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USER GUIDE




Ion Torrent S5™ and Ion Torrent S5™ XL
Sequencer
Catalog Numbers A27211, A27213
Publication Number MAN0010811
Revision A.0




For Research Use Only. Not for use in diagnostic procedures.



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


The information in this guide is subject to change without notice.
DISCLAIMER
LIFE TECHNOLOGIES CORPORATION AND/OR ITS AFFILIATE(S) DISCLAIM ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT, EXPRESSED OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THOSE OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR NON-INFRINGEMENT. TO
THE EXTENT ALLOWED BY LAW, IN NO EVENT SHALL LIFE TECHNOLOGIES AND/OR ITS AFFILIATE(S) BE LIABLE, WHETHER 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 conditions of all
applicable Limited Use Label Licenses.

TRADEMARKS
All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified.
©2015 Thermo Fisher Scientific Inc. All rights reserved.


                                                                                                                                      Contents



                    About this guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
                    Revision history . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
                    Purpose of the guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

               ■    CHAPTER 1 Product information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
                    Contents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
                    Required materials and equipment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
                    Update the software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
                    Instrument installation by trained personnel only . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
                    Nucleic acid contamination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
                    Instrument vibration and clearances . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
                    Static electricity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

               ■    CHAPTER 2 System components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
                    Internet connectivity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
                                           ™
                    Ion Torrent S5 System component positions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 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 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
                                                              ™
                    Update the Ion Torrent S5 System software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
                    Clean the instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19



Ion Torrent S5™ andIon Torrent S5™ XL Instrument User Guide                                                                                                              3
CONFIDENTIAL — For Life Technologies Internal Use Only. Do Not Distribute.


Contents




           ■   APPENDIX A Touchscreen reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
               Clean, Initialize, and Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
               Options and Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
               Touchscreen gauges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
               Chip status icon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
               Alarms/events pop-up . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

           ■   APPENDIX B Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
                                       ™
               Ion Torrent S5 Sequencer alarms and events . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
               Chip Check . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
               Chip calibration (before loading sample) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
               Chip calibration (after loading sample) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
               Initialization—General errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
               Troubleshooting using the controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

           ■   APPENDIX C Supplemental procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
                                                             ™
               Set up and test the Ion Chip Minifuge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
                                           ™
                    Install the Ion Proton Rotor and Buckets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
                    Test the minifuge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 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 . . . . . . . . . . . . . . . . . . . . . . . . . .                                           39
                    Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .    39
                    EMC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .   39
                    Environmental design . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .                  39
               Chemical safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

           ■   Documentation and support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
               Placeholder for related documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
               Customer and technical support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
               Limited product warranty . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43


4                                                              Ion Torrent S5™ andIon Torrent S5™ XL Instrument User Guide
                                                  CONFIDENTIAL — For Life Technologies Internal Use Only. Do Not Distribute.


                                                                             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.




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™ andIon Torrent S5™ XL Instrument User Guide                                                     5
CONFIDENTIAL — For Life Technologies Internal Use Only. Do Not Distribute.


    1                                            Product information


Contents
           The Ion Torrent S5™ and Ion Torrent S5™ XL Systems (Catalog nos. A27212, or
           A27214) contain the following boxes and components.

                                   Ion Torrent S5™ System (Catalog no. A27212)

                              Components                                  Catalog no.

           Ion Torrent S5™ Sequencer                                        A27211

           Ion S5™ Installation Kit                                         A27215


                                  Ion Torrent 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




6                                       Ion Torrent S5™ andIon Torrent S5™ XL Instrument User Guide
                           CONFIDENTIAL — For Life Technologies Internal Use Only. Do Not Distribute.


                                                                                                        Chapter 1 Product information
                                                                                                       Required materials and equipment            1

Required materials and equipment
                                    The following tables list required materials and equipment that are not provided with
                                    the Ion Torrent S5™ Systems.

Table 1 Required materials and equipment for sequencing

  3                                 Description[1]                                     Supplier             Catalog no.             Quantity

         Ion Chip™ Minifuge (120 V or 230 V)                                            Life              4479672 (120V)                 1
                                                                                    Technologies                  or
                                                                                                          4479673 (230V)

         Ion Proton™ Rotor and Buckets Kit                                              Life                  4482578                    1
                                                                                    Technologies

         Uninterruptable Power Supply (UPS) [2]                                           MLS                     —                      1

         Isopropanol (100%)                                                               MLS                     —                     —

         Nuclease-free water molecular biology grade                                      MLS                     —                     —

         Microcentrifuge[3]                                                               MLS                     —                      1

