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Related Manuals for ThermoFisher Scientific invitrogen iSort Series
Summary of Contents for ThermoFisher Scientific invitrogen iSort Series
- Page 1 iSort Automated Cell Sorter ™ Catalog Number A33041 Publication Number MAN0016718 Revision A.0 For Research Use Only. Not for use in diagnostic procedures.
- Page 2 Manufacturer: Cytonome | 9 Oak Park Dr. | Bedford, MA 01730 The information in this document is subject to change without notice. DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, THERMO FISHER SCIENTIFIC AND/OR ITS AFFILIATE(S) WILL NOT BE LIABLE FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING YOUR USE OF IT.
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Page 3: Table Of Contents
Contents About this guide ........................6 1. Product information ......................7 Product description ............................7 Standard items included ..........................7 Required materials not supplied ........................8 Instrument exterior components ........................9 Graphical user interface (GUI)........................14 2. Prepare site for installation ..................... 15 Site preparation workflow ........................... - Page 4 6. Run maintenance functions ....................51 Maintenance screen ............................51 Debubble ................................. 52 Rinse ................................53 Fluidic Flush ..............................54 Damper Flush..............................55 Cleaning Cycles ............................. 56 Initial Cleaning ............................57 Sample Line Cleaning ..........................58 Sheath Fluidics Cleaning ........................61 Calibration and Performance Test screen ....................
- Page 5 Appendix D: Safety ....................... 129 Safety conventions used in this document ....................129 Symbols on instruments ..........................130 Safety labels on instruments ........................132 General instrument safety .......................... 133 Chemical safety ............................134 Chemical waste safety..........................135 Electrical safety ............................136 Physical hazard safety ..........................
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Page 6: About This Guide
About this guide Audience This user guide is for laboratory staff operating, maintaining, and analyzing data using the Invitrogen ™ iSort ™ Automated Cell Sorter. User attention Two user attention words appear in this document. Each word implies a particular level of observation or action as described below. -
Page 7: Product Information
1. Product information Product description iSort Automated The Invitrogen iSort Automated Cell Sorter (Cat. No. A33041) is a compact, ™ ™ ™ automated cell sorter designed for simplicity and affordability. The system contains Cell Sorter a 488-nm laser and is optimized for sorting cells or particles expressing GFP. The iSort ™... -
Page 8: Required Materials Not Supplied
Required materials not supplied The following table lists the materials recommended for use with the iSort ™ Automated Cell Sorter. The sample and collection tubes listed have been tested with the system. Unless otherwise indicated, all materials are available through thermofisher.com. -
Page 9: Instrument Exterior Components
Instrument exterior components Front view Touch-screen monitor Sorting compartment Power button Fluidics compartment USB port, Type A Sample pump compartment Front view with sorting compartment door open Front view with fluidics compartment door open iSort Automated Cell Sorter User Guide ™... - Page 10 Rear view HDMI port (see Important note below) Ethernet connection port USB ports, Type A (2×) Power input port USB port, Type B Air exhausts IMPORTANT! The HDMI port is used by Technical Service representatives to monitor system performance with diagnostic tools. We do not recommend attaching an external monitor to the iSort ™...
- Page 11 Sorting compartment Nozzle assembly Laser interrogation chamber Deflection plates Streamwatch camera window Collection tray (shown in out position) Collection tube holder (shown with two 12 × 75-mm tubes with 5-mL capacity; can hold any combination of 1.5-mL, 5-mL, or 50-mL tubes) Collection tubes (5-mL tubes shown) Sort chamber door (shown open) Sample tube holder (shown in down position)
- Page 12 Sample pump compartment Note: The front of the instrument is facing to the left. Top cover Sample pump dampener Sorting compartment door Sample pump Sample line Rear view of instrument with the top cover open, showing the sample pump compartment iSort Automated Cell Sorter User Guide ™...
- Page 13 Fluidics compartment Waste fluid lines (yellow) Sheath fluid pump assembly Waste container Fluidics compartment door (contains fluidics lines, filters, and the Sheath fluid container sheath pump Sheath fluid lines (clear) Fluid containers (detail) Waste container (2 L capacity) Sheath fluid container (2 L capacity) Waste fluid line with quick Sheath fluid line with quick release release connector...
