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
4
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.
6
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
7

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
8
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
9

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
10
Ion GeneStudio S5 Instrument User Guide

5
3
4
1
2
Ion GeneStudio S5 System, or Ion GeneStudio S5 Plus System configuration
1Ion GeneStudio S5 Sequencer, or Ion GeneStudio S5 Plus Sequencer
2Ion template preparation instrument (Ion Chef™Instrument (shown) or Ion OneTouch™2
System)
3Local area network
4Internet
5Client computer
Internet connectivity
The Ion GeneStudio S5 Sequencer, the Ion GeneStudio S5 Plus Sequencer, or the
Torrent Server (in an Ion GeneStudio S5 Prime System) should be connected to a
network with internet access. Connecting to the Internet allows you to update your
software and access remote system support easily. Software updates through the
network/internet are free. If you do not connect your instrument or server to a
network, software updates must be manually installed via USB.
IMPORTANT! Thermo Fisher Scientic does not support the USB method for
updating software.
Any problems (for example, le corruption, 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 eld
service engineer to correct the problem at your own expense.
In providing outbound access to the Internet from the server, you enable the support
team to provide inbound support. The Ion GeneStudio S5 Sequencer, the Ion
GeneStudio S5 Plus Sequencer, and the 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 access remotely the Ion GeneStudio S5 Sequencer, the Ion
GeneStudio S5 Plus Sequencer, or the Torrent Server, which is required for system
Chapter 2 System components
Internet connectivity
2
Ion GeneStudio S5 Instrument User Guide
11

support. Without remote access, service personnel cannot access, view, and
troubleshoot problems regarding machine performance.
To enable full support, the Torrent Server must have outbound internet access (ports
22, 80, and 443) and be behind an appropriately congured rewall. Although not
recommended, you can enable access to the Torrent Browser (the web server running
on the Torrent Server from the Internet). If you provide such access, you must restrict
access to the server using HTTP and AUTH rewall rules, or a combination of the
two. Implementing and maintaining such restrictions is the responsibility of your
server administrator and not of Thermo Fisher Scientic.
Note: For further support and troubleshooting for Torrent 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
1Touchscreen
2Power button
3Ion S5™Sequencing Reagents cartridge
4Chip clamp
5Ion S5™Wash Solution bottle. Waste reservoir located behind the Wash Solution bottle
(shown on the right).
6Ion S5™Cleaning Solution bottle
7Waste reservoir
Note: The system uses RFID technology to verify that the proper reagents are loaded
in positions 3, 5, and 6. Reagents that exceed their expiration date or usage count
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
Options4Regulatory info.
Chapter 2 System components
Ion GeneStudio S5 System component positions
2
12
Ion GeneStudio S5 Instrument User Guide

Ion GeneStudio S5 Sequencer input and output connections
5
4
2
1
3
1
1USB ports – Connects a USB device to the instrument.
2Ethernet port – An RJ45 port that provides Ethernet (Gigabit) communication between the
sequencer and a local area network.
3Ethernet port – An RJ45 port that provides Ethernet (Gigabit) communication with the Ion
Chef™Instrument.
4On/off switch – Power switch, where the states are on ( | ) or off ( O ).
5Power 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
13

Instrument operation
Power the Ion GeneStudio S5 Sequencer on or off
Note: If the Ion GeneStudio S5 Sequencer is powered on, and the touchscreen is
blank, touch the screen to "wake" the touchscreen.
If the touchscreen is unresponsive, check the power switch on the back of the
instrument to ensure that the switch is in the on (|) position. If the power switch is in
the o (0) position, proceed with step 1. If the power switch is already in the on
position, proceed to step 2.
1. Turn the power switch on the back of the instrument to the on (|) position.
2. Press the power buon on the left side of the instrument.
The buon illuminates. When the instrument touchscreen Main Menu appears,
the instrument is ready for use.
It is not necessary to power o the instrument overnight or over the weekend. If the
instrument will not be used for more than 3 days, power o the instrument as follows:
1. In the Main Menu, press Seings4System Tools4Shut Down.
2. Select either Shut Down or Reboot.
Note: If you select Shut Down, a conrmation message appears. Select Yes to
power o the instrument.
Note: Do not press the power buon during a run. Interrupting power to the
instrument during a run may result in sequencing run failure and loss of sample.
Update the Ion GeneStudio S5 System software
Note: An internet connection is required for the Ion GeneStudio S5 System to receive
alerts that software updates are available.
If an update to the Ion GeneStudio S5 Sequencer software is available, the
Notications/Alarms buon illuminates red in the touchscreen Main Menu. Press the
red Alarms buon to see the detailed messages. If a message states New Software
Available, follow these steps to update the software:
1. In the Main Menu, press Seings4Check for Updates.
2. Press Update to download and install the updates automatically.
3. Press Done.
3
Power on
Power off
14
Ion GeneStudio S5 Instrument User Guide

