C-989-100-12 (1) Chapter 1 Multi-Application Overview Chapter 2 Cell Sorter Preparation Operator’s Guide Chapter 3 Basic Operation Chapter 4 Configuring Experiments Chapter 5 Analysis Chapter 6 Sorting Chapter 7 Window Description Chapter 8 Maintenance Appendix A Operating Principles Appendix B Miscellaneous Index Software Version 3.0 LE-MA900 Series Table of Contents Using the PDF Manual .......................................................... 8 Model Name and Function Table ......................................... 9 Components and Documentation ...................................... 10 Chapter 1 Overview Main Features ...................................................................... 11 Cell Sorter Block Diagram .................................................. 13 System Configuration ......................................................... 14 Name and Function of Parts ............................................... 15 Front Panel ............................................................................... 15 Internal View (Front) ............................................................... 16 Internal View (Side) ................................................................. 22 Rear Panel ................................................................................ 23 Fluidics Cart ............................................................................. 25 Sorting chip .............................................................................. 27 Main Window ........................................................................... 29 Cell Sorter Software Operating Environment ................... 30 LCD Monitor ......................................................................... 31 Chapter 2 Preparation Checking Device Connections ........................................... 32 Preparing a Sample ............................................................. 34 Loading a Sample Tube in a Sample Tube Holder .................. 34 Preparing Automatic Setup Beads ............................................ 34 Sample Temperature Control ................................................... 34 Preparing Collection Tubes and Plates ............................. 36 Attaching the Splash Guard (for use with multi-well plates) (LE-MA900P) ............................................................... 37 Loading a Multi-well Plate (LE-MA900P) .............................. 38 Loading a 384-well PCR Plate (LE-MA900P) ........................ 38 Removing and Attaching the Plate Holder Adapter (LE-MA900P) ............................................................... 38 Configuring Users ............................................................... 39 Adding Users ............................................................................ 39 Editing User Settings ................................................................ 40 Changing Passwords ................................................................ 40 Setting a Cleaning Reminder ............................................. 41 2 Table of Contents Chapter 3 Basic Operation Workflow .............................................................................. 43 System Startup .................................................................... 44 Logging In ............................................................................ 45 Configuring the Instrument ................................................ 46 Using the Sorting Chip .............................................................46 De-bubbling the Sheath Filter ............................................ 48 Cleaning the Sample Line .................................................. 49 Running Automatic Calibration ......................................... 49 Running QC ......................................................................... 51 Running Daily QC ....................................................................51 Running Performance QC ........................................................52 Creating an Experiment ...................................................... 53 Creating a New Experiment .....................................................53 Acquiring Data .................................................................... 55 [Acquisition] Tab Main Functions ...........................................56 Controlling Data Acquisition and Recording ...........................56 Customizing the Worksheet .....................................................57 Analyzing Data .................................................................... 57 Sorting ................................................................................. 59 Sorting into 15 ml Tubes (2-way) ............................................59 Sorting into 5 ml Tubes (4-way) ..............................................61 Sorting into Multi-well Plates (LE-MA900P) ..........................63 Compensating Fluorescence Spillover ............................. 66 Probe Wash ......................................................................... 70 Shutting Down ..................................................................... 70 Shutting Down the Main Unit and Software ............................70 Cleaning the Sheath Line and Shutting Down .........................71 Specifying User Preferences ............................................. 72 Exchanging the Sorting Chip ............................................. 73 Inheriting Auto Calibration Results Between Users ........ 74 Updating the Bead Lot File ................................................ 76 Backing Up/Restoring the Database ................................. 76 Backing up the Database ..........................................................76 Restoring a Database ................................................................77 Chapter 4 Configuring Experiments Creating a Customized Experiment .................................. 78 Configuring an Experiment ................................................ 81 Editing an Experiment ........................................................ 83 Editing a Sample Group ...........................................................83 Editing a Sample Tube .............................................................83 Changing Component Settings .................................................83 Exporting/Importing an Experiment .................................. 84 Exporting an Experiment ..........................................................84 Table of Contents 3 Importing an Experiment ......................................................... 84 Sharing Experiments .......................................................... 85 Searching Experiments ...................................................... 85 Saving Tube Data as FCS Files .......................................... 86 Saving an Experiment as a Template ................................ 87 Configuring Detector Settings ........................................... 87 Basic Configuration Method .................................................... 87 Loading Reference Data Method ............................................. 88 Adjusting Fluorescence Compensation ............................ 90 Using a Target Gate in the Gate Hierarchy .............................. 90 Adjusting the Spillover Matrix Manually ................................ 90 Chapter 5 Analysis Adding a Plot ....................................................................... 93 Editing Plots ........................................................................ 94 Changing Plot Type .................................................................. 95 Changing the Histogram Display View ................................... 95 Duplicating a Plot ..................................................................... 96 Removing a Plot ....................................................................... 96 Changing Axis Scale Type ....................................................... 96 Changing the Axis Parameters ................................................. 97 Adjusting Scale Ranges ............................................................ 97 Adding Gates ....................................................................... 99 Adding a Gate ........................................................................... 99 Copying a Gate ....................................................................... 100 Using Boolean Gates .............................................................. 100 Editing Gates ..................................................................... 102 Displaying Multiple Plots Overlaid .................................. 103 Displaying Plots Overlaid (Overlay Display) ........................ 104 Customizing the Overlay Display .......................................... 105 Deleting Overlay Layers ........................................................ 106 Displaying Statistics ......................................................... 106 Chapter 6 Sorting Sorting Mode ..................................................................... 108 Overview ................................................................................ 108 Single Cell Mode .................................................................... 110 Normal Mode ......................................................................... 110 Semi-Purity Mode .................................................................. 110 Purity Mode ...........................................................................