         P2, P10, P20, P200, P1000 µL pipette set and filtered tips                       MLS                     —                    1 set
                 ®             ®
         Rainin Pipet-Lite XLS with RFID LTS 2 µL to 20 µL                               Rainin               L-20XLS                    1

         Rainin® Pipet-Lite® XLS with RFID LTS 10 µL to 100 µL                           Rainin              L-100XLS                    1

         Rainin® StableRak™ LTS tips 2-20 µL                                             Rainin               SR-L20F                   —

         Rainin® StableRak™ LTS tips 200 µL                                              Rainin              SR-L200F                   —

         0.2-mL MAXYMum Recovery® Thin Wall PCR Tubes, Flat                             Axygen             PCR-02-L-C                 Varies
         Cap (do not use polystyrene tubes)

         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 validated this protocol using these specific materials. Substitution may adversely affect system performance.
[2]   For laboratories that experience frequent power outages or line voltage fluctuations, we recommend that you use an uninterruptable power
      supply that is compatible with 2500 W output or higher.
[3]   Must fit standard 1.5- and 0.2-mL microcentrifuge tubes and generate 15,500 × g.
[4]   As needed to connect laboratory vacuum to liquid trap and liquid trap to P200 pipette tip.




Ion Torrent S5™ andIon Torrent S5™ XL Instrument User Guide                                                                                        7
CONFIDENTIAL — For Life Technologies Internal Use Only. Do Not Distribute.


1   Chapter 1 Product information
    Update the software




Update the software
                          IMPORTANT! Before proceeding, make sure that you have updated the Torrent
                          Suite™ and Ion Torrent S5™ System software to Version 4.4 or later. See “Update the
                          Ion Torrent S5™ System software“ on page 18.



Instrument installation by trained personnel only
                          IMPORTANT! The Ion Torrent 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 43.



Nucleic acid contamination
                          IMPORTANT! A primary source of contamination is DNA fragments from previously
                          processed samples. Do not introduce amplified DNA into the library preparation
                          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 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 electricity
                          IMPORTANT! To avoid possible damage to the chip from static electricity, you must
                          ground yourself on the grounding plate (located next to the chip clamp) prior to
                          handling chips, and do not place chips on non-grounded surfaces such as a bench.
                          Always use the grounding plate to hold chips that are not in the package or inserted
                          in the chip clamp or the Ion PGM™ Chip Minifuge bucket.




8                                                     Ion Torrent S5™ andIon Torrent S5™ XL Instrument User Guide
                                         CONFIDENTIAL — For Life Technologies Internal Use Only. Do Not Distribute.


   2                                                           System components


                           We support the layout in which the Ion Torrent™ Server is directly connected to the
                           Ion Torrent S5™ XL Sequencer, rather than through the local area network from a
                           remote location such as a server room. Data are most robustly transferred from the
                           Ion Torrent S5™ XL Sequencer to the Ion Torrent™ Server when they are directly
                           connected by a standard Category 6 Ethernet cable provided with the installation
                           materials.

                           IMPORTANT! The Ion Torrent 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.



                                                                                     5




                                                                    4
                                 3




                                                                                         Torrent Browser

                                                  1

                                                                                                6

                                                                             2




                           Figure 1 Ion Torrent S5™ XL Sequencer configuration
                             1 Ion Torrent S5™ XL Sequencer                  4 Local area network
                             2 Ion template preparation instrument (Ion      5 Internet
                               Chef™ Instrument (shown) or Ion               6 Client computer
                               OneTouch™ 2 System)
                             3 Ion Torrent™ Server




Ion Torrent S5™ andIon Torrent S5™ XL Instrument User Guide                                                      9
CONFIDENTIAL — For Life Technologies Internal Use Only. Do Not Distribute.


2    Chapter 2 System components
     Internet connectivity




                                                                                             4
                                                                            3
                                            2




                                                                                             Torrent Browser
                                                              1
                                                                                         5




                             Figure 2 Ion Torrent S5™ Sequencer configuration
                               1 Ion Torrent S5™ Sequencer                      3 Local area network
                               2 Ion template preparation instrument (Ion       4 Internet
                                 Chef™ Instrument (shown) or Ion                5 Client computer
                                 OneTouch™ 2 System)



Internet connectivity
                             The Ion Torrent S5™ Sequencer or the Ion Torrent™ Server should be connected to a
                             network with internet access. Connecting to the internet provides you the ability to
                             easily update your software and access remote system support. Software updates
                             through the network/internet are free. If you choose not to connect your instrument or
                             server to a network, software updates will need to be manually installed via USB.

                             IMPORTANT! The USB method for updating is not supported by Thermo Fisher
                             Scientific.