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Page 14: Graphical User Interface (Gui)
Graphical user interface (GUI) The iSort ™ Automated Cell Sorter utilizes a graphical user interface (GUI) accessed by a touch-screen monitor. The integrated iSort software is pre-installed on the instrument. GUI layout and Key functions of the software (Sort, Analyze, Files, Maintenance, and Settings) are displayed on the home screen. -
Page 15: Prepare Site For Installation
2. Prepare site for installation Site preparation workflow IMPORTANT! Do not install the iSort Automated Cell Sorter yourself. A Thermo ™ Fisher Scientific representative will contact you to schedule the installation. When the installation is scheduled: Receive and inspect the system (page 19). Move the crated instrument to the installation site (page 19). -
Page 16: Pre-Installation Requirements
Pre-installation requirements Personnel Responsibilities Instrument • Reviews the site preparation guide for safety information and system maintenance personnel requirements. Coordinates personnel and tasks. • Orders required materials. • Selects the site. • Reviews checklists with appropriate personnel, then with the Thermo Fisher •... -
Page 17: Operating Environment And Site Requirements
Operating environment and site requirements • The iSort ™ Automated Cell Sorter has a footprint (W × D × H) of approximately 67 cm × 41 cm × 49 cm (26.5 in × 16 in × 19 in) with the fluidics compartment door and the top cover closed. -
Page 18: Safety Requirements
Safety requirements Safety practices A safety representative from your facility must ensure that: • Personnel establish and follow all appropriate safety practices and policies to protect laboratory personnel from potential hazards. • All appropriate safety devices and equipment are always available. Required safety The following safety protection and equipment must be available at the installation site:... -
Page 19: Materials Required For Installation
Materials required for installation • Safety glasses, lab coats, and chemical-resistant, disposable gloves (powder-free) • Lint-free tissues • Isopropanol, HPLC-grade or better • 10% bleach solution • Distilled water • 5-mL and 50-mL Polypropylene Falcon ™ tubes • 1.5-mL centrifuge tubes •... -
Page 20: Set Up
Set up IMPORTANT! The following set-up instructions are provided for informational purposes only. Do not attempt the initial set-up of the instrument on your own. Thermo Fisher Scientific service representative will install the iSort ™ Automated Cell Sorter and all of its components and provide some basic operator training. Place the After the instrument has been uncrated, verify all parts are present. -
Page 21: Startup
3. Startup Before you begin Required solutions • Sheath fluid: We recommend using sterile, flow cytometry grade 1X PBS as the carrier for transporting particles through the optical cell. • 100% bleach solution: 5.25% sodium hypochlorite in water. We recommend using laboratory-grade bleach without additives and perfumes. - Page 22 Install the nozzle Before starting up the iSort ™ Automated Cell Sorter, you must reinstall the nozzle tip that has been removed from the nozzle assembly after the last Shut Down procedure (page 98). For instructions on how to install the nozzle tip on the nozzle assembly, see page 101.
- Page 23 Check the system • Check the levels in the fluid containers in the fluidics compartment to ensure that the sheath container is full and the waste container is empty. fluidics If empty, fill the sheath container with sheath fluid. If full, empty the waste container. Before replacing, add 200 mL of full strength bleach solution (5.25% sodium hypochlorite in water) into the emptied waste container to help prevent microbial growth.
- Page 24 After detaching the fluid lines from the containers, slightly lift and pull out the containers from the fluidics compartment. Unscrew the lid and fill the sheath fluid container with the appropriate solution. The sheath fluid container has 2 L capacity, sufficient to process 5 mL of sample. Do not overfill past the 2 L line on the bottle.
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Page 25: Start Up The System
Start up the system Power on the To start up the iSort ™ Automated Cell Sorter, press the illuminated, blue power button located at the bottom-left side of the instrument (page 9) instrument When the Home Screen is displayed, the iSort ™... -
Page 26: Run Initial Cleaning
Run Initial Cleaning Overview Initial Cleaning must be performed before running the first analysis or sort of the day. The initial cleaning process takes approximately 10 minutes. It is not necessary to repeat the initial cleaning cycle before subsequent analysis or sorts. However, if the instrument remains idle for more than 30 minutes, it will prompt you to perform the initial cleaning procedure again to prepare the sample line for further analysis or sort runs. - Page 27 When prompted, place an empty 12 × 75-mm sample tube into the sample tube holder in the down position. Press Continue to begin the back flush component of the initial cleaning cycle, which removes clogs from the sample lines. When prompted, place a fresh 12 × 75-mm sample tube with 3 mL of sheath fluid into the sample tube holder, then move the sample tube holder to the up position.
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Page 28: Run Performance Test
Run Performance Test Overview The Performance Test procedure allows you to track the performance of the iSort ™ Automated Cell Sorter and verify performance against the QC criteria. The procedure requires the use of the Attune ™ Performance Tracking Beads. We recommend that you run the procedure every day to ensure that the system is performing optimally before starting your experiments. - Page 29 On the Calibration & Performance Test screen, select the Sample 4 Peaks option. Briefly vortex the vial of Attune ™ Performance Tracking Beads to mix, then prepare the performance tracking (PT) bead sample by adding the following components into a 12 × 75-mm disposable test tube. Attune Performance Tracking Beads 500 µL...
- Page 30 To review the results of previous performance tests, go to the Calibration & Performance Test screen, then press the Results tab. iSort Automated Cell Sorter User Guide ™...
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Page 31: Analyze And Sort
4. Analyze and Sort Overview The Analysis and Sort applications of the iSort ™ Automated Cell Sorter have similar workflows that contain many identical steps. Therefore, they are described together in this section. • Analysis mode (or non-sorting experiment) is designed for quick verification of sample content and can be performed independently of the Sort workflow. -
Page 32: Prepare Samples
Prepare samples Guidelines for • To maximize success, it is essential that samples are prepared in a single-cell suspension at a density of 10 –10 cells/mL and are free of aggregates. The sample preparation ideal cell concentration is cell type dependent. •... -
Page 33: System Preparation
System preparation Before starting • Make sure that the collection tray is pulled out and there are no collection tubes present. • Place an empty 12 × 75-mm tube into the sample tube holder in the down position. Choose application On the Home Screen, press Sort or Analyze to select the corresponding application. - Page 34 System Preparation System Preparation is a set of procedures that prepares the iSort ™ Automated Cell Sorter for the Analysis or Sort run and ensures optimal instrument performance. • System Preparation is initiated automatically after you have entered the operator name for the Analysis or Sort (page 33) and it takes 10–15 minutes to complete with minimal user input.
