keyword_7_monocyte" />
    <fuge:OntologyIndividual 
      term="Granulocytes" OntologySource_ref="http://www.nlm.nih.gov/mesh/meshhome.html" 
      termAccession="MeSH:D006098" identifier="keyword_8_granulocyte" />
    
    <!-- Number of inhected cells, data properties? -->
    <fuge:DataProperty 
      term="Number of donor HSC cells injected into a recipient mice" 
      termAccession="N/A" identifier="injected_donor_HSC_no" />
    <fuge:DataProperty 
      term="Number of Kit+/sca-1+/Lineage- (KSL) HSC cells injected into a recipient mice" 
      termAccession="N/A" identifier="injected_control_HSC_no" />
    
    <!-- Roles from OBI -->
    <fuge:OntologyIndividual
      term="principal investigator role" OntologySource_ref="http://purl.obofoundry.org/obo/obi.owl" 
      termAccession="OBI:OBI_0000103" identifier="OBI_0000103" />
    <fuge:OntologyIndividual 
      term="laboratory role" OntologySource_ref="http://purl.obofoundry.org/obo/obi.owl"
      termAccession="OBI:OBI_0000184" identifier="OBI_0000184" />
    <fuge:OntologyIndividual 
      term="author role" OntologySource_ref="http://purl.obofoundry.org/obo/obi.owl"
      termAccession="OBI:OBI_0000357" identifier="OBI_0000357" />

    <!-- IT stuff -->
    <fuge:OntologyIndividual 
      term="Extensible Markup Language (XML) Editor"
      termAccession="N/A" identifier="XML_Editor" />
    <fuge:OntologyIndividual 
      term="Flow Cytometry Analysis Software" termAccession="N/A" identifier="FCM_Analysis_SW_OntologyTerm" />
    <fuge:OntologyIndividual 
      term="Mackintosh OSX 10_2_3" termAccession="N/A" identifier="Mackintosh_OSX_10_2_3_OntologyTerm" />

    <!-- Dyes -->
    <fuge:OntologyIndividual 
      term="Texas Red" name="Texas Red" OntologySource_ref="http://www.drmr.com/abcon/trfspec.html"
      termAccession="N/A" identifier="TexasRed_OntologyTerm" />
    <fuge:OntologyIndividual 
      term="Allophycocyanin (APC)" name="Allophycocyanin (APC)" OntologySource_ref="http://www.drmr.com/abcon/APCfspec.html"
      termAccession="N/A" identifier="APC_OntologyTerm" />
    <fuge:OntologyIndividual 
      term="Phycoerythrin (PE)" name="Phycoerythrin (PE)" OntologySource_ref="http://www.drmr.com/abcon/PEfspec.html"
      termAccession="N/A" identifier="PE_OntologyTerm" />
    <fuge:OntologyIndividual 
      term="Fluorescein (FITC)" name="Fluorescein (FITC)" OntologySource_ref="http://www.drmr.com/abcon/Ffspec.html"
      termAccession="N/A" identifier="FITC_OntologyTerm" />
    <fuge:OntologyIndividual 
      term="Peridinin-chlorophyll-protein (PerCP)" name="Peridinin-chlorophyll-protein (PerCP)"
      termAccession="N/A" identifier="PerCP_OntologyTerm" />
    <fuge:OntologyIndividual 
      term="4,6-diamidino-2-phenylindole (DAPI)" name="4,6-diamidino-2-phenylindole (DAPI)"
      termAccession="N/A" identifier="DAPI_OntologyTerm" />