                             Any issues (file corruption, incomplete updates, etc.) updating the sequencer or server
                             in this manner requiring correction of the faulty update is not covered by your Ion
                             Torrent S5™ or Ion Torrent S5™ XL Sequencer warranty or any service contract you
                             may have purchased. You will be required to schedule an on-site Time and Materials
                             visit by a Thermo Fisher 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 software versions
                             and instrument alarms. With your permission, the agent also allows service personnel
                             to remotely log into the Ion Torrent S5™ Sequencer and the Ion Torrent™ Server, which
                             is required for system support. Without remote access, service personnel cannot
                             access, view, and troubleshoot issues regarding machine performance.
                             To enable full support, the Ion Torrent™ Server must have outbound internet access
                             (ports 22, 80, and 443) and be behind an appropriately configured firewall. While not
                             recommended, you can enable access to the Ion Torrent™ Browser (the web server
                             running on the Ion Torrent™ Server from the Internet). If you provide such access, you
                             must restrict access to the server using HTTP and AUTH firewall rules, or a


10                                                       Ion Torrent S5™ andIon Torrent S5™ XL Instrument User Guide
                                            CONFIDENTIAL — For Life Technologies Internal Use Only. Do Not Distribute.


                                                                                       Chapter 2 System components
                                                                              Ion Torrent S5™ System component positions   2

                           combination of the two. Implementing and maintaining such restrictions is the
                           responsibility of the customer's server administrator and not of Thermo Fisher
                           Scientific.
                           Note: For answers to common questions about Ion Torrent™ Server network access
                           requirements, refer to the frequently asked questions (FAQ) and the Torrent Server
                           Administrator Guide in the Torrent Suite section of the Ion Community website (http://
                           ioncommunity.lifetechnologies.com). The FAQ provides information that you can
                           use to prepare Ion Torrent S5™ Systems and servers within the umbrella policies of
                           your site.



Ion Torrent S5™ System component positions
                                                            4




                            1


                                                                                                     5

                            2

                            3
                                                                                                     6




                                                                                                             7


                                1 Touchscreen                                   6 Secondary Wash solution bottle (W3
                                2 Reagent cartridge                               position)
                                3 Power button                                  7 Waste reservoir
                                4 Chip clamp
                                5 Primary Wash solution bottle (W2
                                  position). Waste reservoir located behind
                                  the W2 bottle (shown on the right).

                           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 or usage
                           count will generate an error message prompting the user to replace the reagent before
                           performing the run.
                           Note: RFID regulatory information can be found on the main screen under Options
                           then Regulatory info.




Ion Torrent S5™ andIon Torrent S5™ XL Instrument User Guide                                                                11
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2    Chapter 2 System components
     Ion Torrent S5™ and Ion Torrent S5™ XL Sequencer input and output connections




Ion Torrent S5™ and Ion Torrent S5™ XL Sequencer input and output
connections

                                                                                         3
                             1


                                                                                         4
                             2



                              1   USB ports – Connects the barcode reader            3   On/off switch – Power switch, where the
                                  to the instrument.                                     states are on ( | ) or off ( O ).
                              2   Ethernet port – An RJ45 port that provides         4   Power port – 100-240VAC port that
                                  Ethernet (Gigabit) communication with the              provides power to the instrument.
                                                ™                  ™
                                  Ion Torrent S5 or Ion Torrent S5 XL
                                  Sequencer.




12                                                         Ion Torrent S5™ andIon Torrent S5™ XL Instrument User Guide
                                              CONFIDENTIAL — For Life Technologies Internal Use Only. Do Not Distribute.


   3                                                       Create a Planned Run


                           IMPORTANT! This sequencing kit is compatible with Ion Torrent™ System 4.4 and
                           later. Before proceeding, check for updates to the Ion Torrent™ System and Ion
                           Torrent S5™ or Ion Torrent S5™ XL Sequencer software, and install the updates if
                           available.

                           Note: If you are currently using Ion Reporter™ Software v1.4 with an earlier version
                           of the Torrent Suite™ Software, contact Technical Support for assistance with
                           upgrading to Ion Torrent™ System 4.4.



About planned runs
                           Planned runs contain all the settings used in a sequencing run, including number of
                           flows, kit types, barcodes used (if any), run type (e.g., DNA, RNA, amplicons), and
                           reference file (if any). They provide a fast and convenient way to set up and organize
                           your runs.
                           You create planned runs using the Torrent Browser and then select the appropriate
                           plan in the Select Planned Run screen of the Ion Torrent S5™ or Ion Torrent S5™ XL
                           Sequencer when you are ready 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 want to run (for
                               example, AmpliSeq DNA), then select:
                                 • Upload Plans to upload a .csv format file containing your run information.
                                 • Plan New Run to plan a new run using the generic template for the selected
                                   application.
                                 • Add New Template to create a new planned run template that you can
                                   reuse for the selected application.
                                 • Other options that may be available depending on your selected application,
                                   such as downloading designs from AmpliSeq.com.