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Page 35: Load Sample
Load sample When prompted by the Insert Sample dialog (page 34), open the sort compartment door to access the sample input port and the collection area. Make sure that the sample tube holder is in the down position and the collection tray is pulled out. - Page 36 To initiate sample loading, move the sample tube holder up until it clicks into place, close the sorting compartment door, then press Continue. IMPORTANT! Cell sorting creates aerosols. Exposure to and inhalation of aerosols can potentially be hazardous depending on the cell types you are using.
- Page 37 Within 30 seconds of sample loading, the fluorescence scatter plot on the Define Region screen starts displaying the data from your sample. When you observe data displayed on the screen, you are ready to proceed with your Analysis or Sort (see “Analyze or Sort sample”, page 38). iSort Automated Cell Sorter User Guide ™...
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Page 38: Analyze Or Sort Sample
Analyze or Sort sample Overview As the cells or particles in the sample pass through the optical detection area, they are interrogated by a 488-nm laser, which generates scattered light and fluorescence signals that are displayed in the fluorescence scatter plot on the screen. Scatter plot on Define Regions screen Scatter plot on Sort screen •... - Page 39 Define regions When you observe events appearing on the scatter plot on the Define Regions screen, press the Region 1 or Region 2 button to display the corresponding region on the plot. You can select either or both of the regions to display. In the example below, Region 1 is selected.
- Page 40 Change the position and shape of the regions as necessary so that they enclose the populations of interest on the plot. • To move a region, touch anywhere inside the region, then drag it to the desired location on the plot. •...
- Page 41 Perform The majority of the steps in the Analysis and Sort workflows are identical. Therefore, the workflows are described together. Analysis/Sort • If you are running a Sort, start with Step 1. • If you are running an Analysis, directly go to Step 4 (page 42). When prompted, ensure that the collection tubes are placed in the collection tube holder (page 35), push the collection tray inward until it clicks into place.
- Page 42 To start the Analysis/Sort, press the flashing Play button. The Play button changes to the Pause button, and the counters above the plot display the current Analysis/Sort statistics (see Table 1). Sort screen - Ready Sort screen – Sorting in progress Note: The percentage that appears in a region defined on the plot is not the same as the percentage that appears in the status bar.
- Page 43 To view the statistics for the Total Count, Event Rate, or Abort Rate, press on the center counter window until the desired statistic is displayed (Abort Rate is available only in the Sort workflow). To pause the sample flow during the Analysis/Sort, press the Pause button.
- Page 44 When you are finished with your Analysis or Sort, press the Stop button. • If running Analysis, the sample flow stops and the screen displays the Analysis Complete dialog. • If running Sort, the sample flow and sorting stops, and the screen displays the Sorting Complete dialog.
- Page 45 Rinse When prompted, remove the sample tube from the tube holder, place an empty tube in the sample tube holder, then press Continue. The screen shows the progress of the rinse as the instrument flushes the fluidic lines with sheath fluid. When you are finished with the rinse, press Home to go to the Home screen.
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Page 46: Manage Files
5. Manage files Select files Select files on File Every time an Analysis or a Sort is completed, the data acquired during the run are saved in FCS 3.0 format. These files contain the raw data that can be imported Viewer into any standard flow cytometry analysis software. -
Page 47: Manage Files
Manage files Eject USB To eject the USB drive connected the instrument, press the Eject USB button on the Manage Files menu. When prompted, then remove the USB drive from the USB port. Delete FCS File To delete an FCS file, select the desired file from the File Viewer, then press the Delete FCS File button on the Manage Files menu. - Page 48 Rename FCS File The file naming convention of the iSort ™ Automated Cell Sorter is based on the date and the number of the runs completed on that date. The default file name follows the YYYYMMDD-### format, where YYYY is the year, MM is the month, and DD is the day of the run.
- Page 49 Move FCS File to Moving FCS files to a USB drive copies the files to the selected destination folder on the USB drive and deletes them from the instrument. To move FCS files save from the instrument to a USB drive, press the Move FCS File button on the Manage Files menu.
- Page 50 Copy FCS File to Copying FCS files to a USB drive places a copy of the each selected file in the destination folder on the USB drive without deleting them on the instrument. To copy FCS files save from the instrument to a USB drive, press the Copy FCS File button on the Manage Files menu.
