Thermo Scientific Ion GeneStudio S5 User Manual
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Thermo Scientific Ion GeneStudio S5 User Manual

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Ion GeneStudio S5 Instrument
USER GUIDE
for use with:
Ion GeneStudio S5 Instrument
Ion GeneStudio S5 Plus Instrument
Ion GeneStudio S5 Prime Instrument
Catalog Numbers A38194, A38195, A38196
Publication Number MAN0017528
Revision A.0
For Research Use Only. Not for use in diagnostic procedures.

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Summary of Contents for Thermo Scientific Ion GeneStudio S5

  • Page 1 Ion GeneStudio S5 Instrument USER GUIDE for use with: Ion GeneStudio S5 Instrument Ion GeneStudio S5 Plus Instrument Ion GeneStudio S5 Prime Instrument Catalog Numbers A38194, A38195, A38196 Publication Number MAN0017528 Revision A.0 For Research Use Only. Not for use in diagnostic procedures.
  • Page 2 Description 5 January 2018 New instrument user guide that includes instructions for Ion GeneStudio S5 Series instrument operation and maintenance. Important Licensing Information: These products may be covered by one or more Limited Use Label Licenses. By use of these products, you accept the terms and conditions of all applicable Limited Use Label Licenses.

  • Page 3: Table Of Contents

    Ion GeneStudio S5 System component positions ........
  • Page 4 Chemical safety ..............60 Ion GeneStudio S5 Instrument User Guide...
  • Page 5 Customer and technical support ..........62 Ion GeneStudio S5 Instrument User Guide...

  • Page 6: About This Guide

    A38194), Ion GeneStudio S5 Plus (Cat. No. A38195), and Ion GeneStudio S5 Prime (Cat. No. A38196) Sequencers. Note: In this user guide, Ion GeneStudio S5 Sequencer or System refers generically to the three Ion GeneStudio S5 Sequencers or Systems, unless otherwise specified.

  • Page 7: Chapter 1 Product Information

    Product information Contents The Ion GeneStudio S5 (Cat. No. A38194), Ion GeneStudio S5 Plus (Cat. No. A38195), and Ion GeneStudio S5 Prime (Cat. No. A38196) Systems contain the following boxes and components. Ion GeneStudio S5 System (Cat. No. A38194) Components Part No.

  • Page 8: Required Materials And Equipment Not Supplied

    2500 W output or higher. Must fit standard 1.5- and 0.2-mL microcentrifuge tubes and generate 15,500 × As needed to connect laboratory vacuum to liquid trap and liquid trap to P200 pipette tip. Ion GeneStudio S5 Instrument User Guide...

  • Page 9: Instrument Installation By Trained Personnel Only

    Instrument vibration and clearances IMPORTANT! Significant vibration during sequencing may add noise and reduce the quality of the measurements. The Ion GeneStudio S5 System must be installed on a bench that is free from vibrations or in contact with equipment that can cause vibrations to the bench (freezers, pumps, and other similar equipment).

  • Page 10: Chapter 2 System Components

    System components Ion GeneStudio S5 System component configuration and layout The Ion GeneStudio S5 Sequencer uses a virtual server, and the Ion GeneStudio S5 Plus Sequencer is equipped with an internal Torrent Server. These instruments are not connected to an external Torrent Server. The Ion GeneStudio S5 Prime System includes the Ion GeneStudio S5 Prime Sequencer and an external Torrent Server.

  • Page 11: Internet Connectivity

    USB device that require correction of the faulty update is not covered by your Ion GeneStudio S5, Ion GeneStudio S5 Plus, or Ion GeneStudio S5 Prime Sequencer warranty or any service contract you may have bought.

  • Page 12: Ion Genestudio S5 System Component Positions

    Chapter 2 System components Ion GeneStudio S5 System component positions support. Without remote access, service personnel cannot access, view, and troubleshoot problems regarding machine performance. To enable full support, the Torrent Server must have outbound internet access (ports 22, 80, and 443) and be behind an appropriately configured firewall. Although not recommended, you can enable access to the Torrent Browser (the web server running on the Torrent Server from the Internet).

  • Page 13: Ion Genestudio S5 Sequencer Input And Output Connections

    Chapter 2 System components Ion GeneStudio S5 Sequencer input and output connections Ion GeneStudio S5 Sequencer input and output connections USB ports – Connects a USB device to the instrument. Ethernet port – An RJ45 port that provides Ethernet (Gigabit) communication between the sequencer and a local area network.

  • Page 14: Chapter 3 Instrument Operation

    Instrument operation Power the Ion GeneStudio S5 Sequencer on or off Note: If the Ion GeneStudio S5 Sequencer is powered on, and the touchscreen is blank, touch the screen to "wake" the touchscreen. Power on If the touchscreen is unresponsive, check the power switch on the back of the instrument to ensure that the switch is in the on (|) position.

