Thermo Scientific A38194 User Manual Download Page 15

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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).

Chip type

Number of

reads

Read

length/output

Instrument run time

Ion GeneStudio S5

Sequencer

Ion GeneStudio S5

Plus Sequencer

Ion GeneStudio S5

Prime Sequencer

Ion 510

™

Chip

2–3 M

200 bases

0.3–0.5 Gb

4.5 hours

3 hours

400 bases

0.6–1 Gb

10.5 hours

5 hours

Ion 520

™

Chip

4–6 M

200 bases

0.6–1 Gb

7.5 hours

3.5 hours

3 hours

400 bases

1.2–2 Gb

12 hours

5.5 hours

3–4 M

600 bases

0.5–1.5 Gb

12 hours

5.5 hours

Ion 530

™

Chip

15–20 M

200 bases

3–4 Gb

10.5 hours

5 hours

4 hours

400 bases

6–8 Gb

21.5 hours

8 hours

6.5 hours

9–12 M

600 bases

1.5–4.5 Gb

21 hours

8 hours

7 hours

Ion 540

™

Chip

60–80 M

200 bases

10–15 Gb

19 hours

10 hours

6.5 hours

Ion 550

™

Chip

100–130 M

200 bases

20–25 Gb

—

11.5 hours

8.5 hours

Chapter 3

Instrument operation

Ion GeneStudio S5 instrument run times

Ion GeneStudio S5 Instrument User Guide

Summary of Contents for A38194

Page 1: ...tic procedures 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 ...

Page 2: ...17528 Revision Date Description A 0 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 Trademarks All trade...

Page 3: ...y 11 Ion GeneStudio S5 System component positions 12 Ion GeneStudio S5 Sequencer input and output connections 13 CHAPTER 3 Instrument operation 14 Power the Ion GeneStudio S5 Sequencer on or off 14 Power on 14 Power off 14 Update the Ion GeneStudio S5 System software 14 Ion GeneStudio S5 instrument run times 15 Maintain the sequencer 16 Required materials 16 Clean or decontaminate the sequencer 16...

Page 4: ...ticles 45 Solid state buffer leak 46 Pulse clean the sequencer 46 APPENDIX C Supplemental procedures 48 Set up and test the Ion Chip Minifuge 48 Install the Ion S5 Ion Proton Rotor and Buckets 48 Test the minifuge 50 APPENDIX D Instrument warranty 52 APPENDIX E Safety 54 Safety alerts on this instrument 54 Location of safety labels on this instrument 55 Safety information for instruments not manuf...

Page 5: ... Documentation and support 62 Related documentation 62 Customer and technical support 62 Contents Ion GeneStudio S5 Instrument User Guide 5 ...

Page 6: ...n 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 The Ion S5 Sequencer and the Ion S5 XL Sequencer are no longer available for purchase and are replaced by the Ion GeneStudio S5 Sequencer and Ion GeneS...

Page 7: ...n S5 Installation Kit A27215 Ion GeneStudio S5 Prime System Cat No A38196 Components Part No Ion GeneStudio S5 Prime Sequencer A37260 Ion Torrent Server A36305 Ion S5 Installation Kit A27215 Ion S5 Installation Kit Part No A27215 Not available for separate purchase Contents Part No Quantity Storage Ion 540 Chip Kit A27765 4 pack 15 C to 30 C Ion S5 Sequencing Solutions A27767 1 Ion S5 Sequencing R...

Page 8: ...s P2 P10 P20 P200 P1000 and appropriate low retention filtered tips MLS Isopropanol 100 MLS Nuclease free water molecular biology grade MLS Standard laboratory vacuum line or vacuum pump MLS Liquid trap MLS Tygon tubing 4 MLS Vortex mixer MLS 1 IMPORTANT Thermo Fisher Scientific has verified the procedures in this user guide using these specific materials Substitution may adversely affect system p...

Page 9: ...ration laboratory or work area 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 IMPORTANT Place the instrume...