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Page 51: Run Maintenance Functions
6. Run maintenance functions Maintenance screen The Maintenance screen allows you to execute various instrument maintenance, cleaning, and calibration functions. To access the Maintenance screen, press the Maintenance button on the Home screen. Debubble (page 52) Calibration and Performance Test (page 66) Rinse (page 52) Tubing Life (page 82) Fluidic Flush (page 54) -
Page 52: Debubble
Debubble The Debubble function is a user-initiated function for clearing air bubbles from the fluidics lines of the system. Air bubbles in the fluidics lines may cause fluctuations in the system pressure, which can result in problems with the stream from the nozzle and adversely affect droplet formation. -
Page 53: Rinse
Rinse The Rinse function removes clogs from the sample and probe lines by back flushing the lines, and can be used to prevent sample carryover between runs. Clogs in the system can affect sample flow, stream alignment, and droplet formation. Run Rinse Select Rinse from the Maintenance screen. -
Page 54: Fluidic Flush
Fluidic Flush The Fluidic Flush function washes the fluidic lines of the system with buffer or sheath fluid to prevent sample carryover between runs. Required solutions Sheath fluid (1X PBS, flow cytometry grade) Run Fluidic Flush Select Fluidic Flush from the Maintenance screen. Place a new tube containing 3 mL of sheath fluid or buffer in the sample tube holder. -
Page 55: Damper Flush
Damper Flush The Damper Flush function removes contamination from the pulse damper in the sample line. Required solutions Sheath fluid (1X PBS, flow cytometry grade) Run Damper Flush Select Damper Flush from the Maintenance screen. Place a new tube containing 3 mL of sheath fluid in the sample tube holder. Move the sample tube holder up until it clicks into place, then press Continue. -
Page 56: Cleaning Cycles
Cleaning Cycles Cleaning Cycles Cleaning Cycles screen allows you to run Initial Cleaning, Sample Line Cleaning, and Sheath Fluidics Cleaning (decontamination) functions. screen Initial Cleaning (page 57) Sample Line Cleaning (page 58) Sheath Fluidics Cleaning (page 61) To access the Cleaning Cycles screen, press Cleaning Cycles on the Maintenance screen. -
Page 57: Initial Cleaning
Initial Cleaning Overview Initial Cleaning is required before the first analysis or sort of the day. It is not necessary to repeat the initial cleaning before the subsequent analysis or sort runs. However, if the instrument remains idle for more than 30 minutes, you will be prompted to perform the initial cleaning again to prepare the sample line for further runs. -
Page 58: Sample Line Cleaning
Sample Line Cleaning Overview Sample Line Cleaning is a four step cleaning sequence that sanitizes and rinses the sample lines of the system to prevent cross-contamination and carryover between samples. The procedure is similar to the cleaning procedure used in the Shut Down procedure (page 88), but the instrument does not power off when the cycle is completed. - Page 59 When prompted, press Continue to begin the sample line cleaning. When prompted, place a tube containing 3 mL of 10% bleach solution into the sample tube holder. Move the sample tube holder up until it stops, then press Continue to initiate the first step of the cleaning process.
- Page 60 When prompted, remove the tube containing the Attune ™ Wash Solution from the sample tube holder, and replace with a tube containing deionized water. Move the sample tube holder up until it stops, then press Continue to initiate the third step of the cleaning process. When prompted at the completion of the third step of the cleaning process, click Continue to initiate the fourth step.
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Page 61: Sheath Fluidics Cleaning
Sheath Fluidics Cleaning Overview Sheath Fluidics Cleaning is used for decontaminating the fluidics lines of the iSort ™ Automated Cell Sorter. Running the sheath fluidics cleaning also requires you to change the 0.2-µm sheath fluid filter. The entire procedure takes approximately 2 hours to complete. - Page 62 When prompted, ensure that you have all of the required materials at hand to perform the sheath fluidics cleaning, then press Continue. The instrument will pressurize the fluidics system and initiate the sheath fluidics cleaning. When prompted, remove the sample tube (if present) from the sample tube holder and replace it with an empty tube.
- Page 63 When the damper flush is completed, the instrument drains the sheath fluid from the fluidics lines and internal reservoirs into the waste container. When prompted, fill a new sample tube with 5 mL of cleaning solution (10% bleach solution), place it in the sample tube holder, then move the sample tube holder in the up position.
- Page 64 12. When prompted, empty the waste container and the sheath fluid container holding the remaining cleaning solution. 13. Thoroughly rinse the sheath fluid container to remove any traces of the cleaning solution, then completely fill it up with deionized water (~ 2 L). 14.
- Page 65 18. Move the sample tube holder in the up position, then press Continue to begin the damper flush cycles. The instrument performs three cycles of damper flush. 19. At the completion of the first and second damper flush cycles, the instrument prompts you to place a new sample tube containing 3 mL of sheath fluid in the sample tube holder in the up position.
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Page 66: Calibration And Performance Test Screen
Calibration and Performance Test screen The Calibration and Performance Test screen contains the controls to run the daily performance test and perform various calibration functions. Performance Test (page 67) Flow Rate Calibration (page 74) Drop Delay Calibration (page 68) Gimbal Adjustment (page 78) To access the Calibration and Performance Test screen, select the Calibration &... -
Page 67: Performance Test
Performance Test Overview The Performance Test procedure allows you to track the performance of the iSort ™ Automated Cell Sorter and verify it against the QC criteria. The procedure requires the use of the Attune ™ Performance Tracking Beads. IMPORTANT! We recommend that you run the procedure every day to ensure that the system is performing optimally before starting your experiments. -
Page 68: Drop Delay Calibration
Drop Delay Calibration Overview The drop delay value represents the distance between the point of interrogation of the sample and the exact point where the sample stream breaks off into droplets that contain the particle of interest. Therefore, the stability of the break-off dictates the accuracy of the sorting. - Page 69 When prompted, press Continue to initiate the calibration process. If you are not authorized to run the Drop Delay Calibration, press Cancel to abort the operation. If needed, the instrument will prompt you to prepare the sample line. To prepare the sample line, press Continue. To proceed with Drop Delay Calibration without preparing the sample line, press Skip.