    <!-- Antibodies -->
    <fuge:OntologyIndividual identifier="anti-CD4-OntologyTerm" term="anti-CD4" name="anti-CD4" termAccession="N/A" />
    <fuge:OntologyIndividual identifier="anti-CD8-OntologyTerm" term="anti-CD8" name="anti-CD8" termAccession="N/A" />
    <fuge:OntologyIndividual identifier="anti-CD45R-OntologyTerm" term="anti-CD45R" name="anti-CD45R" termAccession="N/A" />
    <fuge:OntologyIndividual identifier="anti-Gr1-OntologyTerm" term="anti-Gr1" name="anti-Gr1" termAccession="N/A" />
    <fuge:OntologyIndividual identifier="anti-CD11b-OntologyTerm" term="anti-CD11b" name="anti-CD11b" termAccession="N/A" />
    <fuge:OntologyIndividual identifier="anti-CD45.1-OntologyTerm" term="anti-CD45.1" name="anti-CD45.1" termAccession="N/A" />
    <fuge:OntologyIndividual identifier="anti-CD45.2-OntologyTerm" term="anti-CD45.2" name="anti-CD45.2" termAccession="N/A" />
    
    <!-- Analytes -->
    <fuge:OntologyIndividual identifier="CD4-OntologyTerm"
      term="CD4" name="CD4" termAccession="http://www.genecards.org/cgi-bin/carddisp.pl?gene=CD4" 
      OntologySource_ref="http://www.genecards.org/cgi-bin/carddisp.pl?gene=CD4" />
    <fuge:OntologyIndividual identifier="CD8-OntologyTerm" 
      term="CD8" name="CD8" termAccession="http://www.genecards.org/cgi-bin/carddisp.pl?gene=CD8" 
      OntologySource_ref="http://www.genecards.org/cgi-bin/carddisp.pl?gene=CD8" />
    <fuge:OntologyIndividual identifier="CD45-OntologyTerm"
      term="CD45" name="CD45" termAccession="http://www.genecards.org/cgi-bin/carddisp.pl?gene=CD45" 
      OntologySource_ref="http://www.genecards.org/cgi-bin/carddisp.pl?gene=CD45" />
    <fuge:OntologyIndividual identifier="Gr1-OntologyTerm" term="Gr1" name="Gr1" termAccession="N/A" />
    <fuge:OntologyIndividual identifier="CD11b-OntologyTerm" termAccession="http://www.genecards.org/cgi-bin/carddisp.pl?gene=CD11b" 
      term="CD11b" name="CD11b" OntologySource_ref="http://www.genecards.org/cgi-bin/carddisp.pl?gene=CD11b" />
    <fuge:OntologyIndividual identifier="CD45.1-OntologyTerm" term="CD45.1" name="CD45.1" termAccession="N/A" />
    <fuge:OntologyIndividual identifier="CD45.2-OntologyTerm" term="CD45.2" name="CD45.2" termAccession="N/A" />
    <fuge:OntologyIndividual identifier="DNA_of_Membrane-compromised_Cells-OntologyTerm" term="DNA of Membrane-compromised Cells" 
      name="DNA of Membrane-compromised Cells" termAccession="N/A" />
    
    <!-- Organism details -->
    <fuge:OntologyIndividual term="male" name="male" identifier="male_OntologyTerm" 
      termAccession="PATO:0000384" 
      OntologySource_ref="http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PATO" />
    
    <fuge:OntologyIndividual term="Mus Musculus, C57BL/6J:Pep3b" name="Mus Musculus, C57BL/6J:Pep3b" identifier="MusMusculus_C57BL-6J_Pep3b" 
      termAccession="http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&amp;id=10090&amp;lvl=3&amp;keep=1&amp;srchmode=1&amp;unlock&amp;mod=1#modif" 
      OntologySource_ref="http://www.ncbi.nlm.nih.gov/Taxonomy/" />
    
    <fuge:OntologyIndividual term="computationally post acquisition" termAccession="N/A" identifier="SW_compensation" />
    <fuge:OntologyIndividual term="Biological sample" termAccession="N/A" identifier="Biological_Sample_OntologyTerm" />
    <fuge:OntologyIndividual term="Expected/analyzed types of cells: red blood cells, lymphoid and myeloid properties, Ly-5.1 vs. Ly-5.2."
      termAccession="N/A" identifier="SampleCharacteristicDescription_OntologyTerm" >
      <fuge:_descriptions>
        <fuge:Description text="Expected/analyzed types of cells: red blood cells, lymphoid and myeloid properties, 
          Ly-5.1 vs. Ly-5.2. After lysing red blood cells, samples are stained for lymphoid and myeloid properties 
          in addition to the specific form (Ly-5.1 or Ly-5.2) of the alloantigen ptprc (protein tyrosine phosphatase 
          receptor type c polypeptide) to detect donor and recipient respectively." />
      </fuge:_descriptions>
    </fuge:OntologyIndividual>
   
