Thermo Scientific Torrent S5 XL User Manual Download Page 18

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Confirm that the instrument door is closed, then press Next to begin the

sequencing run.
The system calibrates the chip (~1 minute), then begins the sequencing run. If

chip calibration fails, see ts_Error message: Failed: Reseat chip then press Next to

recalibrate_Ion Proton Sequencer.

IMPORTANT!

During a run, do not open the instrument door, and avoid

touching the instrument. Touching the instrument during the sequencing run

may reduce the quality of the measurements.

When the run is complete, the touchscreen returns to the Main Menu. Use the Torrent

Suite Browser to review the results.

Update the Ion Torrent S5

™

System software

Note:

An internet connection is required for the Ion Torrent S5

™

System to receive

alerts that software updates are available.
If an update to the Ion Torrent S5

™

Sequencer software is available, the red “Alarms

and Events” pop-up appears in the touchscreen Main Menu to alert you. Press the red

pop-up to see the detailed messages. If a message states New Software Available,

update the software as follows:

Reviewer:

How do users with instruments not connected to the internet receive

notification that software updates are available, and how do they update the

software?

In the Main Menu, select Options

Updates.

Select the Released Updates checkbox, then press Check.

When the message Press Update to begin update process appears, press Update.

Note:

If the message All Software Current appears, press Back to return to the

Main Menu.

In the warning/confirmation dialog, press Ok. The software update progress bar

will appear.

When the message Update Done displays, follow the onscreen prompts to restart

the instrument.

IMPORTANT!

After updates are installed, the instrument must be restarted.

Note:

In some cases, the instrument restarts automatically after software

installation.

Chapter 4

Instrument operation

Update the Ion Torrent S5

™

System software

Ion Torrent S5

™

andIon Torrent S5

™

XL Instrument User Guide

CONFIDENTIAL — For Life Technologies Internal Use Only. Do Not Distribute.

Summary of Contents for Torrent S5 XL

Page 1: ...nly Not for use in diagnostic procedures CONFIDENTIAL For Life Technologies Internal Use Only Do Not Distribute Ion Torrent S5 and Ion Torrent S5 XL Sequencer Catalog Numbers A27211 A27213 Publication Number MAN0010811 Revision A 0 ...

Page 2: ...IN CONTRACT TORT WARRANTY OR UNDER ANY STATUTE OR ON ANY OTHER BASIS FOR SPECIAL INCIDENTAL INDIRECT PUNITIVE MULTIPLE OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT INCLUDING BUT NOT LIMITED TO THE USE THEREOF 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 conditio...

Page 3: ...tions 11 Ion Torrent S5 and Ion Torrent S5 XL Sequencer input and output connections 12 CHAPTER 3 Create a Planned Run 13 About planned runs 13 Create a planned run 13 Planned run wizard key fields 14 CHAPTER 4 Instrument operation 16 Power the Ion Torrent S5 or Ion Torrent S5 XL Sequencer on or off 16 Power on 16 Power off 16 Chip handling guidelines 16 Select the planned run and perform the run ...

Page 4: ...fuge 32 APPENDIX D Safety 34 Symbols on this instrument 34 Conformity symbols on this instrument 35 Safety alerts on this instrument 36 Location of safety labels on this instrument 36 Safety information for instruments not manufactured by Thermo Fisher Scientific 37 Instrument safety 37 General 37 Electrical 37 Cleaning and decontamination 38 Safety and electromagnetic compatibility EMC standards ...

Page 5: ...ix in this document Revision history Revision Date Description A 0 November 2014 Ion Torrent S5 and Ion Torrent S5 XL Instrument User Guide for compliance testing Purpose of the guide The Ion Torrent S5 and Ion Torrent S5 XL Instrument User Guide Pub no MAN0010811 provides reference information for using the Ion Torrent S5 or Ion Torrent S5 XL Sequencer s Cat nos A27211 and A27213 Ion Torrent S5 a...

Page 6: ...orrent S5 XL System Catalog no A27214 Components Catalog no Ion Torrent S5 XL Sequencer A27213 Ion S5 Installation Kit A27215 Ion S5 Installation Kit Catalog no A27215 Components Color Quantity Volume Storage Ion 520 530 OT2 Kit 4 2 C to 8 C Ion 540 Chip Kit 4 15 C to 30 C Ion Torrent S5 Sequencing Kit 4 2 C to 8 C Ion S5 Controls Kit 1 2 C to 8 C 1 6 Ion Torrent S5 andIon Torrent S5 XL Instrument...

Page 7: ...Tubes Flat Cap do not use polystyrene tubes Axygen PCR 02 L C Varies 1 5 mL or 1 7 mL microcentrifuge tubes MLS Varies Ice buckets and ice Aluminum heat block capable of maintaining 50 C MLS Vortex mixer with a rubber platform MLS 1 Thermal cycler with a heated lid MLS 1 Standard laboratory vacuum line or vacuum pump MLS 1 Liquid trap MLS 1 Tygon tubing 4 MLS 1 1 Thermo Fisher Scientific has valid...

Page 8: ... add noise and reduce the quality of the measurements The Ion Torrent 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 instrument at least 40 in 1 meter away from major sources of electronic noise such as refrigerators or microwaves Static electricit...