  • Page 15: Ion Genestudio S5 Instrument Run Times

    The instrument automatically restarts when the software update is complete. Ion GeneStudio S5 instrument run times Approximate Ion GeneStudio S5 instrument run times for a given chip type, read length, and number of reads are shown in the following table. Run times indicate typical time from run start to BAM file delivery (1 run/initialization).

  • Page 16: Maintain The Sequencer

    10% bleach solution. 5. Wipe the affected surfaces with 70% isopropanol, then allow to air-dry. Perform the The Ion GeneStudio S5 Sequencers require cleaning before initialization. Cleaning is normally performed automatically at the completion of the previous sequencing run. sequencer...
  • Page 17 5. Place a used sequencing chip in the chip clamp, then push the chip clamp in all the way to engage. 6. Close the instrument door, then press Next. Cleaning takes ~35 minutes to complete. On completion, the instrument door automatically unlocks and the chip and cartridge clamps disengage. Ion GeneStudio S5 Instrument User Guide...

  • Page 18: Perform An Instrument Reset Run With An Initialized, Unused Sequencing

    Maintain the sequencer Perform an Cleaning is normally performed at completion of a sequencing run automatically. If an Ion GeneStudio S5 is initialized and instrument reset run with an • a sequencing run is not started within 24 hours after initialization, or initialized, unused •...

  • Page 19: Appendix A Touchscreen Reference

    • The Run program walks you through steps leading up to and through sequencing, including: – Placing a loaded chip on the instrument ™ – Selecting a Planned Run created in the Torrent Suite Software – Performing sequencing Ion GeneStudio S5 Instrument User Guide...

  • Page 20: Settings

    In the Settings menu, users can view and/or change instrument settings, manage data and network configurations, and update the installed software. Network Settings The Network Settings menu allows you to configure IP address, Torrent Server, and FTP settings. Ion GeneStudio S5 Instrument User Guide...
  • Page 21 Enter one of the following IP addresses in the TSUrl field for your instrument: • Ion GeneStudio S5/Ion GeneStudio S5 Plus Sequencer: 192.168.122.249 • Ion GeneStudio S5 Prime Sequencer: 192.168.201.1 Ion GeneStudio S5 Instrument User Guide...
  • Page 22 Enter the following IP address in the FTPserver field for your instrument: • Ion GeneStudio S5/Ion GeneStudio S5 Plus Sequencer: 192.168.122.249 • Ion GeneStudio S5 Prime Sequencer: 192.168.201.1 Update Server Allows users to update the software update server.

  • Page 23: System Tools

    1. Press the screen within the row of the product to view an RFID Tag Detail page. 2. Press Done to return. Ion GeneStudio S5 Instrument User Guide...
  • Page 24 2. Press Chip Calibration to start the chip calibration. 3. In the dropdown lists, select the Image to display and the type of Calibration to perform. 4. Press Cancel to quit the chip calibration. Ion GeneStudio S5 Instrument User Guide...
  • Page 25 Ion ™ Wash Solution is not flowing. Example Reagent Check for an Ion 540 ™ Chip ™ Example Reagent Check for an Ion 550 Chip Ion GeneStudio S5 Instrument User Guide...
  • Page 26 Drives in <Filesystem> screen opens. 3. Press the screen within the row of the Drive to view details of the disk drive. The Details for <Drive> screen opens. 4. Press Done to return to the previous screen. Ion GeneStudio S5 Instrument User Guide...
  • Page 27 Torrent Browser. You can then download the file and email it to Technical Support. To retrieve the file using the Torrent Browser, navigate to Help4Instrument Diagnostics, then follow the on-screen instructions. Ion GeneStudio S5 Instrument User Guide...

  • Page 28: Check For Software Updates

    When software updates are available users will receive a Notification through the home screen. software updates 1. In the Settings menu, press Check for Updates. The Software Update screen lists the available updates. 2. Press Update to automatically download and install the updates. Ion GeneStudio S5 Instrument User Guide...

  • Page 29: Data Management

    Experiment Name row of the individual experiment to be transferred. 2. Press Transfer. 3. Select the radio button of the action to be performed. 4. Select the radio button of the files to be transferred. 5. Press OK. Ion GeneStudio S5 Instrument User Guide...
  • Page 30 Experiment Name row of the individual experiment to be analyzed, then press Analysis. 2. Select the Stop Analysis or Restart Analysis radio button, then press OK. 3. If performing a re-analysis, follow the on-screen instructions, then press OK. Ion GeneStudio S5 Instrument User Guide...

  • Page 31: Manually Delete Run Data

    Manage. 2. Press Select All to select all the available experiments, or touch the screen in the Experiment Name row of the individual experiment to be managed. 3. Press Delete Selected. Ion GeneStudio S5 Instrument User Guide...

