ThermoFisher 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 B.0

Life Technologies Holdings Pte Ltd | Block 33 | Marsiling Industrial Estate Road 3 | #07-06, Singapore 739256
For descriptions of symbols on product labels or product documents, go to thermofisher.com/symbols-definition.
The information in this guide is subject to change without notice.
DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, THERMO FISHER SCIENTIFIC INC. 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
B.0 22 February 2022 Update the quantity of the Ion S5™Cartridge Tool in the Ion S5™Installation Kit.
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.
©2022 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 ............................................................ 12
Ion GeneStudio™S5 System component positions ................................. 13
Ion GeneStudio™S5 Sequencer input and output connections ....................... 14
■CHAPTER 3 Instrument operation ............................................... 15
Power the Ion GeneStudio™S5 Sequencer on or o ................................ 15
Power on ................................................................. 15
Power o ................................................................. 15
Update the Ion GeneStudio™S5 System software .................................. 16
Ion GeneStudio™S5 instrument run times ......................................... 16
Maintain the sequencer ......................................................... 18
Materials required .......................................................... 18
Clean or decontaminate the sequencer ....................................... 18
Perform the sequencer cleaning manually ..................................... 18
Perform an instrument reset run with an initialized sequencer that is loaded
with an unused Reagents cartridge ........................................ 20
Ion GeneStudio™S5 Instrument User Guide 3

■APPENDIX A Touchscreen reference ............................................ 21
Clean, Initialize, and Run ........................................................ 21
Settings ....................................................................... 22
Network Settings .......................................................... 22
System Tools .............................................................. 25
Check for software updates ................................................. 31
Data management ......................................................... 32
Manually delete run data .................................................... 34
Perform the instrument Clean operation ...................................... 35
Instrument settings ........................................................ 36
Touchscreen icons ............................................................. 38
Alarms, Notifications, and Events ................................................ 40
■APPENDIX B Troubleshooting .................................................... 43
Instrument alarms and events ................................................... 43
Initialization fails ............................................................... 44
Troubleshooting using control libraries ............................................ 46
Troubleshooting using Control Ion Sphere™Particles ............................... 46
Solid-state buer leak .......................................................... 47
Pulse clean the sequencer .................................................. 47
■APPENDIX C Supplemental procedures ........................................ 49
Set up and test the Ion Chip™Minifuge ........................................... 49
Install the Ion S5™/Ion Proton™Rotor and Buckets ............................ 49
Test the minifuge .......................................................... 51
■APPENDIX D Instrument warranty ............................................... 53
■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 safety ........................................................... 57
Safety and electromagnetic compatibility (EMC) standards .......................... 58
Safety ................................................................... 58
EMC ..................................................................... 58
Environmental design ...................................................... 59
Chemical safety ................................................................ 60
Contents
4Ion GeneStudio™S5 Instrument User Guide

■Documentation and support ....................................................... 62
Related documentation ......................................................... 62
Customer and technical support ................................................. 62
Limited product warranty ........................................................ 63
Contents
Ion GeneStudio™S5 Instrument User Guide 5

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.
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 specified.
The Ion S5™and Ion S5™XL Instruments continue to be supported by Thermo Fisher Scientific. 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 Instruments.
6Ion 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
1
Ion GeneStudio™S5 Instrument User Guide 7

Ion S5 Installation Kit (Part No. A27215; Not available for separate purchase.) (continued)
Contents Part No. Quantity Storage
Ion S5™Cartridge Tool A28308 1 15°C to 30°C
Ion S5™Chip Balance Pack A29022 1
Required materials and equipment not supplied
Unless otherwise indicated, all materials are available through thermofisher.com. "MLS" indicates that
the material is available from fisherscientific.com or another 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)
Minifuge Proton Rotor and Bucket Kit (required for use only with the
Ion OneTouch™2 System.)
4482578
(Optional) Uninterruptible 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 can adversely
affect system performance.
[2] For laboratories that experience frequent power outages or line voltage fluctuations, we recommend that you use an uninterruptible 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
8Ion 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 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 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 Ion Torrent™Server. These instruments are not connected to an external
Ion Torrent™Server. The Ion GeneStudio™S5 Prime System includes the Ion GeneStudio™S5 Prime
Sequencer and an external Ion Torrent™Server.
We support the layout in which the external Ion 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 Ion 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 Ion 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 Ion
Torrent™Server.
2
10 Ion GeneStudio™S5 Instrument User Guide

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)
3Ion Torrent™Server
4Local area network
5Internet
6Client computer
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
Chapter 2 System components
Ion GeneStudio™S5 System component configuration and layout 2
Ion GeneStudio™S5 Instrument User Guide 11

Internet connectivity
The Ion GeneStudio™S5 Sequencer, the Ion GeneStudio™S5 Plus Sequencer, or the Ion 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 Scientific does not support the USB method for updating software.
Any problems (for example, file 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 field 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 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 access remotely the Ion GeneStudio™S5 Sequencer, the
Ion GeneStudio™S5 Plus Sequencer, or the Ion Torrent™Server, which is required for system support.
Without remote access, service personnel cannot access, view, and troubleshoot problems 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. Although not recommended, you can enable
access to the 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 combination of the two. Implementing and maintaining such restrictions is the responsibility of your
server administrator and not of Thermo Fisher Scientific.
Note: For further support and troubleshooting for Ion Torrent™Server network access requirements,
see Software Administration in Torrent Suite™Software Help.
Chapter 2 System components
Internet connectivity
2
12 Ion GeneStudio™S5 Instrument User Guide