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 le 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 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
9–12 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
3
Ion GeneStudio S5 Instrument User Guide
15

Maintain the sequencer
• Lint-free wipes
• 70% isopropanol
•(Optional) 10% bleach solution
In the event of a spill or leak on or inside the instrument, perform the following steps.
Note: Dispose of all waste in appropriate liquid or solid waste containers.
1. Remove the Ion S5™ Wash Solution bole, then remove and empty the waste
reservoir.
2. Remove the Ion S5™ Sequencing Reagents cartridge.
3. Inspect the waste and nucleotide reagent bays for liquid.
4. Using absorbent paper soak up as much liquid as possible, then wash the
aected area with 10% bleach solution.
5. Wipe the aected surfaces with 70% isopropanol, then allow to air-dry.
The Ion GeneStudio S5 Sequencers require cleaning before initialization. Cleaning is
normally performed automatically at the completion of the previous sequencing run.
To enable two sequencing runs on a single initialization, you must deselect the
"Enable post-run clean" checkbox for the rst 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
allow the subsequent initialization to proceed until a manual cleaning has been
performed.
If an Ion GeneStudio S5 Sequencer is initialized and
• a sequencing run is not started within 24 hours, or
• a run is not started or completed due to a power failure or an abort
do not perform a manual cleaning. An instrument reset run is required before
reinitialization. See “Perform an instrument reset run with an initialized, unused
Sequencing Reagents cartridge“ on page 18 for more information.
Required
materials
Clean or
decontaminate the
sequencer
Perform the
sequencer
cleaning manually
Chapter 3 Instrument operation
Maintain the sequencer
3
16
Ion GeneStudio S5 Instrument User Guide

When a cleaning is necessary, use the following procedure:
1. On the home screen, press Seings4Clean Instrument.
The instrument door unlocks allowing access to the consumables.
2. Remove the Ion S5™ Wash Solution bole to access the waste reservoir, then
remove and empty the waste reservoir.
1
2
3
3. Reinstall the empty waste reservoir and a used Ion S5™ Wash Solution bole.
4. Ensure the Ion S5™ Sequencing Reagents cartridge and Ion S5™ Wash Solution
bole are properly installed.
IMPORTANT! Perform the cleaning with a used reagent cartridge and wash
solution bole installed. The cleaning procedure pumps cleaning solution into
the wash solution bole 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 press Next.
Cleaning takes ~35 minutes to complete. On completion, the instrument door
automatically unlocks and the chip and cartridge clamps disengage.
Chapter 3 Instrument operation
Maintain the sequencer
3
Ion GeneStudio S5 Instrument User Guide
17

Cleaning is normally performed at completion of a sequencing run automatically. If
an Ion GeneStudio S5 is initialized and
•a sequencing run is not started within 24 hours after initialization, or
• a sequencing run is not completed due to a power failure or an abort, and <200
ows occurred before the stoppage
an instrument reset run is required to ensure proper cleaning before reinitialization.
Do NOT perform a manual cleaning with an unused, initialized Ion S5™ Sequencing
Reagents cartridge.
Note:
·If a power failure or abort occurs during the second of two runs started after a
single initialization, a manual cleaning (page 16) is sucient.
·If the number of ows that occurred before a power failure or abort is unknown,
perform an instrument reset run.
To perform an instrument reset run, use the following procedure 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 Review.
5. In the Select Run screen, press Edit, then in the Detail screen set the number of
ows to 200. Ensure that the Post-Run/Clean checkbox is selected, then press
Close.
6. Press Start run, then press Accept to conrm that Post-Run Clean is enabled, and
to start the run.
When the instrument reset run completes, the instrument automatically performs the
cleaning procedure. After cleaning, the touchscreen returns to the main menu.
Perform an
instrument reset
run with an
initialized, unused
Sequencing
Reagents
cartridge
Chapter 3 Instrument operation
Maintain the sequencer
3
18
Ion GeneStudio S5 Instrument User Guide

Touchscreen reference
Clean, Initialize, and Run
Ion GeneStudio S5
In the Home screen, the Clean, Initialize, and Run programs lead you through the
necessary steps to prepare the instrument for sequencing and to start a sequencing
run. Press the main dial to start a program. Simple, easy to follow instructions are
provided on the touchscreen.
• Cleaning must be performed before each initialization to ensure that the reagents
from the previous run are cleared from the uid lines. The Clean program is
normally 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 cartridge, wash solution, and cleaning solution
• 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 Suite™ Software
– Performing sequencing
A
Ion GeneStudio S5 Instrument User Guide
19

Settings
In the Seings menu, users can view and/or change instrument seings, manage data
and network congurations, and update the installed software.
The Network Seings menu allows you to congure IP address, Torrent Server, and
FTP seings.
Network Settings
Appendix A Touchscreen reference
Settings
A
20
Ion GeneStudio S5 Instrument User Guide