    <fuge:DataProperty identifier="6_months_data_property"
      term="6 months" name="6 months" termAccession="N/A" value="6" dataType="integer" />
    
    <!-- Catalog numbers as data properties -->
    <fuge:DataProperty term="Catalog Number 553648" termAccession="N/A" identifier="catalogNumber_553648" value="553648" />
    <fuge:DataProperty term="Catalog Number 553028" termAccession="N/A" identifier="catalogNumber_553028" value="553028" />
    <fuge:DataProperty term="Catalog Number 553092" termAccession="N/A" identifier="catalogNumber_553092" value="553092" />
    <fuge:DataProperty term="Catalog Number 551461" termAccession="N/A" identifier="catalogNumber_551461" value="551461" />
    <fuge:DataProperty term="Catalog Number 557397" termAccession="N/A" identifier="catalogNumber_557397" value="557397" />
    <fuge:DataProperty term="Catalog Number 553775" termAccession="N/A" identifier="catalogNumber_553775" value="553775" />
    <fuge:DataProperty term="Catalog Number 552950" termAccession="N/A" identifier="catalogNumber_552950" value="552950" />
    <fuge:DataProperty term="Catalog Number 7034" termAccession="N/A" identifier="catalogNumber_7034" value="7034" />
    
    <!-- Clone numbers as data properties -->
    <fuge:DataProperty term="Clone Number H129.19" termAccession="N/A" identifier="dp_H129.19_CloneNumber" value="H129.19" />
    <fuge:DataProperty term="Clone Number 53-6.7" termAccession="N/A" identifier="dp_53-6.7_CloneNumber" value="53-6.7" />
    <fuge:DataProperty term="Clone Number RA3-6B2" termAccession="N/A" identifier="dp_RA3-6B2_CloneNumber" value="RA3-6B2" />
    <fuge:DataProperty term="Clone Number 1A8" termAccession="N/A" identifier="dp_1A8_CloneNumber" value="1A8" />
    <fuge:DataProperty term="Clone Number M1/70" termAccession="N/A" identifier="dp_M1-70_CloneNumber" value="M1/70" />
    <fuge:DataProperty term="Clone Number A20" termAccession="N/A" identifier="dp_A20_CloneNumber" value="A20" />
    <fuge:DataProperty term="Clone Number 104" termAccession="N/A" identifier="dp_104_CloneNumber" value="104" />
    