Page 9: ...rrent S5 System must be connected to the Ion Torrent Server by a standard Category 6 Ethernet cable We do not troubleshoot data transfer issues associated with an indirect connection between the Ion Torrent S5 XL Sequencer and the Ion Torrent Server Torrent Browser 3 4 5 6 2 1 Figure 1 Ion Torrent S5 XL Sequencer configuration 1 Ion Torrent S5 XL Sequencer 2 Ion template preparation instrument Ion...

Page 10: ...her Scientific field service engineer to correct the problem at your own expense In providing outbound access to the internet from the server you enable the Thermo Fisher Scientific support team to provide inbound support Both the Ion Torrent S5 Sequencer and the Ion Torrent Server run a remote monitor agent that can provide service personnel with critical system information such as installed soft...

Page 11: ... 7 1 2 3 5 6 4 1 Touchscreen 2 Reagent cartridge 3 Power button 4 Chip clamp 5 Primary Wash solution bottle W2 position Waste reservoir located behind the W2 bottle shown on the right 6 Secondary Wash solution bottle W3 position 7 Waste reservoir Note The system utilizes RFID technology to verify that the proper reagents are loaded in positions 2 5 and 6 Reagents that exceed their expiration date ...

Page 12: ...th the Ion Torrent S5 or Ion Torrent S5 XL Sequencer 3 On off switch Power switch where the states are on or off O 4 Power port 100 240VAC port that provides power to the instrument Chapter 2 System components Ion Torrent S5 and Ion Torrent S5 XL Sequencer input and output connections 2 12 Ion Torrent S5 andIon Torrent S5 XL Instrument User Guide CONFIDENTIAL For Life Technologies Internal Use Onl...

Page 13: ...dy to perform the run see t_Start the sequencing run Note For additional information see the Torrent Suite User Interface Guide available on the Ion Community at ioncommunity lifetechnologies com Create a planned run 1 Open Torrent Browser for the Ion Torrent Server connected to your Ion Torrent S5 or Ion Torrent S5 XL Sequencer 2 Select the Plan tab select Templates locate the application you wan...

Page 14: ...ressRNA barcode set which contains all 16 barcodes in the Ion Xpress RNA BC01 16 Kit If you are not using barcodes with DNA libraries Leave the Barcode field blank RNA libraries prepared using the Ion Total RNA Seq Kit v2 Select RNA_Barcode_None from the drop down list This will ensure that the proper trimming is performed on the resulting sequence when the RNA library does not have a barcode Plug...

Page 15: ...hresholds Set thresholds for Bead Loading Key Signal and Usable Sequence In the Ion Proton Torrent Browser Monitor4Runs in Progress tab an alert is displayed if the values for a run fall below the selected thresholds Chapter 3 Create a Planned Run Planned run wizard key fields 3 Ion Torrent S5 andIon Torrent S5 XL Instrument User Guide 15 CONFIDENTIAL For Life Technologies Internal Use Only Do Not...

Page 16: ...ry to power off the instrument overnight or over the weekend If the instrument will not be used for more than 3 days power off the instrument as follows 1 In the Main Menu select Tools Shut Down 2 Ensure the post run cleaning is complete then press Shut Down 3 After you exit the main touchscreen press the Halt button then OK when prompted The instrument will power down Chip handling guidelines To ...

Page 17: ...g this procedure 1 Secure the chip loaded with template positive Ion Sphere Particles in the chip clamp close the instrument door then press Next 2 In the drop down list select a planned run that you created in the Torrent Suite Software then press Next Note You can also select Planned Run none then enter your run information on the following screen but selecting a predefined planned run is recomm...

Page 18: ...Press the red pop up to see the detailed messages If a message states New Software Available update the software as follows Reviewer How do users with instruments not connected to the internet receive notification that software updates are available and how do they update the software 1 In the Main Menu select Options4Updates 2 Select the Released Updates checkbox then press Check 3 When the messa...

Page 19: ...ottle then remove and empty the waste reservoir 2 Remove the nucleotide reagent cartridge 3 Visually inspect the waste and nucleotide reagent bays for liquid 4 Using absorbent paper soak up as much liquid as possible then wash the affected area with 10 bleach solution 5 Wipe the affected surfaces with IPA wipes then allow to air dry Chapter 4 Instrument operation Clean the instrument 4 Ion Torrent...

Page 20: ...be performed before each run to prepare the run reagents The Initialize program walks you through the following steps Specifying the sequencing kit Loading the reagent and wash solutions After this step the instrument performs a reagent check Abbreviated instructions are provided on the touchscreen for detailed instructions see The Run program walks you through steps leading up to and through sequ...

Page 21: ...iew by support personnel For troubleshooting if directed to do so by Technical Support Reagent Check Measures the pH of all reagents on the instrument This task is normally performed by the instrument as part of the Initialize program If directed to do so by Technical Support or as part of a troubleshooting procedure see Appendix B Troubleshooting RFID Lists the product product expiration date and...

Page 22: ...ulator pressure If the icon is red see Manifold temperature If the icon is red see Chip block temperature If the icon is red see Percent instrument hard drive and SSD in use If the icon is red see LAN local area network status Icon turns red when instrument is not connected to the network Instrument status Green shown ready to use Red pulsing in use Appendix A Touchscreen reference Touchscreen gau...

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