- Page 70 Make sure that the collection tray is pulled out, then press Continue. When prompted, add Attune Performance Tracking Beadst in a sample tube, ™ then place the sample tube with the calibration beads in the tube holder. Push the tube holder upward until it stops, then press Continue to start the sample flow.
- Page 71 11. On the Drop Delay Calibration screen, verify the presence of the calibration beads in the fluorescence scatter plot. 12. Ensure that the event rate counter located above the scatter plot registers an event rate of between 100 and 500, then press Continue.
- Page 72 14. When prompted, examine the puddles deposited on the slide under a fluorescent microscope for the first calibration point: Using a fluorescent microscope, count the calibration beads in the left and right puddles. b. Enter the number of the beads in the left and right puddles using the dropdown menus on the touchscreen.
- Page 73 17. After the instrument adjusts the calibration parameters based on the final calibration point, the instrument displays the “Drop Delay Calibration Successful” message. 18. Press Home to complete the Drop Delay Calibration procedure. 19. When prompted, replace the sample tube with the calibration beads with an empty tube in the tube holder, then press Continue to start the final rinse procedure.
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Page 74: Flow Rate Calibration
Flow Rate Calibration Overview The Flow Rate Calibration function allows authorized users and service personnel to troubleshoot and fine tune the flow rate value. The sample flow rate of the iSort ™ Automated Cell Sorter is fixed at 1.4 mL per hour and cannot be adjusted. - Page 75 When prompted to prepare the Performance Test sample, briefly vortex the vial of Attune ™ Performance Tracking Beads to mix, then add the following components into a 12 × 75-mm disposable test tube. Attune ™ Performance Tracking Beads 500 µL 5% Tween 20 in deionized water 2 µL...
- Page 76 Make sure that the collection tray is pulled out, then press Continue. When prompted, place the sample tube with the performance tracking beads in the tube holder, push the tube holder upward until it stops, then press Continue to start the sample flow When prompted, enter the calibration sample volume (200–4500 µL) using the numeric keypad on the touchscreen, then press Finished.
- Page 77 On the Flow Rate Calibration screen, verify the presence of the performance tracking beads in the fluorescence scatter plot, which consist of equal concentrations of beads of four fluorescence emission intensities. 10. After the instrument automatically adjusts the flow rate calibration parameters, it displays the “Recalibration Successful”...
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Page 78: Gimbal Adjustment
Gimbal Adjustment Overview The Gimbal Adjustment function allows you to manually adjust the position and the tilt of the nozzle stage so that the sample stream is properly aligned with the system optics. The alignment is accomplished by means of the three gimbal knobs located on the nozzle stage. - Page 79 When prompted, press Proceed to begin the Gimbal Adjustment process. If you are not authorized to adjust the nozzle gimbal, press Cancel to abort the operation. Make sure that the collection tray is pulled out, then press Continue. The instrument automatically aligns the stream before guiding you through the gimbal adjustment process.
- Page 80 When prompted, press Continue to repeat the automatic Jet Align procedure. Note: Any adjustment made to the nozzle gimbal requires the repeat of the Jet Align procedure. When prompted, turn the Gimbal knobs A and B as instructed on the screen, then press Continue.
- Page 81 After completing the alignment, the instrument automatically measures the nozzle tilt to ensure that it is within specifications, then measures the gimbal angle. 10. If further adjustments are required, the instrument provides you with the necessary instructions, and rechecks the nozzle tilt for proper alignment. Follow the instructions provided until the instrument displays the “Gimbal Adjustment Passed”...
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Page 82: Tubing Life
Tubing Life Tubing Life screen The Tubing Life screen allows you to check the remaining tubing life for the sample, sheath, and waste pumps, and to reset the tubing life counter after replacement. To access the Tubing Life screen, press Tubing Life on the Maintenance screen. Check remaining On the Tubing Life screen, select Sample Pump, Sheath Pump, or Waste Pump to check the remaining tubing life for the corresponding pump. - Page 83 The instrument displays the remaining tubing life for the selected pump. Click Continue to return to the Tubing Life screen. Reset tubing life IMPORTANT! Make sure that you reset the tubing life counter after replacing the counter tubing for the sample, sheath, or the waste pump. Reset the counter only after you have replaced the existing tubing.
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Page 84: System Update
System Update System Update The System Update screen allows you to update the firmware and software for the iSort ™ Automated Cell Sorter. screen To access the System Update screen, press System Update on the Maintenance screen. Firmware and Periodically, Thermo Fisher Scientific makes improvements to the iSort ™... - Page 85 Update firmware Insert the USB flash drive containing the latest iSort ™ firmware version into the USB port located at the front of the instrument (see page 9). On the System Update screen, select Firmware Update to open the Firmware Update screen. Select the latest iSort ™...