  • Page 32: Perform The Instrument Clean Operation

    18 for more information. 1. In the Settings menu, press Clean Instrument. The Clean procedure begins automatically. 2. Follow the on-screen instructions (see page 16 for more information), then press Next. Ion GeneStudio S5 Instrument User Guide...

  • Page 33: Instrument Settings

    The user interface returns to the Home screen when the cleaning is complete. Instrument The Instrument Settings menu provides information about the instrument and allows the user to set the instrument name and language. Settings Ion GeneStudio S5 Instrument User Guide...
  • Page 34 Appendix A Touchscreen reference Settings Item Description When/How to use About Provides instrument details. To view instrument reference information or access regulatory information. Regulatory Info Lists instrument-specific regulatory information. To view instrument regulatory information. Ion GeneStudio S5 Instrument User Guide...
  • Page 35 For troubleshooting if directed to do so Calibration by Technical Support. Touch the red cross with your finger or a stylus each time it appears. In total, you will touch the screen 4 times, once in each corner. Ion GeneStudio S5 Instrument User Guide...
  • Page 36 OK. Service Options For use by trained service personnel. For troubleshooting if directed to do so by Technical Support. Language To set the user interface language. Set to customer preference during instrument installation. Ion GeneStudio S5 Instrument User Guide...

  • Page 37: Touchscreen Icons

    Sequencing in progress Instrument ready Error Chip status – Absent Chip status – Standby Chip status – Connecting Chip status – Ready Chip status – Imaging Chip status – Error Manifold air pressure – Good Ion GeneStudio S5 Instrument User Guide...
  • Page 38 Refer to the Torrent Suite ™ Software help for more information on archiving data. Indicator turns yellow when disk space is ≥67% full, indicator turns red when ≥90% full. Ion GeneStudio S5 Instrument User Guide...

  • Page 39: Alarms, Notifications, And Events

    = the low voltage threshold, HH.HH = the high voltage threshold. Indicates a voltage drop on the motherboard. CPU temperature check failed, Where X is the processor number. Physical Id X. Indicates that the processor is over heating. Ion GeneStudio S5 Instrument User Guide...
  • Page 40 “Network Settings“ on server is properly connected, see page 20. page 13 for the Ethernet port No Connectivity to FTP server. Reconfigure the FTP server as location. needed, see “Network Settings“ on page 20. Ion GeneStudio S5 Instrument User Guide...
  • Page 41 13 for the Ethernet port location. Newer Software Available Notification that software updates are Update your software. See “Check for available. software updates“ on page 28. Ion GeneStudio S5 Instrument User Guide...

  • Page 42: Appendix B Troubleshooting

    Wait 30 seconds, then press the button on the side of the instrument to power on the instrument. • If the red "Alarms" and/or "Events" message still appears in the main menu, contact Technical Support. Ion GeneStudio S5 Instrument User Guide...

  • Page 43: Initialization Fails

    2. Press Retry. 3. If the initialization completes without failure, touch Home, then continue with your sequencing run. 4. If the Reagent Check continues to fail, contact Technical Support. Ion GeneStudio S5 Instrument User Guide...
  • Page 44 • Bottle seal was not tight. 1. Finger-tighten the bottles. • Bottle was damaged or 2. If the bottle continues to defective. leak, replace the bottle. 3. If leak check continues to fail, contact Technical Support. Ion GeneStudio S5 Instrument User Guide...

  • Page 45: Troubleshooting Using Control Libraries

    2 Instrument, or the ™ Ion Chef Instrument. ™ 2. Use the ISPs in an Ion GeneStudio S5 run. 3. If AQ20 throughput is still below specification, verify the quality of unenriched and enriched ISPs to identify a problem in template preparation.

  • Page 46: Solid-State Buffer Leak

    Test Fragments. Pulse clean the You should only pulse clean your Ion GeneStudio S5 Sequencer if directed by Technical Support, or your Field Service Engineer (FSE), to recover instrument sequencer performance from a diagnosed solid-state buffer leak.
  • Page 47 4. Close the instrument door, then touch Next. The pulse cleaning procedure begins automatically. The user interface returns to the main menu when the cleaning is complete and the sequencer is ready to be initialized. Ion GeneStudio S5 Instrument User Guide...

  • Page 48: Appendix C Supplemental Procedures

    Minifuge (Cat. No. 4479672 or 4479673) is used to load sequencing ™ chips manually for use on Ion PGM , Ion Proton , and Ion GeneStudio S5 sequencing ™ ™ platforms. To accommodate the larger chip size, Ion Proton and Ion GeneStudio S5 ™...
  • Page 49 3. Tighten the set screw (arrow) with a 1.5-mm hex wrench. Note: A newer version of the rotor lacks a set screw. In this case, simply press the rotor firmly onto the motor shaft to install. Ion GeneStudio S5 Instrument User Guide...

