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Ion GeneStudio
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 B.0
For Research Use Only. Not for use in diagnostic procedures.
™
S5 Instrument
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Troubleshooting
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Related Manuals for ThermoFisher Scientific ION GeneStudio S5
Summary of Contents for ThermoFisher 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 B.0 For Research Use Only. Not for use in diagnostic procedures.
- Page 2 Life Technologies Holdings Pte Ltd | Block 33 | Marsiling Industrial Estate Road 3 | #07-06, Singapore 739256 For descriptions of symbols on product labels or product documents, go to thermofisher.com/symbols-definition. The information in this guide is subject to change without notice. DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, THERMO FISHER SCIENTIFIC INC.
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Page 3: Table Of Contents
Contents About this guide ............6 Purpose of the guide . - Page 4 Contents ■ APPENDIX A Touchscreen reference ..........21 Clean, Initialize, and Run .
- Page 5 Contents ■ Documentation and support ............62 Related documentation .
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Page 6: About This Guide
About this guide CAUTION! ABBREVIATED SAFETY ALERTS. Hazard symbols and hazard types specified in procedures may be abbreviated in this document. For the complete safety information, see the “Safety” appendix in this document. IMPORTANT! Before using this product, read and understand the information in the “Safety” appendix in this document. -
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
Chapter 1 Product information Required materials and equipment not supplied Ion S5 Installation Kit (Part No. A27215; Not available for separate purchase.) (continued) Contents Part No. Quantity Storage ™ Ion S5 Cartridge Tool A28308 15°C to 30°C ™ Ion S5 Chip Balance Pack A29022 Required materials and equipment not supplied... -
Page 9: Instrument Installation By Trained Personnel Only
Chapter 1 Product information Instrument installation by trained personnel only Instrument installation by trained personnel only ™ IMPORTANT! The Ion GeneStudio S5 System is installed by trained service personnel and must not be relocated without assistance from trained service personnel. See “Customer and technical support” on page Nucleic acid contamination IMPORTANT! A primary source of contamination is DNA fragments from previously processed... -
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 Ion Torrent Server. These instruments are not connected to an external ™... - Page 11 Chapter 2 System components Ion GeneStudio ™ S5 System component configuration and layout Ion GeneStudio ™ S5 Prime System configuration Ion GeneStudio ™ S5 Prime Sequencer Ion Torrent ™ Server Ion template preparation instrument Local area network (Ion Chef ™ Instrument (shown) or Ion OneTouch ™...
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Page 12: Internet Connectivity
Chapter 2 System components Internet connectivity Internet connectivity ™ ™ ™ The Ion GeneStudio S5 Sequencer, the Ion GeneStudio S5 Plus Sequencer, or the Ion Torrent ™ Server (in an Ion GeneStudio S5 Prime System) should be connected to a network with internet access. -
Page 13: Ion Genestudio ™ S5 System Component Positions
Chapter 2 System components Ion GeneStudio ™ S5 System component positions ™ Ion GeneStudio S5 System component positions Ion GeneStudio S5 Ion GeneStudio S5 Ion GeneStudio S5 Touchscreen Power button Ion S5 ™ Sequencing Reagents cartridge Chip clamp ™ ™... -
Page 14: 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 15: 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 16: Update The Ion Genestudio ™ S5 System Software
Chapter 3 Instrument operation Update the Ion GeneStudio ™ S5 System software ™ Update the Ion GeneStudio S5 System software ™ Note: An internet connection is required for the Ion GeneStudio S5 System to receive alerts that software updates are available. ™... - Page 17 Chapter 3 Instrument operation Ion GeneStudio ™ S5 instrument run times (continued) Instrument run time Number of Read Chip type ™ ™ ™ Ion GeneStudio Ion GeneStudio Ion GeneStudio reads length/output Sequencer Plus Sequencer Prime Sequencer 600 bases ™ Ion 530 Chip 9–12 M 21 hours...
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Page 18: Maintain The Sequencer
Chapter 3 Instrument operation Maintain the sequencer Maintain the sequencer Materials required • Lint-free wipes • 70% isopropanol • (Optional) 10% bleach solution Clean or decontaminate the sequencer In the event of a spill or leak on or inside the instrument, perform the following steps. Note: Dispose of all waste in appropriate liquid or solid waste containers. - Page 19 Chapter 3 Instrument operation Maintain the sequencer 1. On the home screen, press Settings4Clean Instrument. The instrument door unlocks allowing access to the consumables. 2. Remove the Ion S5 ™ Wash Solution bottle to access the waste reservoir, then remove and empty the waste reservoir.