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Page 86: View Log
View Log View Log screen The iSort ™ Automated Cell Sorter keeps track of actions and errors that occur in the software and saves them as a searchable list accessible through the View Log screen. You can use the log for troubleshooting and, if necessary, reference it when consulting Technical Support. -
Page 87: Remote Service
Remote Service Overview Remote Service screen allows you to download and launch the Remote Service application. Remote Service application is a real-time remote instrument diagnostics tool that allows our service engineers and the Remote Service Center support team to help get a failed instrument up and running as quickly as possible using remote monitoring and diagnostic tools. -
Page 88: Shut Down
7. Shut Down Daily Shut Down You must perform the Shut Down procedure after the last Analysis or Sort of the day, then remove the nozzle tip for cleaning and storage. The Shut Down procedure sanitizes the system fluidics with 10% bleach solution, flushes it with a detergent solution, then rinses it with deionized water to complete the cleaning process. - Page 89 Press Continue to confirm the Shut Down. The instrument initiates the Shut Down procedure. When prompted, place a tube containing 3 mL of 10% bleach solution into the sample tube holder. Move the sample tube holder up until it stops, then press Continue to start the Shut Down Cleaning –...
- Page 90 When prompted, remove the tube containing the Wash Solution from the sample tube holder, and replace with a tube containing deionized water. Move the sample tube holder up until it stops, then press Continue to initiate the Shut Down Cleaning – Step 3. After completing the Shut Down Cleaning –...
- Page 91 Prepare instrument When the Shut Down procedure is completed and the system is powered off, leave the sample tube of deionized water in the sample tube holder in the up for Shut Down position. Remove the nozzle from the holder, then remove the nozzle tip from the nozzle assembly, and clean it in an ultrasonic bath (sonicator) as described on page 98.
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Page 92: Settings
8. Settings Settings screen The Settings screen allows you to start and stop fluid flow, set Stop Analysis criteria, and review system version information. To access the Settings screen, press the Settings button on the Home screen. • To save the changes that you have made in the Settings screen as default, press Save as Default. - Page 93 About (Version To view system version information about the iSort ™ Automated Cell Sorter, press About on the Settings Screen. Information) The Version Information screen opens and shows the Build Number, FPGA Firmware Version, and BoB (Break Out Board) Version information for the system.
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Page 94: Instrument Care And Maintenance
9. Instrument care and maintenance Planned maintenance schedule To ensure reliability of the iSort ™ Automated Cell Sorter, you must perform basic preventative maintenance procedures on a regular basis. In addition, certain maintenance and parts replacement procedures must be performed by the Thermo Fisher Scientific field service engineers (FSE) annually. The following table lists the routine maintenance procedures that keep the iSort ™... - Page 95 Procedure Frequency Materials required User Clean or replace waste and As needed Full strength bleach solution (5.25% sodium sheath bottles hypochlorite), 10% bleach solution, distilled water, iSort Waste Bottle (Cat. No. A33412), ™ iSort Sheath Bottle (Cat. No. A33413) ™...
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Page 96: General Care
General care • When cleaning optical elements, use only optical-grade materials to avoid scratching soft lens coatings. We recommend using TexWipe ™ TX761MD Microdenier Swabs (Cat. No. A36701) and deionized water. • Use the appropriate cleaning solutions for each component, as indicated in the instructions for cleaning and decontamination. - Page 97 Remove and clean The deflection plates must be removed and cleaned on a regular basis to prevent any buildup of deposits. Significant buildup of sheath fluid deposits due to clogs the deflection or misalignment of the nozzle tip can cause arcing between the deflection plates, plates which can damage the instrument.
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Page 98: Remove And Clean The Nozzle Tip
Remove and clean the nozzle tip Overview The nozzle is responsible for accepting sample and sheath flows, for producing a focused and stable stream through the 85-µm nozzle tip, and for creating and charging droplets. For optimal performance, the nozzle tip must be removed and cleaned in an ultrasonic cleaning bath following instrument Shut Down at the end of the day. - Page 99 Unscrew the small black cap that secures the nozzle tip to the nozzle assembly using the torque wrench provided with the instrument. Remove the ceramic nozzle tip and the O-ring. IMPORTANT! Be very careful when handling the nozzle tip. Hold the nozzle tip only by its base and never handle it with bare hands.
- Page 100 While the nozzle tip is in the ultrasonic cleaning bath, loosely screw the small black cup back on the nozzle assembly, then cover it with the black rubber protector containing deionized water. If you have removed the nozzle tip after performing the Shut Down operation (page 88), store the nozzle tip in the detergent solution at room temperature until the next time you need to use the instrument.
- Page 101 Reinstall the nozzle IMPORTANT! Hold the nozzle tip only by its base and never handle it with bare hands. Always use clean gloves when handling the nozzle tip. Rinse the nozzle tip with deionized water, then reinsert it into the nozzle assembly.
- Page 102 Tighten the black cap with the torque wrench (provided with the instrument) until you hear two clicks. Do not overtighten. Note: Loose coupling of the nozzle tip to the nozzle assembly can result in decreased system performance. Reinsert the nozzle assembly into the Nozzle stage. The nozzle assembly should snap into place by the magnetic fastener.
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Page 103: Replace Peristaltic Pump Tubing
Replace peristaltic pump tubing The peristaltic pump tubing for the sample and sheath pumps is a consumable part and requires regular replacement for the instrument to continue normal operation. Additionally, all other tubing in the system can be replaced by a trained technician, if there are concerns relating to the cleanliness of the tubing or contamination. -
Page 104: Replace Sample Pump Tubing
Replace sample pump tubing In general, we recommend that you replace peristaltic pump tubing for the sample line (Cat. No. A33303) when prompted by the instrument. Normally, the sample pump tubing needs to be replaced every 10 weeks based on 20 hours per week average run time (or every 200 hours of run time). - Page 105 Remove the shoe that secures the sample line to the rollers on the back of the sample pump. To do this, push the left arm of the shoe inward to release the notch that secures it to the pump assembly and rotate the shoe away from the pump, then pull the shoe away from the rollers.