    <!-- Wavelengths as data properties -->
    <fuge:DataProperty term="407 nm" termAccession="N/A" identifier="dp_407nm" value="407" />
    <fuge:DataProperty term="430 nm" termAccession="N/A" identifier="dp_430nm" value="430" />
    <fuge:DataProperty term="470 nm" termAccession="N/A" identifier="dp_470nm" value="470" />
    <fuge:DataProperty term="483 nm" termAccession="N/A" identifier="dp_483nm" value="483" />
    <fuge:DataProperty term="488 nm" termAccession="N/A" identifier="dp_488nm" value="488" />
    <fuge:DataProperty term="493 nm" termAccession="N/A" identifier="dp_493nm" value="493" />
    <fuge:DataProperty term="502 nm" termAccession="N/A" identifier="dp_502nm" value="502" />
    <fuge:DataProperty term="515 nm" termAccession="N/A" identifier="dp_515nm" value="515" />
    <fuge:DataProperty term="545 nm" termAccession="N/A" identifier="dp_545nm" value="545" />
    <fuge:DataProperty term="556 nm" termAccession="N/A" identifier="dp_556nm" value="556" />
    <fuge:DataProperty term="562 nm" termAccession="N/A" identifier="dp_562nm" value="562" />
    <fuge:DataProperty term="588 nm" termAccession="N/A" identifier="dp_588nm" value="588" />
    <fuge:DataProperty term="595 nm" termAccession="N/A" identifier="dp_595nm" value="595" />
    <fuge:DataProperty term="600 nm" termAccession="N/A" identifier="dp_600nm" value="655" />
    <fuge:DataProperty term="620 nm" termAccession="N/A" identifier="dp_620nm" value="620" />
    <fuge:DataProperty term="633 nm" termAccession="N/A" identifier="dp_633nm" value="633" />
    <fuge:DataProperty term="650 nm" termAccession="N/A" identifier="dp_650nm" value="650" />
    <fuge:DataProperty term="655 nm" termAccession="N/A" identifier="dp_655nm" value="655" />
    <fuge:DataProperty term="665 nm" termAccession="N/A" identifier="dp_665nm" value="665" />
    <fuge:DataProperty term="670 nm" termAccession="N/A" identifier="dp_670nm" value="670" />
    <fuge:DataProperty term="685 nm" termAccession="N/A" identifier="dp_685nm" value="685" />
    <fuge:DataProperty term="735 nm" termAccession="N/A" identifier="dp_735nm" value="735" />
    <fuge:DataProperty term="750 nm" termAccession="N/A" identifier="dp_750nm" value="750" />
    <fuge:DataProperty term="810 nm" termAccession="N/A" identifier="dp_810nm" value="810" />

    <!-- Voltages as data properties -->
    <fuge:DataProperty term="220 V" termAccession="N/A" identifier="dp_220V" value="220" />
    <fuge:DataProperty term="330 V" termAccession="N/A" identifier="dp_330V" value="330" />
    <fuge:DataProperty term="500 V" termAccession="N/A" identifier="dp_500V" value="500" />
    <fuge:DataProperty term="550 V" termAccession="N/A" identifier="dp_550V" value="550" />

    <!-- Powers as data properties -->
    <fuge:DataProperty term="15 mW" termAccession="N/A" identifier="dp_15mW" value="15" />
    
    <!-- Reagent model/make -->
    <fuge:OntologyIndividual term="BD-CD4-TxRed" termAccession="N/A" identifier="BD-CD4-TxRed_Term" />
    <fuge:OntologyIndividual term="BD-CD8-TxRed" termAccession="N/A" identifier="BD-CD8-TxRed_Term" />
    <fuge:OntologyIndividual term="BD-CD45R-APC" termAccession="N/A" identifier="BD-CD45R-APC_Term" />
    <fuge:OntologyIndividual term="BD-Gr1-PE" termAccession="N/A" identifier="BD-Gr1-PE_Term" />
    <fuge:OntologyIndividual term="BD-CD11b-PE" termAccession="N/A" identifier="BD-CD11b-PE_Term" />
    <fuge:OntologyIndividual term="BD-CD45.1-FITC" termAccession="N/A" identifier="BD-CD45.1-FITC_Term" />
    <fuge:OntologyIndividual term="BD-CD45.2-PerCP" termAccession="N/A" identifier="BD-CD45.2-PerCP_Term" />
    <fuge:OntologyIndividual term="Exalpha-DAPI" termAccession="N/A" identifier="Exalpha-DAPI_Term" />
    