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Page 20: Perform An Instrument Reset Run With An Initialized Sequencer That Is Loaded With An Unused Reagents Cartridge
Chapter 3 Instrument operation Maintain the sequencer Perform an instrument reset run with an initialized sequencer that is loaded with an unused Reagents cartridge ™ Cleaning is normally automatically performed at completion of a sequencing run. If an Ion GeneStudio S5 System is initialized, an instrument reset run is required to ensure proper cleaning before reinitialization in one of the following situations. -
Page 21: Appendix A Touchscreen Reference
Touchscreen reference Clean, Initialize, and Run Ion GeneStudio S5 In the Home screen, the Clean, Initialize, and Run programs lead you through the necessary steps to prepare the instrument for sequencing and to start a sequencing run. Press the main dial to start a program. -
Page 22: Settings
Appendix A Touchscreen reference Settings Settings In the Settings menu, users can view and/or change instrument settings, manage data and network configurations, and update the installed software. Note: The Service tools option is for use by trained service personnel only. Network Settings ™... - Page 23 Appendix A Touchscreen reference Settings Item Description When/How to use IP Address Allows users to set or change the IP configuration (DHCP 1. Select either the DHCP or Configuration or Static IP). Static IP radio button. 2. Touch the screen in the field you want to edit to activate the field.
- Page 24 Appendix A Touchscreen reference Settings (continued) Item Description When/How to use FTP Server Allows users to change the FTP Server IP address and When a change to the FTP Server IP Configuration user information. address or user information is required. Enter the following IP address in the FTPserver field for your instrument: •...
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Page 25: System Tools
Appendix A Touchscreen reference Settings (continued) Item Description When/How to use Update Server Allows users to update the software update server. When a change to the URL for the software update server is required. The values on this screen are set at installation. - Page 26 Appendix A Touchscreen reference Settings Item Description When/How to use RFID Lists the product, product expiration date, and remaining To determine if reagents that were left uses of the product. on an instrument during a period of instrument shutdown have expired. 1.
- Page 27 Appendix A Touchscreen reference Settings (continued) Item Description When/How to use Chip Calibration Checks the status of a chip. 1. Insert a chip into the chip clamp. 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.
- Page 28 Appendix A Touchscreen reference Settings (continued) Item Description When/How to use Reagent Check Reagent Check, performed by the instrument as part of If directed to do so by Technical initialization, confirms that initialization passes by testing Support as part of a troubleshooting reagent flow and signal detection.
- Page 29 Appendix A Touchscreen reference Settings (continued) Item Description When/How to use Filesystems Provides real-time drive activity status and disk space Use if directed to do so as part of a and disks used. troubleshooting procedure: 1. In the System Tools menu, press Filesystems and disks.
- Page 30 Appendix A Touchscreen reference Settings (continued) Item Description When/How to use Pulse clean Provides step by step instruction to perform a pulse Use if directed to do so by Technical clean of the instrument if a solid‑state buffer leak occurs. Support as part of a troubleshooting procedure: 1.
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Page 31: Check For Software Updates
Appendix A Touchscreen reference Settings (continued) Item Description When/How to use Shut Down Access to "Shut Down" and "Reboot" commands. If directed to do so by Technical Support as part of a troubleshooting procedure. Note: It is not necessary/recommended to shut down the instrument overnight or over the weekend. -
Page 32: Data Management
Appendix A Touchscreen reference Settings Data management The Data management function allows users to delete run data manually, analyze the data, or transfer ™ the data to the Ion Torrent Server. Under normal conditions, run data are automatically transferred to the server, then deleted from the instrument hard drive. - Page 33 Appendix A Touchscreen reference Settings (continued) Item Description When/How to use Analysis Allows the user to stop or reanalyze the data of individual 1. Tap the screen in the Experiment Controls runs. Name row of the individual experiment to be analyzed, then press Analysis.
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Page 34: Manually Delete Run Data
Appendix A Touchscreen reference Settings Manually delete run data To troubleshoot data management problems the Data Management function allows users to delete run data manually, or transfer the data to the server. Under normal conditions, run data are automatically ™ transferred to the Ion Torrent Server, then deleted from the instrument hard drive. -
Page 35: Perform The Instrument Clean Operation
Appendix A Touchscreen reference Settings Perform the instrument Clean operation The Clean program is normally performed automatically at the completion of the previous sequencing run. Perform a Clean if the sequencing run: • was aborted or had a power failure during the second of two runs started after a single initialization. •... -
Page 36: Instrument Settings
Appendix A Touchscreen reference Settings Instrument settings The Instrument Settings menu provides information about the instrument and allows you to set the instrument name and calibrate the touchscreen. Ion GeneStudio ™ S5 Instrument User Guide... - Page 37 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. Instrument To change the instrument name. Name Ion GeneStudio ™...