- Page 106 Remove the bracket that secures the sample tube dampener and the fluidic lines to the instrument. Unscrew the sample pump dampener and detach from the instrument. Unscrew the screw above the Lucite block that secures the sample line to the instrument.
- Page 107 Remove the dampener and the sample pump tubing from the instrument. Install new sample Attach the new sample pulse dampener into the remaining tubing, then place the sample pulse damper back into its holder. pump tubing Make sure that the sample pulse dampener is upright, then attach the bracket that secures the sample tube dampener and the fluidic lines to the instrument.
- Page 108 Insert the sample line through the screw and the clear Lucite block that secures the sample injection port to the instrument. When the sample line is positioned correctly, tighten the screw. Insert the sample pump tubing into the shoe, making sure that the tubing remains slack.
- Page 109 When you are finished replacing the sample pump tubing, close the top the cover and the sorting compartment door, then power on the instrument. In the MaintenanceTubing Life screen, select Sample Pump. In the Sample Pump Life dialog, press Replacement Complete to reset the sample tube life counter to 100%.
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Page 110: Replace Sheath Pump Tubing
Replace sheath pump tubing In general, we recommend that you replace peristaltic pump tubing for the sheath line (Cat. No. A33297) when prompted by the instrument. Normally, the sample pump tubing needs to be replaced every 10 weeks based on 20 hours per week average run time (or every 200 hours of run time). - Page 111 To release the sheath pump tubing from the pump roller assembly, swing the locking lever clockwise and out of the slot in the clamping bracket, as indicated by the yellow arrow. Sheath line pump tubing Clamping bracket Pump roller assembly Locking lever Swing the clamping bracket away from the pump roller assembly, as indicated by the yellow arrow.
- Page 112 Gently pull the fittings that connect the tubing to the sheath fluid lines towards you, then out to the side until all four fittings are freed from the pump assembly. Gently lift the sheath pump tubing and remove it from the pump roller assembly.
- Page 113 After you have removed both sheath pump tubes from the pump roller assembly, twist and pull apart the fittings to disconnect the sheath pump tubes from the fluid lines (clear lines). Discard the used sheath pump tubing. Install new sheath To connect the new sheath pump tubing (Cat.
- Page 114 Insert the fittings into the bottom slots in the pump assembly to secure them. Align the sheath pump tubing to the center of bottom rollers, keeping it away from the edges where it could possibly get pinched or caught in a gap. Repeat the process for the top set of the sheath pump tubing, gently sliding it into position and centering it within the top rollers.
- Page 115 Swing the locking lever counterclockwise and engage it with the slot in the clamping bracket to secure the sheath pump tubing within the pump roller assembly. When you are finished replacing the sheath pump tubing, close the fluidics compartment door, then power on the instrument. In the MaintenanceTubing Life screen, select Sheath Pump.
- Page 116 11. After replacing the sheath pump and sheath tubing, sheath fluid must flow for 20 minutes to calibrate the new tubing. When prompted, prompted, press Continue to start the flow. Note: If you press Cancel, the tubing lifetime counter will not be reset. 12.
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Page 117: Replace Fluidics Filters
Replace fluidics filters Replace sheath inlet The 0.2-µm sheath inlet filter (Cat. No. A33307) is located in the sheath fluid line between the sheath fluid container and the sheath pump. It should be replaced each filter time sheath fluidics cleaning is performed (page 60). Sheath fluid container Sheath fluid line 0.2-µm sheath inlet filter... - Page 118 Remove the sheath inlet filter from the sheath line by disconnecting the Luer fittings on each end. Attach the replacement 0.2-µm sheath inlet filter (Cat. No. A33307) by connecting the Luer fittings to the sheath lines on each end. Note: The 0.2-µm sheath inlet filter is directional. Make sure that the blue arrow on the filter is aligned with the fluid flow and it is pointing to the sheath pump.
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Page 119: Appendix A: Troubleshooting
Appendix A: Troubleshooting Use the following flowcharts to troubleshoot issues that may be encountered when operating the iSort ™ Automated Cell Sorter. For additional information, refer to the tables that follow the flowcharts (pages 124–125). If you are unable to resolve the issue with the information provided or there are any other questions or concerns, contact Technical Support (page 139). - Page 120 iSort Automated Cell Sorter User Guide ™...
- Page 121 iSort Automated Cell Sorter User Guide ™...
- Page 122 iSort Automated Cell Sorter User Guide ™...
- Page 123 iSort Automated Cell Sorter User Guide ™...