    <!-- Instrumentation terms, some from OBI -->
    <fuge:OntologyIndividual term="Becton Dickinson" termAccession="N/A" identifier="BD_OntologyTerm" />
    <fuge:OntologyIndividual term="FACSAria" termAccession="OBI:OBI_0400040" identifier="OBI_0400040" 
      OntologySource_ref="http://purl.obofoundry.org/obo/obi.owl" />
    <fuge:OntologyIndividual term="Cuvette" termAccession="N/A" identifier="Cuvette_OntologyTerm" />
    <fuge:OntologyIndividual term="Band pass filter" termAccession="OBI:OBI_0400013" identifier="OBI_0400013" 
      name="Band pass filter" OntologySource_ref="http://purl.obofoundry.org/obo/obi.owl" />
    <fuge:OntologyIndividual term="Long pass filter" termAccession="OBI:OBI_0400067" identifier="OBI_0400067" 
      name="Long pass filter" OntologySource_ref="http://purl.obofoundry.org/obo/obi.owl" />
    <fuge:OntologyIndividual term="Photodiode" termAccession="OBI:OBI_0400083" identifier="OBI_0400083" 
      name="Photodiode" OntologySource_ref="http://purl.obofoundry.org/obo/obi.owl" />
    <fuge:OntologyIndividual term="Photomultiplier tube" termAccession="OBI:OBI_0400084" identifier="OBI_0400084" 
      name="Photomultiplier tube" OntologySource_ref="http://purl.obofoundry.org/obo/obi.owl" />
    <fuge:OntologyIndividual term="Solid state laser" termAccession="OBI:OBI_0400096" identifier="OBI_0400096" 
      name="Solid state laser" OntologySource_ref="http://purl.obofoundry.org/obo/obi.owl" />
    <fuge:OntologyIndividual term="HeNe laser" termAccession="OBI:OBI_0400053" identifier="OBI_0400053" 
      name="HeNe laser" OntologySource_ref="http://purl.obofoundry.org/obo/obi.owl" />
    <fuge:OntologyIndividual term="List-mode data file" termAccession="OBI:OBI_0000021" identifier="OBI_0000021" 
      name="List-mode data file" OntologySource_ref="http://purl.obofoundry.org/obo/obi.owl" />
    <fuge:OntologyIndividual term="Spillover Matrix in Gating-ML" termAccession="N/A" identifier="SpilloverMatrixInGating-ML_OntologyTerm" 
      name="Spillover Matrix in Gating-ML" />
    <fuge:OntologyIndividual term="Gating-ML File Format" termAccession="N/A" identifier="Gating-ML_File_Format_OntologyTerm" 
      name="Gating-ML File Format" />
    
    <!-- Instrumentation individuals - make/models -->
    <fuge:OntologyIndividual term="BD LP 502 filter" termAccession="N/A" identifier="BD_LP502_OntologyTerm" />
    <fuge:OntologyIndividual term="BD LP 556 filter" termAccession="N/A" identifier="BD_LP556_OntologyTerm" />
    <fuge:OntologyIndividual term="BD LP 595 filter" termAccession="N/A" identifier="BD_LP595_OntologyTerm" />
    <fuge:OntologyIndividual term="BD LP 655 filter" termAccession="N/A" identifier="BD_LP655_OntologyTerm" />
    <fuge:OntologyIndividual term="BD LP 735 filter" termAccession="N/A" identifier="BD_LP735_OntologyTerm" />
    
    <fuge:OntologyIndividual term="BD BP 450/40 filter" termAccession="N/A" identifier="BD_BP450_40_OntologyTerm" />
    <fuge:OntologyIndividual term="BD BP 488/10 filter" termAccession="N/A" identifier="BD_BP488_10_OntologyTerm" />
    <fuge:OntologyIndividual term="BD BP 530/30 filter" termAccession="N/A" identifier="BD_BP530_30_OntologyTerm" />
    <fuge:OntologyIndividual term="BD BP 575/26 filter" termAccession="N/A" identifier="BD_BP575_26_OntologyTerm" />
    <fuge:OntologyIndividual term="BD BP 610/20 filter" termAccession="N/A" identifier="BD_BP610_20_OntologyTerm" />
    <fuge:OntologyIndividual term="BD BP 660/20 filter" termAccession="N/A" identifier="BD_BP660_20_OntologyTerm" />
    <fuge:OntologyIndividual term="BD BP 675/20 filter" termAccession="N/A" identifier="BD_BP675_20_OntologyTerm" />
    <fuge:OntologyIndividual term="BD BP 780/60 filter" termAccession="N/A" identifier="BD_BP780_60_OntologyTerm" />
    