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Page 38: Touchscreen Icons
Appendix A Touchscreen reference Touchscreen icons (continued) Item Description When/How to use Screen 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, one time in each corner. - Page 39 Appendix A Touchscreen reference Touchscreen icons Number Icon Description Network connectivity – connected Network connectivity – not connected Instrument idle Sequencing in progress Instrument ready Error Chip status – Absent Chip status – Standby Chip status – Connecting Chip status – Ready Chip status –...
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Page 40: Alarms, Notifications, And Events
Alarms, Notifications, and Events Alarms, Notifications, and Events If the Alarms/Notifications indicator appears, press the indicator to open the Notifications screen, then press Alarms or Events see detailed messages. Ion GeneStudio S5 Ion GeneStudio S5 Alarms and Notifications indicator. Alarm... - Page 41 Appendix A Touchscreen reference Alarms, Notifications, and Events (continued) Alarm Description Recommended Action CPU temperature check failed, Where X is the processor number. Contact Technical Support. Physical Id X. Indicates that the processor is over heating. Front/Rear FanX speed below Where X is the fan number and YYYY Contact Technical Support.
- Page 42 Appendix A Touchscreen reference Alarms, Notifications, and Events (continued) Alarm Description Recommended Action ™ No Connectivity to Torrent Server. Check that the Ethernet cable Reconfigure the Ion Torrent Server connecting the instrument to the as needed, see “Network Settings” server is properly connected, see on page page 14 for the Ethernet port...
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Page 43: Appendix B Troubleshooting
• Available Tap the red Alarms icon to see detailed Menu software messages. updates were • If a message states "Newer Ion GeneStudio S5 detected. Software Available": • Connectivity IMPORTANT! After updates are issues were installed, the instrument must be detected. -
Page 44: Initialization Fails
Appendix B Troubleshooting Initialization fails Initialization fails Observation Possible cause Recommended action Chip Check fails • The chip clamp was not 1. Open the chip clamp, closed. remove the chip, and look for signs of water • The chip was not outside the flow cell. - Page 45 Appendix B Troubleshooting Initialization fails Observation Possible cause Recommended action Reagent Check fails A wash failure was detected. 1. Perform a manual cleaning of the sequencer, see page 2. Replace the Reagents cartridge, Wash Solution bottle, and Cleaning Solution bottle, then repeat initialization of the sequencer.
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Page 46: Troubleshooting Using Control Libraries
Appendix B Troubleshooting Troubleshooting using control libraries Troubleshooting using control libraries Observation Possible cause Recommended action Ion Sphere ™ Test Fragments • Chip loading was poor. 1. Confirm that the Control Ion Sphere ™ are not present in the Test ™... -
Page 47: Solid-State Buffer Leak
Appendix B Troubleshooting Solid-state buffer leak ™ c. Add 150 µL of Ion S5 Annealing Buffer to the tube. 4. Anneal the sequencing primer to the enriched ISPs, then follow the remaining procedures in your appropriate user guide to load a chip and start the sequencing run. Solid-state buffer leak Observation Possible cause... - Page 48 Appendix B Troubleshooting Solid-state buffer leak 3. Follow the onscreen prompts to prepare the instrument. ™ • Install new bottles of Ion S5 Cleaning Solution in both the Wash and Cleaning solution positions. ™ • Replace the Ion S5 Sequencing Reagents cartridge with an empty used cartridge. •...
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Page 49: Appendix C Supplemental Procedures
Supplemental procedures ™ Set up and test the Ion Chip Minifuge ™ ™ Note: The Ion Chip Minifuge is only required when using the Ion OneTouch 2 System for template ™ ™ preparation. Ion Chef Instrument users do not require an Ion Chip Minifuge. - Page 50 Appendix C Supplemental procedures Set up and test the Ion Chip ™ Minifuge 2. Press the Ion S5 ™ ™ /Ion Proton Rotor down onto the motor shaft to install. Insert motor shaft here 3. Tighten the set screw (arrow) with a 1.5-mm hex wrench. Note: A newer version of the rotor lacks a set screw.