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 Ion S5™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.
·RFID regulatory information can be found on the main screen under Options4Regulatory info.
Chapter 2 System components
Ion GeneStudio™S5 System component positions 2
Ion GeneStudio™S5 Instrument User Guide 13

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/o switch – Power switch, where the states are on ( | ) or o ( 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
14 Ion GeneStudio™S5 Instrument User Guide

Instrument operation
Power the Ion GeneStudio™S5 Sequencer on or o
Note: If the Ion GeneStudio™S5 Sequencer is powered on, and the touchscreen is blank, touch the
screen to "wake" the touchscreen.
Power on
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 button on the left side of the instrument.
The button illuminates. When the instrument touchscreen Main Menu appears, the instrument is
ready for use.
Power o
It is not necessary to power o the instrument overnight or over the weekend. If the instrument will not
be used for more than three days, power o the instrument as follows:
1. In the Main Menu, tap Settings4System Tools4Shut Down.
2. Select either Shut Down or Reboot.
Note: If you select Shut Down, a confirmation message appears. Select Yes to power o the
instrument.
Note: Do not press the power button during a run. Interrupting power to the instrument during a run
can result in sequencing run failure and loss of sample.
3
Ion GeneStudio™S5 Instrument User Guide 15

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 Notifications/Alarms
button illuminates red in the touchscreen Main Menu. Press the red Alarms button 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 Settings4Check for Updates.
2. Press Update to download and install the updates automatically.
3. Press Done.
The instrument automatically restarts when the software update is complete.
Ion GeneStudio™S5 instrument run times
Approximate Ion GeneStudio™S5 instrument run times for a given chip type, read length, and number
of reads are shown in the following table. Run times indicate typical time from run start to BAM file
delivery (1 run/initialization).
Chip type Number of
reads
Read
length/output
Instrument run time
Ion GeneStudio™S5
Sequencer
Ion GeneStudio™S5
Plus Sequencer
Ion GeneStudio™S5
Prime Sequencer
Ion 510™Chip 2–3 M
200 bases
0.3–0.5 Gb 4.5 hours 3 hours 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
Chapter 3 Instrument operation
Update the Ion GeneStudio™S5 System software
3
16 Ion GeneStudio™S5 Instrument User Guide

(continued)
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 530™Chip 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 17

Maintain the sequencer
Materials required
•Lint-free wipes
•70% isopropanol
•(Optional) 10% bleach solution
Clean or decontaminate the sequencer
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 bottle, 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.
Perform the sequencer cleaning manually
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 first
sequencing run. The post-run cleaning is then performed normally after the second sequencing run.
However, if the "Enable post-run clean" checkbox is deselected for the second run, the cleaning is
not performed after either run. If the second sequencing run is not performed, or the cleaning is not
performed automatically after the second run, the instrument will not 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 sequencer that is loaded with an unused Reagents
cartridge” on page 20 for more information.
When a cleaning is necessary, use the following procedure:
Chapter 3 Instrument operation
Maintain the sequencer
3
18 Ion GeneStudio™S5 Instrument User Guide

1. On the home screen, press Settings4Clean Instrument.
The instrument door unlocks allowing access to the consumables.
2. Remove the Ion S5™Wash Solution bottle 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 bottle.
4. Ensure the Ion S5™Sequencing Reagents cartridge and Ion S5™Wash Solution bottle are properly
installed.
IMPORTANT! Perform the cleaning with a used reagent cartridge and wash solution bottle
installed. The cleaning procedure pumps cleaning solution into the wash solution bottle and
reagent cartridge making them unsuitable for sequencing.
5. Place a used sequencing chip in the chip clamp, then push the chip clamp in all the way to
engage.
6. Close the instrument door, then 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 19

Perform an instrument reset run with an initialized sequencer that is loaded
with an unused Reagents cartridge
Cleaning is normally automatically performed at completion of a sequencing run. If an Ion GeneStudio™
S5 System is initialized, an instrument reset run is required to ensure proper cleaning before
reinitialization in one of the following situations.
•A sequencing run is not started within 24 hours after initialization.
•A sequencing run is not completed due to a power failure or an abort, and <200 flows occurred
before the stoppage.
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 is sucient (see page 18).
·If the number of flows 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, tap 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 tap Next.
4. When prompted, select Planned Run (none). Ensure that the Enable post-run clean checkbox is
selected, then tap Review.
5. In the Select Run screen, tap Edit, then in the Detail screen set the number of flows to 200.
Ensure that the Post-Run/Clean checkbox is selected, then tap Close.
6. Tap Start run, then tap Accept to confirm 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.
Chapter 3 Instrument operation
Maintain the sequencer
3
20 Ion GeneStudio™S5 Instrument User Guide