    <!--Characteristic being measured, maybe the cell ontology could be used here?  -->
    <fuge:OntologyIndividual term="T helper" termAccession="N/A" identifier="T_helper_OntologyTerm" />
    <fuge:OntologyIndividual term="T suppresor" termAccession="N/A" identifier="T_suppresor_OntologyTerm" />
    <fuge:OntologyIndividual term="B cell" termAccession="N/A" identifier="B_cells_OntologyTerm" />
    <fuge:OntologyIndividual term="Granulocyte" termAccession="N/A" identifier="Granulocytes_OntologyTerm" />
    <fuge:OntologyIndividual term="Monocyte" termAccession="N/A" identifier="Monocytes_OntologyTerm" />
    <fuge:OntologyIndividual term="Donor leukocytes" termAccession="N/A" identifier="Donor_leukocytes_OntologyTerm" />
    <fuge:OntologyIndividual term="Recipient leukocytes" termAccession="N/A" identifier="Recipient_leukocytes_OntologyTerm" />
    <fuge:OntologyIndividual term="Cell viability" termAccession="N/A" identifier="Cell_viability_OntologyTerm" />
    <fuge:OntologyIndividual term="Hematopoietic Stem Cell" termAccession="N/A" identifier="HSC_OntologyTerm" />
    <fuge:OntologyIndividual term="Kit+/sca-1+/Lineage- Hematopoietic Stem Cell" termAccession="N/A" identifier="KSL_HSC_OntologyTerm" />

    <!-- Units, is there an ontology useful for these? -->
    <fuge:OntologyIndividual term="µl" name="µl" termAccession="N/A" identifier="micro_liter_unit_OntologyTerm" />
    <fuge:OntologyIndividual term="number of cells" termAccession="N/A" identifier="Cell_Unit_OntologyTerm" />
    <fuge:OntologyIndividual term="rad (irradiation unit)" termAccession="N/A" identifier="rad_irradiation_unit_OntologyTerm" />
    <fuge:OntologyIndividual term="cells per ml" termAccession="N/A" identifier="CellsPerML_Unit_OntologyTerm" />
    <fuge:OntologyIndividual term="V (Volts)" termAccession="N/A" identifier="V_Unit_OntologyTerm" />
        
    <!-- Phenotypes and genotypes of the mice -->
    <fcm:Phenotype term="Black Pep3b Mouse" termAccession="N/A" identifier="black_Pep3b_mouse_phenotype" />
    <fcm:Phenotype term="White W41/W41 Mouse" termAccession="N/A" identifier="White_W41_W41_mouse_phenotype" />
    <fcm:Genotype term="Ly-5 Congenic C57BL-6 Mouse" termAccession="N/A" identifier="Ly-5_Congenic_C57BL-6_mouse_genotype" />
    <fcm:Genotype term="C57BL/6J W41/W41 Mouse" termAccession="N/A" identifier="C57BL/6J_W41/W41_mouse_genotype" />
 
    <fuge:OntologySource ontologyURI="http://purl.obofoundry.org/obo/obi.owl" name="OBI" identifier="http://purl.obofoundry.org/obo/obi.owl">
    </fuge:OntologySource> 
    <fuge:OntologySource ontologyURI="http://www.nlm.nih.gov/mesh/meshhome.html" name="MESH" identifier="http://www.nlm.nih.gov/mesh/meshhome.html">
    </fuge:OntologySource> 
    <fuge:OntologySource ontologyURI="http://www.drmr.com/abcon/trfspec.html" name="DRMR" identifier="http://www.drmr.com/abcon/trfspec.html">
    </fuge:OntologySource> 
    <fuge:OntologySource ontologyURI="http://www.genecards.org/cgi-bin/carddisp.pl?gene=" name="GeneCard" identifier="http://www.genecards.org/cgi-bin/carddisp.pl?gene=">
    </fuge:OntologySource>     
 
  </fuge:OntologyCollection>
  
  <fuge:Provider identifier="JSpidlen" name="Josef Spidlen (XML created in oXygen)" Software_ref="oXygen" />
  
</fuge:FuGE>