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Page 51: Test The Minifuge
Appendix C Supplemental procedures Set up and test the Ion Chip ™ Minifuge 4. Install the two buckets. Position the buckets with the larger semi-circular cut-outs facing out, and ensure that the buckets hang freely. Correct orientation Incorrect orientation Test the minifuge 1. - Page 52 Appendix C Supplemental procedures Set up and test the Ion Chip ™ Minifuge 2. Place the two chips prepared in step 1 in the centrifuge buckets, with the chip notch pointing out. Add 55 µL of nuclease-free water to each chip loading well (do not inject into the chip loading port).
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Page 53: Appendix D Instrument Warranty
Instrument warranty ™ For new Ion Torrent instruments, Life Technologies warrants to and only to buyer for twelve (12) ™ ™ months from the date of shipping, that the Ion Torrent software and Ion Torrent instruments are free from defects in material and workmanship and conform to Life Technologies’ published specifications ™... -
Page 54: Appendix E Safety
Safety WARNING! GENERAL SAFETY. Using this product in a manner not specified in the user documentation may result in personal injury or damage to the instrument or device. Ensure that anyone using this product has received instructions in general safety practices for laboratories and the safety information provided in this document. -
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 labels on this instrument ™ Ion GeneStudio S5 Series sequencers have warnings at the location shown: Ion Torrent S5™ XL Sequencer 1234987 00000000 For Research Use Only. Not for use in diagnostic procedures Rated 100-240V AC 50/60Hz, 14.5-6.5A EMC Class A... -
Page 56: Instrument Safety
Appendix E Safety Instrument safety Instrument safety General CAUTION! Do not remove instrument protective covers. If you remove the protective instrument panels or disable interlock devices, you may be exposed to serious hazards including, but not limited to, severe electrical shock, laser exposure, crushing, or chemical exposure. Cleaning and decontamination CAUTION! Cleaning and Decontamination. -
Page 57: Electrical Safety
Appendix E Safety Instrument safety Electrical safety WARNING! Ensure appropriate electrical supply. For safe operation of the instrument: · Plug the system into a properly grounded receptacle with adequate current capacity. · Ensure the electrical supply is of suitable voltage. ·... -
Page 58: Safety And Electromagnetic Compatibility (Emc) Standards
Appendix E Safety Safety and electromagnetic compatibility (EMC) standards Safety and electromagnetic compatibility (EMC) standards The instrument design and manufacture complies with the following standards and requirements for safety and electromagnetic compatibility. Safety Reference Description EU Directive 2014/35/EU European Union “Low Voltage Directive” IEC 61010-1 Safety requirements for electrical equipment for measurement, control, and laboratory use –... -
Page 59: Environmental Design
Appendix E Safety Safety and electromagnetic compatibility (EMC) standards Environmental design Waste and hazardous substances Reference Description Directive 2012/19/EU European Union “WEEE Directive” – Waste electrical and electronic equipment Directive 2011/65/EU European Union “RoHS Directive” – Restriction of hazardous substances in electrical and electronic equipment Radio compliance Reference... -
Page 60: Chemical Safety
Appendix E Safety Chemical safety Chemical safety WARNING! GENERAL CHEMICAL HANDLING. To minimize hazards, ensure laboratory personnel read and practice the general safety guidelines for chemical usage, storage, and waste provided below. Consult the relevant SDS for specific precautions and instructions: ·... - Page 61 Appendix E Safety Chemical safety · Veiller à utiliser des récipients à déchets primaire et secondaire. (Le récipient primaire contient les déchets immédiats, le récipient secondaire contient les fuites et les écoulements du récipient pri‐ maire. Les deux récipients doivent être compatibles avec les matériaux mis au rebut et conformes aux exigences locales, nationales et communautaires en matière de confinement des récipients.) ·...
- Page 62 Documentation and support Related documentation Title Pub. No. Ion 510 ™ & Ion 520 ™ & Ion 530 ™ Kit – Chef User Guide MAN0016854 ™ Ion 540 Kit – Chef User Guide MAN0010851 ™ Ion 550 Kit − Chef User Guide MAN0017275 ™...
- Page 63 Documentation and support Limited product warranty Limited product warranty Life Technologies Corporation and/or its affiliate(s) warrant their products as set forth in the Life Technologies' General Terms and Conditions of Sale at www.thermofisher.com/us/en/home/ global/terms-and-conditions.html. If you have any questions, please contact Life Technologies at www.thermofisher.com/support.
- Page 64 Ion GeneStudio S5 Instrument_UG_MAN0017528-v3- GUID-1CCD8367-1337-4D12-9FE0-54DC22DF51FE-2022/02/22 18:08:37 en 18:12:34.668Z thermofisher.com/support | thermofisher.com/askaquestion thermofisher.com 22 February 2022...
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