                            3. When you have completed your selections, click Plan Run to save your
                               selections. The run is listed on the Planned Runs page under the name you
                               specified.



Ion Torrent S5™ andIon Torrent S5™ XL Instrument User Guide                                                     13
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3    Chapter 3 Create a Planned Run
     Planned run wizard: key fields




Planned run wizard: key fields
                                      Field name                                 Description

                             IonReporter             If Ion Reporter™ Software is installed and enabled and you want to
                                                     analyze the run data using the software, select the account and
                                                     workflow.

                             Application             Select the sequencing application you are performing.

                             Library Kit Type        Select the kit used to prepare the library.

                             Template Kit            Select the instrument and kit used to prepare the templated Ion
                                                     PI™ Ion Sphere™ Particles.

                             Sequencing Kit          Select the Ion Torrent S5™ Sequencing Kit.

                             Chip Type               Select the chip type you are using.

                             Flows                   Enter the appropriate number of flows for the sequencing kit and
                                                     read length.

                             Barcode Set             If you are using barcodes with:
                             (optional)               • DNA libraries: Select the IonXpress barcode set, which
                                                        includes all barcodes in the Ion Xpress™ Barcode Adapters
                                                        1‑96 Kits.
                                                      • RNA libraries prepared using the Ion Total RNA-Seq Kit v2:
                                                        Select the IonXpressRNA 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.

                             Plugins                 Select and configure the appropriate plugins for your application.

                             Project                 Select or add a project within which to group your run data. You
                                                     can include runs in multiple projects, and remove runs from a
                                                     project at any time.

                             Run Plan Name           Enter a name for the run.

                             Reference Library       Select a reference library uploaded to the Torrent Server, if any.

                             Target Regions and      Select the Target Regions and/or HotSpot Regions BED file on the
                             Hotspot Regions         Torrent Server, if any.




14                                                         Ion Torrent S5™ andIon Torrent S5™ XL Instrument User Guide
                                              CONFIDENTIAL — For Life Technologies Internal Use Only. Do Not Distribute.


                                                                                Chapter 3 Create a Planned Run
                                                                                      Planned run wizard: key fields   3

                                Field name                                    Description

                           Enter a sample         Specify the Sample Name, ID, and Description for each sample in
                           name...                the run (number of samples will change based on the number of
                                                  barcodes and/or chips selected).

                           Monitoring             Set thresholds for Bead Loading, Key Signal, and Usable
                           Thresholds             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.




Ion Torrent S5™ andIon Torrent S5™ XL Instrument User Guide                                                            15
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     4                                          Instrument operation


Power the Ion Torrent S5™ or Ion Torrent S5™ XL Sequencer on or
off
Power on       Note: If the Ion Torrent S5™ Sequencer is powered on, and the touchscreen is blank,
               touch the screen to "wake" the touchscreen.

                1. Locate the power switch on the back of the instrument and turn to the on (|)
                   position.

                2. Press the power button on the left side of the instrument. The button should
                   illuminate. When the instrument touchscreen Main Menu appears, the
                   instrument is ready for use.

Power off      It is not necessary 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 place a loaded chip in the chip clamp:
               Reviewer: need new photos for this process

               Slide the metal tab out to access the chip
               holder.




16                                         Ion Torrent S5™ andIon Torrent S5™ XL Instrument User Guide
                              CONFIDENTIAL — For Life Technologies Internal Use Only. Do Not Distribute.


                                                                                  Chapter 4 Instrument operation
                                                                           Select the planned run and perform the run   4

                           If necessary, remove the chip currently in
                           the clamp.




                           Place the appropriate loaded chip in the
                           chip clamp with the chip notch in the
                           bottom ‑front corner.
                           Note: Do not force the chip into the clamp.
                           If the chip does not fit easily in the clamp,
                           confirm that the notch is oriented as shown
                           in the photo.


                           Slide the metal tab in until it clicks to
                           engage the clamp.




                           Close the instrument door.                      need new photo of closing the door.



Select the planned run and perform the run
                           Prepare and load the Ion 520™, Ion 530™, or Ion 540™ Chip before performing 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 recommended.

                            3. Confirm the pre-populated settings are correct, or make changes using the
                               buttons and drop-down lists if necessary.