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Page 124: Error Messages And Warnings
The following tables list a number of issues that may be encountered when operating the iSort ™ Automated Cell Sorter. Symptoms, possible causes, and recommended actions are provided. If you are unable to resolve the issue with the information provided or there are any other questions or concerns, contact Technical Support (page 139). -
Page 125: Fluidics Issues
Fluidics issues Observation Possible cause Recommended action System preparation fails Sheath pump tubing is worn Replace the Sheath pump tubing. before completing the out. checking pressure step. Error Message: Flow instability Air bubbles in the system, The System will attempt another Debubble detected. -
Page 126: Appendix B: Technical Specifications
Appendix B: Technical specifications Note: Technical specifications of the iSort ™ Automated Cell Sorter are subject to change without notice. For the latest product information, see the product page at thermofisher.com/iSort. Physical Dimensions (H × D × W): 49 × 41 × 67 cm (19 × 16 × 26.5 inches) characteristics Weight: 41 kg (89 lb) Footprint: Approximately 92 cm ×... - Page 127 Sort performance Automation: Auto alignment (auto drop delay calibration, auto droplet monitoring, auto stream to laser alignment) Sort technology: Jet-in air Sort purity: >99% (sample dependent; see Note below) Sensitivity: <250 molecules of equivalent fluorescein Signal dynamic range: 1 to 10,000 (4 orders of magnitude) Note: Sort purity is dependent on sample preparation and experimental protocol.
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Page 128: Appendix C: Ordering Information
Appendix C: Ordering information Accessory products The following accessory products and consumables for use with the iSort ™ Automated Cell Sorter are available separately from Thermo Fisher Scientific. For and consumables more information, go to thermofisher.com or contact Technical Support (page 139). Product Amount Cat. -
Page 129: Appendix D: Safety
Appendix D: Safety Safety conventions used in this document Safety alert words Three safety alert words appear in this document at points where you need to be aware of relevant hazards. Each alert word—CAUTION, WARNING, DANGER— implies a particular level of observation or action, as defined below: CAUTION! –... -
Page 130: Symbols On Instruments
Symbols on instruments Electrical symbols The following table describes the electrical symbols that may be displayed on Thermo Fisher Scientific instruments. on instruments Symbol Description Indicates the On position of the main power switch. Indicates the Off position of the main power switch. Indicates a standby switch by which the instrument is switched on to the Standby condition. - Page 131 Safety symbols The following table describes the safety symbols that may be displayed on Thermo Fisher Scientific instruments. Each symbol may appear by itself or in combination with text that explains the relevant hazard (see “Safety labels on instruments”). These safety symbols may also appear next to DANGERS, WARNINGS, and CAUTIONS that occur in the text of this and other product- support documents.
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Page 132: Safety Labels On Instruments
Safety labels on instruments The following CAUTION, WARNING, and DANGER statements may be displayed on Thermo Fisher Scientific instruments in combination with the safety symbols described in the preceding section. Hazard English Français Symbol CAUTION! Hazardous chemicals. Read the ATTENTION! Produits chimiques dangereux. Safety Data Sheets (SDSs) before handling. -
Page 133: General Instrument Safety
General instrument safety WARNING! PHYSICAL INJURY HAZARD. Use this product only as specified in this document. Using this instrument in a manner not specified by Thermo Fisher Scientific may result in personal injury or damage to the instrument. Moving and lifting CAUTION! PHYSICAL INJURY HAZARD The instrument is to be moved and the instrument... -
Page 134: Chemical Safety
Chemical safety Chemical hazard WARNING! CHEMICAL HAZARD. Before handling any chemicals, refer to warning the Safety Data Sheet (SDS) provided by the manufacturer, and observe all relevant precautions. WARNING! CHEMICAL HAZARD. All chemicals in the instrument, including liquid in the lines, are potentially hazardous. Always determine what chemicals have been used in the instrument before changing reagents or instrument components. -
Page 135: Chemical Waste Safety
Chemical waste safety Chemical waste CAUTION! HAZARDOUS WASTE. Refer to Safety Data Sheets (SDSs) and hazard local regulations for handling and disposal. Chemical waste To minimize the hazards of chemical waste: safety guidelines • Read and understand the Safety Data Sheets (SDSs) provided by the manufacturers of the chemicals in the waste container before you store, handle, or dispose of chemical waste. -
Page 136: Electrical Safety
Electrical safety DANGER! ELECTRICAL SHOCK HAZARD. Severe electrical shock can result from operating the iSort Automated Cell Sorter without its instrument ™ panels in place. Do not remove instrument panels. High‐voltage contacts are exposed when instrument panels are removed from the instrument. Fuses WARNING! FIRE HAZARD. -
Page 137: Physical Hazard Safety
Physical hazard safety Moving parts WARNING! PHYSICAL INJURY HAZARD. Moving parts can crush and cut. Keep hands clear of moving parts while operating the instrument. Disconnect power before servicing the instrument. Biological hazard safety WARNING! BIOHAZARD. Biological samples such as tissues, body fluids, and blood of humans and other animals have the potential to transmit infectious diseases. -
Page 138: Safety And Electromagnetic Compatibility (Emc) Standards
Safety and electromagnetic compatibility (EMC) standards This instrument has been tested and founded to be in compliance with applicable requirements of the following safety and electromagnetic standards: • IEC 61010-1:2010 (3 Ed.), EN 61010-1:2010 (3 Ed.). Electrical Equipment for Measurement, Control, and Laboratory Use – Part 1: General Requirements. •... -
Page 139: Documentation And Support
Documentation and support Obtaining support Technical support For the latest services and support information for all locations, visit www.thermofisher.com. At the website, you can: • Access worldwide telephone and fax numbers to contact Technical Support and Sales facilities • Search through frequently asked questions (FAQs) •... - Page 140 thermofisher.com/support | thermofisher.com/askaquestion thermofisher.com 19 October 2018...
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