Page 10: ...ata are most robustly transferred from the Ion GeneStudio S5 Prime Sequencer to the Torrent Server when they are connected directly by a standard Category 6 Ethernet cable that is provided with the installation materials IMPORTANT The Ion GeneStudio S5 Prime Sequencer must be connected to the Torrent Server by a standard Category 6 Ethernet cable We do not troubleshoot data transfer problems that ...

Page 11: ...ruption incomplete updates resulting from update of the sequencer or server using a 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 You are required to schedule an on site Time and Materials visit by a field service engineer to correct th...

Page 12: ...rent Server network access requirements see Software Administration in Torrent Suite Software Help Ion GeneStudio S5 System component positions 7 2 3 5 6 4 1 Ion GeneStudio S5 Ion GeneStudio S5 Ion GeneStudio S5 1 Touchscreen 2 Power button 3 Ion S5 Sequencing Reagents cartridge 4 Chip clamp 5 Ion S5 Wash Solution bottle Waste reservoir located behind the Wash Solution bottle shown on the right 6 ...

Page 13: ...n the sequencer and a local area network 3 Ethernet port An RJ45 port that provides Ethernet Gigabit communication with the Ion Chef Instrument 4 On off switch Power switch where the states are on or off O 5 Power port 100 240VAC port that provides power to the instrument Chapter 2 System components Ion GeneStudio S5 Sequencer input and output connections 2 Ion GeneStudio S5 Instrument User Guide ...

Page 14: ...power off the instrument as follows 1 In the Main Menu press Settings4System Tools4Shut Down 2 Select either Shut Down or Reboot Note If you select Shut Down a confirmation message appears Select Yes to power off the instrument Note Do not press the power button during a run Interrupting power to the instrument during a run may result in sequencing run failure and loss of sample Update the Ion Gen...

Page 15: ...encer Ion 510 Chip 2 3 M 200 bases 0 3 0 5 Gb 4 5 hours 3 hours 3 hours 400 bases 0 6 1 Gb 10 5 hours 5 hours 5 hours Ion 520 Chip 4 6 M 200 bases 0 6 1 Gb 7 5 hours 3 5 hours 3 hours 400 bases 1 2 2 Gb 12 hours 5 5 hours 5 5 hours 3 4 M 600 bases 0 5 1 5 Gb 12 hours 5 5 hours 5 5 hours Ion 530 Chip 15 20 M 200 bases 3 4 Gb 10 5 hours 5 hours 4 hours 400 bases 6 8 Gb 21 5 hours 8 hours 6 5 hours 9...

Page 16: ...ost run clean checkbox for the first sequencing run The post run cleaning is then performed normally after the second sequencing run However if the Enable post run clean checkbox is deselected for the second run the cleaning is not performed after either run If the second sequencing run is not performed or the cleaning is not performed automatically after the second run the instrument will not all...

Page 17: ...n bottle are properly installed IMPORTANT Perform the cleaning with a used reagent cartridge and wash solution bottle installed The cleaning procedure pumps cleaning solution into the wash solution bottle and reagent cartridge making them unsuitable for sequencing 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 pre...

Page 18: ...e before reinitialization 1 In the instrument touchscreen main menu press Run The instrument door unlocks and the chip clamp disengages 2 Ensure that a used sequencing chip is in the chip clamp then push the chip clamp in all the way to engage 3 Close the instrument door then press Next 4 When prompted select Planned Run none Ensure that the Enable post run clean checkbox is selected then press Re...

Page 19: ...ly performed automatically at the completion of the previous sequencing run Perform a Clean if for any reason the sequencing run was not properly completed Follow the instructions that are provided on the touchscreen The Initialize program must be performed before each run to load and prepare the run reagents The Initialize program walks you through Emptying the waste reservoir Loading the reagent...

Page 20: ...tings manage data and network configurations and update the installed software The Network Settings menu allows you to configure IP address Torrent Server and FTP settings Network Settings Appendix A Touchscreen reference Settings A 20 Ion GeneStudio S5 Instrument User Guide ...