Ion Torrent S5™ andIon Torrent S5™ XL Instrument User Guide                                                             17
CONFIDENTIAL — For Life Technologies Internal Use Only. Do Not Distribute.


4    Chapter 4 Instrument operation
     Update the Ion Torrent S5™ System software



                             4. 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?

                             1. In the Main Menu, select Options4Updates.

                             2. Select the Released Updates checkbox, then press Check.

                             3. 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.

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

                             5. 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.




18                                                        Ion Torrent S5™ andIon Torrent S5™ XL Instrument User Guide
                                             CONFIDENTIAL — For Life Technologies Internal Use Only. Do Not Distribute.


                                                                              Chapter 4 Instrument operation
                                                                                          Clean the instrument     4

Clean the instrument
                           Required materials:
                            • absorbent paper towels
                            • isopropyl alcohol (IPA) wipes
                            • (optional)– 10% bleach solution
                           To clean or decontaminate the instrument in the event of a spill or leak on or inside
                           the instrument:
                           Note: Dispose of all waste in appropriate liquid or solid waste containers.

                            1. Remove the W2 reagent bottle, 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.




Ion Torrent S5™ andIon Torrent S5™ XL Instrument User Guide                                                        19
CONFIDENTIAL — For Life Technologies Internal Use Only. Do Not Distribute.


     A                                    Touchscreen reference



Clean, Initialize, and Run




                The Clean, Initialize, and Run programs lead you through the necessary steps to
                prepare the instrument for sequencing and start a sequencing run.
                 • The Clean program can be used to perform a wash solution cleaning. Cleaning
                   must be performed before each initialization to ensure that the reagents from the
                   previous run are cleared from the fluid lines. Follow the instructions provided on
                   the touchscreen.
                 • The Initialize program must 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
                   sequencing, including:
                    – Placing a loaded chip on the instrument.
                     – Selecting a planned run created in the Torrent Server Software.
                     – Performing sequencing.




20                                         Ion Torrent S5™ andIon Torrent S5™ XL Instrument User Guide
                              CONFIDENTIAL — For Life Technologies Internal Use Only. Do Not Distribute.


                                                                              Appendix A Touchscreen reference
                                                                                                  Options and Tools   A

Options and Tools




                            • The Options menu gives you access to software updates. See “Update the
                              software“ on page 8 for details.
                            • The Tools menu gives you access to troubleshooting tools and to the instrument
                              Shut Down and Reboot commands. See the following table for details.

Table 2 Tools menu options

   Item                              Description                                            When to use

Data Mgnt Allows you to manually delete run data or transfer the data        To troubleshoot data management
          the server. Under normal conditions, run data is                   issues. See .
          automatically transferred to the Ion Proton™ Torrent Server,
          then deleted from the instrument hard drive.

Noise       Provides real-time measurement of electrical noise               For troubleshooting if directed to do so
Screen      readings on the chip.                                            by Technical Support.

Upload      Allows upload of diagnostics files for review by support         For troubleshooting if directed to do so
diags       personnel.                                                       by Technical Support.

Reagent     Measures the pH of all reagents on the instrument. This task If directed to do so by Technical Support
Check       is normally performed by the instrument as part of the       or as part of a troubleshooting procedure
            Initialize program.                                          (see Appendix B, “Troubleshooting“).

RFID        Lists the product, product expiration date, and remaining        To determine if reagents, left on an
            uses of the product.                                             instrument during a period of instrument
                                                                             shutdown, have expired.

Shut Down Access to "Shut Down" and "Reboot" commands.                       If directed to do so as part of a
                                                                             troubleshooting procedure.
            Note: It is not necessary/recommended to shut down the
            instrument overnight or over the weekend. If necessary to
            shut down the instrument, see “Power off“ on page 16.




Ion Torrent S5™ andIon Torrent S5™ XL Instrument User Guide                                                             21
CONFIDENTIAL — For Life Technologies Internal Use Only. Do Not Distribute.


A    Appendix A Touchscreen reference
     Touchscreen gauges




Touchscreen gauges
                          Touch the Gauges icon in the lower right corner of the touchscreen to show or hide
                          the instrument gauges.

                                                                           regulator          chip block
                                                                           pressure          temperature
                                                              manifold              manifold           disc
                                                              pressure            temperature         space       LAN


                                                 u
                               touch to expand             touch to collapse                        instrument status


                               Icon                                            Description

                                          Manifold pressure.
                                          If the icon is red, see .

                                          Regulator 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.




22                                                     Ion Torrent S5™ andIon Torrent S5™ XL Instrument User Guide
                                          CONFIDENTIAL — For Life Technologies Internal Use Only. Do Not Distribute.



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