Thermo Scientific Ion GeneStudio S5 User manual

For Research Use Only. Not for use in diagnostic 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

Manufacturer: Life Technologies Holdings Pte Ltd | Block 33 | Marsiling Industrial Estate Road 3 | #07-06, Singapore 739256
The information in this guide is subject to change without notice.
DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, LIFE TECHNOLOGIES AND/OR ITS AFFILIATE(S) WILL NOT BE LIABLE FOR SPECIAL, INCIDENTAL,
INDIRECT, PUNITIVE, MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING YOUR
USE OF IT.
Revision history: Pub. No. MAN0017528
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 trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. MAXYMum Recovery is a
trademark of Axygen, Inc. Tygon is a trademark of Saint-Gobain Performance Plastics Corp.
©2018 Thermo Fisher Scientific Inc. All rights reserved.

Contents
About this guide ............................................................ 6
Purpose of the guide ............................................................ 6
■CHAPTER 1 Product information ....................................... 7
Contents ....................................................................... 7
Required materials and equipment not supplied .................................... 8
Instrument installation by trained personnel only ................................... 9
Nucleic acid contamination ....................................................... 9
Instrument vibration and clearances ............................................... 9
■CHAPTER 2 System components ...................................... 10
Ion GeneStudio S5 System component configuration and layout ...................... 10
Internet connectivity ............................................................ 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
Perform the sequencer cleaning manually .................................... 16
Perform an instrument reset run with an initialized, unused Sequencing
Reagents cartridge ........................................................ 18
Ion GeneStudio S5 Instrument User Guide
3

■APPENDIX A Touchscreen reference ................................. 19
Clean, Initialize, and Run ........................................................ 19
Settings ....................................................................... 20
Network Settings .......................................................... 20
System Tools .............................................................. 23
Check for software updates ................................................. 28
Data Management ......................................................... 29
Manually delete run data ................................................... 31
Perform the instrument Clean operation ...................................... 32
Instrument Settings ........................................................ 33
Touchscreen icons ............................................................. 37
Alarms, Notifications, and Events ................................................ 39
■APPENDIX B Troubleshooting ......................................... 42
Sequencer alarms and events ................................................... 42
Initialization fails ............................................................... 43
Troubleshooting using control libraries ........................................... 45
Troubleshooting using Control Ion Sphere™Particles ............................... 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 manufactured by Thermo Fisher Scientific ..... 55
Instrument safety .............................................................. 56
General .................................................................. 56
Cleaning and decontamination ............................................... 56
Electrical ................................................................. 57
Safety and electromagnetic compatibility (EMC) standards .......................... 58
Safety .................................................................... 58
EMC ...................................................................... 58
Environmental design ...................................................... 59
Chemical safety ................................................................ 60
Contents
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Ion GeneStudio S5 Instrument User Guide

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

About this guide
CAUTION! ABBREVIATED SAFETY ALERTS. Hazard symbols and hazard
types specied 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.
Purpose of the guide
The Ion GeneStudio S5 Instrument User Guide (Pub. No. MAN0017528) provides
reference information for using and maintaining the Ion GeneStudio S5 (Cat. No.
A38194), Ion GeneStudio S5 Plus (Cat. No. A38195), and Ion GeneStudio S5 Prime
(Cat. No. A38196) Sequencers.
Note: In this user guide, Ion GeneStudio S5 Sequencer or System refers generically to
the three Ion GeneStudio S5 Sequencers or Systems, unless otherwise specied.
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 GeneStudio
S5 Prime Sequencer, respectively. Both of the Ion S5™ and Ion S5™ XL Sequencers
continue to be supported by Thermo Fisher Scientic. See the Ion S5™ and Ion S5™ XL
Instrument User Guide (Pub. No. MAN0010811) for reference information for the Ion
S5™ and Ion S5™ XL Sequencers.
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Ion GeneStudio S5 Instrument User Guide

Product information
Contents
The Ion GeneStudio S5 (Cat. No. A38194), Ion GeneStudio S5 Plus (Cat. No. A38195),
and Ion GeneStudio S5 Prime (Cat. No. A38196) Systems contain the following boxes
and components.
Ion GeneStudio S5 System (Cat. No. A38194)
Components Part No.
Ion GeneStudio S5 Sequencer A37904
Ion S5™Installation Kit A27215
Ion GeneStudio S5 Plus System (Cat. No. A38195)
Components Part No.
Ion GeneStudio S5 Plus Sequencer A37259
Ion 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 Reagents A27768 1 –30°C to –10°C
Ion 540™Control Ion Spheres A28195 1
Ion 540™Loading Reagents OT2 A27897 1
Ion S5™Cartridge Tool A28308 2 15°C to 30°C
Ion S5™Chip Balance Pack A29022 1
1
Ion GeneStudio S5 Instrument User Guide
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Required materials and equipment not supplied
Unless otherwise indicated, all materials are available through thermosher.com.
MLS: Fisher Scientic (sherscientic.com) or other major laboratory supplier.
3Item[1] Source
Ion Chip™Minifuge (120 V or 230 V; required for use only with the Ion OneTouch™2
System.)
4479672 (120V) or
4479673 (230V)
Ion S5™/Ion Proton™Rotor and Buckets Kit (required for use only with the
Ion OneTouch™2 System.)
4482578
( Optional ) Non-interruptible Power Supply (UPS) [2] MLS
Thermal cycler with a heated lid MLS
Microcentrifuge[3] MLS
1.5-mL or 1.7-mL microcentrifuge tubes MLS
0.2-mL MAXYMum Recovery™Thin Wall PCR Tubes, Flat Cap (do not use
polystyrene tubes)
Axygen, PCR-02-L-C
Pipettes (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 performance.
[2] For laboratories that experience frequent power outages or line voltage fluctuations, we recommend that you use an non-interruptible 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.
Chapter 1 Product information
Required materials and equipment not supplied
1
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Ion GeneStudio S5 Instrument User Guide

Instrument installation by trained personnel only
IMPORTANT! The Ion GeneStudio S5 System is installed by trained service personnel
and must not be relocated without assistance from trained service personnel. See
“Customer and technical support“ on page 62.
Nucleic acid contamination
IMPORTANT! A primary source of contamination is DNA fragments from previously
processed samples. Do not introduce amplied DNA into the library preparation
laboratory or work area.
Instrument vibration and clearances
IMPORTANT! Signicant 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 instrument at least 40 in. (1 meter) away from major sources
of electronic noise such as refrigerators or microwaves.
Chapter 1 Product information
Instrument installation by trained personnel only
1
Ion GeneStudio S5 Instrument User Guide
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System components
Ion GeneStudio S5 System component configuration and layout
The Ion GeneStudio S5 Sequencer uses a virtual server, and the Ion GeneStudio S5
Plus Sequencer is equipped with an internal Torrent Server. These instruments are not
connected to an external Torrent Server. The Ion GeneStudio S5 Prime System
includes the Ion GeneStudio S5 Prime Sequencer and an external Torrent Server.
We support the layout in which the external Torrent Server is connected directly to the
Ion GeneStudio S5 Prime Sequencer, instead of through a local area network from a
remote location such as a server room. Data 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 are associated with an indirect connection between the Ion
GeneStudio S5 Prime Sequencer and the Torrent Server.
6
5
4
2
1
3
Ion GeneStudio S5 Prime System configuration
1Ion GeneStudio S5 Prime Sequencer
2Ion template preparation instrument
(Ion Chef™Instrument (shown) or
Ion OneTouch™2 System)
3Torrent Server
4Local area network
5Internet
6Client computer
2
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Ion GeneStudio S5 Instrument User Guide