  • Page 50: Test The Minifuge

    Aspirate the remaining isopropanol from the flow cells for 5–10 seconds. Confirm that the chips are dry. Note: To aspirate the isopropanol, attach a P200 pipette tip to a vacuum line, then place the pipette tip in the chip loading port. Ion GeneStudio S5 Instrument User Guide...
  • Page 51 The chips have air bubbles after the Contact Technical Support. additional 10 minute centrifugation... The chips remain completely filled... The centrifuge is ready to use for chip loading. Ion GeneStudio S5 Instrument User Guide...

  • Page 52: Appendix D Instrument Warranty

    WITH RESPECT TO Ion Torrent PRODUCT AND ARE IN LIEU OF ALL OTHER ™ WARRANTIES, STATUTORY, EXPRESS OR IMPLIED, ALL OF WHICH OTHER WARRANTIES ARE EXPRESSLY DISCLAIMED, INCLUDING WITHOUT LIMITATION ANY IMPLIED WARRANTY OF MERCHANTABILITY, FITNESS FOR Ion GeneStudio S5 Instrument User Guide...
  • Page 53 OBTAINED THROUGH THE USE OF ANY PRODUCT (INCLUDING, WITHOUT LIMITATION, ANY CLAIM OF INACCURATE, INVALID OR INCOMPLETE RESULTS), WHETHER ARISING FROM A STATUTE OR OTHERWISE IN LAW OR FROM A COURSE OF PERFORMANCE, DEALING OR USAGE OF TRADE. Ion GeneStudio S5 Instrument User Guide...

  • Page 54: Appendix E Safety

    CAUTION! Hazardous waste. Refer MISE EN GARDE! Déchets to SDS(s) and local regulations for dangereux. Lire les fiches handling and disposal. signalétiques (FS) et la réglementation locale associées à la manipulation et à l’élimination des déchets. Ion GeneStudio S5 Instrument User Guide...

  • Page 55: Location Of Safety Labels On This Instrument

    Appendix E Safety Safety information for instruments not manufactured by Thermo Fisher Scientific Location of safety Ion GeneStudio S5 Series sequencers have warnings at the location shown: labels on this instrument Safety and regulatory Ion Torrent S5™ XL Sequencer 1234987 00000000 For Research Use Only.

  • Page 56: Instrument Safety

    Service clientèle). · Avant d’utiliser une méthode de nettoyage ou de décontamination (autre que celles recommandées par le fabricant), les utilisateurs doivent vérifier auprès de celui-ci qu’elle ne risque pas d’endommager l’appareil. Ion GeneStudio S5 Instrument User Guide...

  • Page 57: Electrical

    WARNING! Déconnecter l’alimentation. Pour déconnecter entièrement l’alimentation, détacher ou débrancher le cordon d’alimentation. Placer l’instrument de manière à ce que le cordon d’alimentation soit accessible. Ion GeneStudio S5 Instrument User Guide...

  • Page 58: Safety And Electromagnetic Compatibility (Emc) Standards

    Electromagnetic Disturbance Characteristics of Industrial, Scientific, and Medical (ISM) Radiofrequency Equipment Industrial, Scientific and Medical (ISM) ICES-003, Issue 5 Radio Frequency Generators U.S. Standard Radio Frequency Devices FCC Part 15 Subpart B (47 CFR) Ion GeneStudio S5 Instrument User Guide...

  • Page 59: Environmental Design

    : (1) l'appareil ne doit pas produire de brouillage, et (2) l'utilisateur de l'appareil doit accepter tout brouillage radioélectrique subi, même si le brouillage est susceptible d'en compromettre le fonctionnement. Ion GeneStudio S5 Instrument User Guide...

  • Page 60: Chemical Safety

    : lunettes de sûreté, gants ou vêtements de protection). · Limiter l’inhalation des produits chimiques. Ne pas laisser les récipients de produits chimiques ouverts. Ils ne doivent être utilisés qu’avec une ventilation adéquate (par exemple, sorbonne). Ion GeneStudio S5 Instrument User Guide...
  • Page 61 éliminés en respectant toutes les réglementations locales, nationales et/ou communautaires en vigueur. · IMPORTANT ! Les matériaux représentant un danger biologique ou radioactif exigent parfois une manipulation spéciale, et des limitations peuvent s’appliquer à leur élimination. Ion GeneStudio S5 Instrument User Guide...
  • Page 62 MAN0010844 Ion 540 ™ Kit – OT2 User Guide MAN0010850 Ion GeneStudio S5 System Site Preparation Guide MAN0017529 Customer and technical support Visit thermofisher.com/support for the latest in services and support, including: • Worldwide contact telephone numbers • Product support, including: –...

This manual is also suitable for:

A38194A38195A38196

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