Page 21: ...w information then press Done Torrent Server Configuration Allows users to change the Torrent Server IP address and user information 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 When a change to the Torrent Server IP address or user information is req...

Page 22: ...formation is required Update Server Allows users to update the software update server Enter the following IP address in the UpdateUrl 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 When a change to the URL for the software update server is required The values on this screen are set at installation Do not ...

Page 23: ...ct product expiration date and remaining uses of the product To determine if reagents that were left on an instrument during a period of instrument shutdown have expired 1 Press the screen within the row of the product to view an RFID Tag Detail page 2 Press Done to return System Tools Appendix A Touchscreen reference Settings A Ion GeneStudio S5 Instrument User Guide 23 ...

Page 24: ...al Support 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 4 Press Cancel to quit the chip calibration Appendix A Touchscreen reference Settings A 24 Ion GeneStudio S5 Instrument User Guide ...

Page 25: ...agent Check for an Ion 550 Chip If directed to do so by Technical Support as part of a troubleshooting procedure Press Run to start the reagent check Press Last Trace to review the most recent reagent check result trace Note Reagent Check confirms that the chip calibration passes and will only fail if the chip is defective or Ion S5 Wash Solution is not flowing Appendix A Touchscreen reference Set...

Page 26: ...k Drives The Filesystems screen opens 2 Press the screen within the row of the Filesystem you want to view then press Details The Disk 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 Appendix A Touchscreen reference Settings A 26 Ion GeneStudio S5 Inst...

Page 27: ...nt door then press Next The pulse cleaning procedure starts automatically Upload Diagnostics Allows upload of instrument diagnostics files for review by support personnel For troubleshooting if directed to do so by Technical Support Note The system must be connected to an active network port If no network is present the file is pushed to the Torrent Browser You can then download the file and email...

Page 28: ...f on page 14 If directed to do so by Technical Support as part of a troubleshooting procedure When software updates are available users will receive a Notification through the home screen 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 Check for software updates Appendix A Touchsc...

Page 29: ...rom the instrument If the instrument hard drive becomes full see Manually delete run data on page 31 Transfer data Transfer run data from the instrument hard drive to the Torrent Server 1 Touch the screen in the 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 tra...

Page 30: ...een in the 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 Appendix A Touchscreen reference Settings A 30 Ion GeneStudio S5 Instrument User Guide ...

Page 31: ... then deleted from the instrument hard drive 1 In the Settings menu press Data Management to access the Data Management screen then press 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 Manually delete run data Appendix A Touchscreen reference Settings A Ion GeneStudi...

Page 32: ...ANT Do NOT perform a manual cleaning with an unused initialized Ion S5 Sequencing Reagents cartridge Perform an instrument reset run instead See Perform an instrument reset run with an initialized unused Sequencing Reagents cartridge on page 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...

Page 33: ...leaning is complete The Instrument Settings menu provides information about the instrument and allows the user to set the instrument name and language Instrument Settings Appendix A Touchscreen reference Settings A Ion GeneStudio S5 Instrument User Guide 33 ...

Page 34: ... To view instrument reference information or access regulatory information Regulatory Info Lists instrument specific regulatory information To view instrument regulatory information Appendix A Touchscreen reference Settings A 34 Ion GeneStudio S5 Instrument User Guide ...

Page 35: ...alibration For troubleshooting if directed to do so 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 Appendix A Touchscreen reference Settings A Ion GeneStudio S5 Instrument User Guide 35 ...

Page 36: ...lt settings press 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 Appendix A Touchscreen reference Settings A 36 Ion GeneStudio S5 Instrument User Guide ...

Page 37: ...ot connected 2 Instrument idle Sequencing in progress Instrument ready Error 3 Chip status Absent Chip status Standby Chip status Connecting Chip status Ready Chip status Imaging Chip status Error 4 Manifold air pressure Good Appendix A Touchscreen reference Touchscreen icons A Ion GeneStudio S5 Instrument User Guide 37 ...

Page 38: ... there is an alarm contact Technical Support 8 Instrument File System Space the percent of file space used is indicated 1 The instrument checks for sufficient disk space before each run and notifies the user if there is not enough 9 Torrent Server File System Space the percent of file space used is indicated Note If the indicator turns red archive data from the server to free up disk space Refer t...

Page 39: ...he drive that failed Indicates that a drive is failing Failed to mount the results filesystem One or more drives are missing from the RAID that makes up sw_results System sensor check failed ipmi sensors A component on the motherboard is failing or has failed System sensor check failed CC CC V LL LL HH HH Where CC CC current voltage LL LL the low voltage threshold HH HH the high voltage threshold ...

Page 40: ...r failure Air compressor is either leaking or has stopped working Non fatal alarms Instrument must be cleaned before starting another run Maximum number of runs since last clean has been exceeded Perform an instrument cleaning See Perform the sequencer cleaning manually on page 16 Ambient temperature is above the threshold of 35 C Verify the temperature in the lab Contact Technical Support if the ...

Page 41: ...operly connected see page 13 for the Ethernet port location If the problem persists contact Technical Support Newer Software Available Notification that software updates are available Update your software See Check for software updates on page 28 Appendix A Touchscreen reference Alarms Notifications and Events A Ion GeneStudio S5 Instrument User Guide 41 ...

Page 42: ...installation is complete follow the onscreen prompts to restart the instrument Note In some cases the instrument restarts automatically after software installation If a message states No Connectivity to Torrent Server No Connectivity to ftp server or Network Manager not connected disconnect and re connect the ethernet cable confirm that the router is operational and verify that the network is up a...

Page 43: ...ext If the chip fails replace it with a new chip then press Chip Check 5 If Chip Check continues to fail there could be a problem with the chip socket Contact Technical Support Reagent Check fails A chip failure was detected 1 Replace the used sequencing chip used during initialization with a different used chip 2 Press Retry 3 If the initialization completes without failure touch Home then contin...

Page 44: ...eck continues to fail contact Technical Support Ensure that you install the Ion S5 Wash Solution bottle with the instrument door fully open If you install the bottle impeded by a partially closed door the port can be obstructed and a faulty installation and wash failure can result Bottle leak check fails Bottle seal was not tight Bottle was damaged or defective 1 Finger tighten the bottles 2 If th...

Page 45: ...neTouch 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 4 If ISP quality is good but AQ20 throughput is below specification contact Technical Support Troubleshooting using Control Ion Sphere Particles To prepare Contro...

Page 46: ...ument performance from a diagnosed solid state buffer leak Note You must contact Technical Support or your FSE to diagnose whether a solid state buffer leak has occurred and obtain the required materials to perform the pulse cleaning 1 Ensure that the sequencer has completed a normal post run cleaning In the main menu Display text Description Run Instrument requires cleaning before a pulse cleanin...

Page 47: ...eagents cartridge with an empty used cartridge Install a used sequencing chip 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 Appendix B Troubleshooting Solid state buffer leak B Ion GeneStudio S5 Instrument User Guide 47 ...

Page 48: ...commodate the larger chip size Ion Proton and Ion GeneStudio S5 sequencer users must install the Ion S5 Ion Proton Rotor and Buckets Cat No 4482578 test the minifuge to confirm that no liquid is lost during centrifugation before using the minifuge to load chips for the first time Note The following protocols may also be used to convert the Ion Chip Minifuge back for use with Ion PGM sequencing chi...

Page 49: ...e 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 Appendix C Supplemental procedures Set up and test the Ion Chip Minifuge C Ion GeneStudio S5 Instrument User Guide 49 ...

Page 50: ...each injection remove the expelled liquid from the opposite port Note Use 50 µL volume of isopropanol if testing Ion PGM sequencing chips b 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 Test the minifuge Appendix C ...

Page 51: ...air bubbles A small volume of liquid will remain in the loading well this is normal Result Action The chips are NOT completely filled Contact Technical Support The chips ARE completely filled Centrifuge the chips for an additional 10 minutes then check the chips again for air bubbles especially near the inlet and outlet ports The chips have air bubbles after the additional 10 minute centrifugation...

Page 52: ...g the Ion Torrent Product directly from Life Technologies are not transferable and do not extend to the benefit of any other person or entity unless otherwise expressly stated in writing by Life Technologies ANY PRODUCT NOT COVERED BY AN EXPRESS WRITTEN WARRANTY IS SOLD AND PROVIDED AS IS WITHOUT WARRANTY OF ANY KIND STATUTORY EXPRESS OR IMPLIED Any description of Ion Torrent Product recited in Li...

Page 53: ...CLUDING 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 Appendix D Instrument warranty Set up and test the Ion Chip Minifuge D Ion GeneStudio S5 Instrument User Guide 53 ...

Page 54: ...ment gloves gowns eye protection etc To obtain SDSs see the Documentation and Support section in this document Safety alerts on this instrument Additional text may be used with one of the symbols described above when more specific information is needed to avoid exposure to a hazard See the following table for safety alerts found on the instrument English Français CAUTION Hazardous chemicals Read t...

Page 55: ...d regulatory symbols Ion GeneStudio S5 Sequencer labels Safety information for instruments not manufactured by Thermo Fisher Scientific Some of the accessories provided as part of the instrument system are not designed or built by Thermo Fisher Scientific Consult the manufacturer s documentation for the information needed for the safe use of these products Location of safety labels on this instrum...

Page 56: ...e manufacturer users should confirm with the manufacturer that the proposed method will not damage the equipment CAUTION Nettoyage et décontamination Utiliser uniquement les méthodes de nettoyage et de décontamination indiquées dans la documentation du fabricant destinée aux utilisateurs L opérateur ou toute autre personne responsable est tenu d assurer le respect des exigences suivantes Ne pas ut...

Page 57: ...itif de mise à la terre est déconnecté La continuité de la mise à la terre est impérative pour le fonctionnement de l instrument en toute sécurité WARNING Power Supply Line Cords Use properly configured and approved line cords for the power supply in your facility WARNING Cordons d alimentation électrique Utiliser des cordons d alimentation adaptés et approuvés pour raccorder l instrument au circu...

Page 58: ...laboratory use Part 2 010 Particular requirements for laboratory equipment for the heating of materials Reference Description Directive 2014 30 EU European Union EMC Directive EN 61326 1 Electrical Equipment for Measurement Control and Laboratory Use EMC Requirements Part 1 General Requirements AS NZS CISPR 22 2009 A1 2010 Limits and Methods of Measurement of Electromagnetic Disturbance Characteri...

Page 59: ...rmo Fisher Scientific can void your authority to operate this equipment under Federal Communications Commissions rules Canada This device complies with Industry Canada licence exempt RSS standard s Operation is subject to the following two conditions 1 this device may not cause interference and 2 this device must accept any interference including interference that may cause undesired operation of ...

Page 60: ... if necessary the waste generated by the particular applications reagents and substrates used in your laboratory Ensure that the waste is stored transferred transported and disposed of according to all local state provincial and or national regulations IMPORTANT Radioactive or biohazardous materials may require special handling and disposal limitations may apply WARNING PRÉCAUTIONS GÉNÉRALES EN CA...

Page 61: ... locales nationales et communautaires en matière de confinement des récipients Une fois le récipient à déchets vidé il doit être refermé hermétiquement avec le couvercle fourni Caractériser par une analyse si nécessaire les déchets générés par les applications les réactifs et les substrats particuliers utilisés dans le laboratoire Vérifier que les déchets sont convenablement stockés transférés tra...

Page 62: ...n 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 Product FAQs Software patches and updates Training for many applications and instruments Order and web support Product documentation including User guides manuals and protocols Certificates of Analysis Safety...

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