For testing of Food and Environmental samples only.
Ion 510™ & Ion 520™ & Ion 530™ Food
Protection Kit–Chef
USER GUIDE
Instructions for automated template preparation, chip loading,
and sequencing for the Thermo Scientific™ Next Generation
Sequencing Food Authenticity Workflow
for use with:
Ion GeneStudio™ S5 Food Protection System
Ion Chef™ Food Protection Instrument
Ion 510™ Food Protection Chip Kit
Ion 520™ Food Protection Chip Kit
Ion S5™ Food Protection Controls Kit Plus
Catalog Numbers A39476 and A39477
Publication Number MAN0017967
Revision A.0
Manufacturer: Life Technologies Corporation | 5781 Van Allen Way | Carlsbad, CA 92008
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. MAN0017967
Revision Date Description
A.0 18 October 2018 New document.
TRADEMARKS: All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. SGS DNA is a registered
trademark of Scandinavian Gene Synthesis.
©2018 Thermo Fisher Scientific Inc. All rights reserved.
Contents
■CHAPTER 1 Product information ....................................... 6
Product description ............................................................. 6
Library compatibility ........................................................ 6
Software compatibility ....................................................... 6
Kit contents and storage ......................................................... 7
Kit summary ............................................................... 7
Ion Chef™ reagents and materials ............................................. 7
Ion S5™ reagents ........................................................... 8
Related products ................................................................ 8
Instruments ................................................................ 8
Compatible Ion Chip™ kits .................................................... 8
Ion S5™ Food Protection Controls Kit Plus ...................................... 9
Compatible library preparation kits ........................................... 9
Required materials not supplied .................................................. 9
About the Ion Chef™ Food Protection System ...................................... 10
Ion Chef™ Food Protection Instrument components ............................ 10
Interior hardware and consumables .......................................... 11
About the Ion Chef™ System touchscreen interface ............................. 12
Workflow ..................................................................... 13
■CHAPTER 2 Before you begin .......................................... 14
Precautions ................................................................... 14
Avoid nucleic acid contamination ............................................. 14
Avoid chip damage ......................................................... 14
Protection by equipment .................................................... 14
Guidelines for using Ion Chef™ reagents and consumables .......................... 14
Prepare the instrument for use .................................................. 15
■CHAPTER 3 Create a Planned Run .................................... 16
About Planned Runs ............................................................ 16
Create an NGS Food Authenticity template ........................................ 16
Plan an NGS Food Authenticity run using the template .............................. 19
Planned Run wizard key fields ................................................... 21
Ion 510
™
& Ion 520
™
& Ion 530
™
Food Protection Kit–Chef User Guide
3
■CHAPTER 4 Run the Ion Chef™ Food Protection System ............ 22
Materials required ............................................................. 22
Dilute the library pools ......................................................... 23
Dilute the sample library pool ............................................... 23
Dilute the control library (if used) ............................................ 23
Prepare the consumables ....................................................... 23
Add the diluted library pools to the Ion Chef™ Library Sample Tube ................... 24
Load the Ion Chef™ Food Protection System ....................................... 24
Load the pipette tip racks and PCR Plate ...................................... 26
Load the Reagents and Solutions cartridges .................................. 28
Load the Recovery Tubes and Enrichment Cartridge v2 ......................... 29
Load the Chip-loading centrifuge ............................................ 31
Confirm that consumables are correctly installed .............................. 33
Single chip loading workflow ................................................ 33
Ion Chef™ pre-run checklist ................................................. 35
Start the Ion Chef™ Food Protection Instrument run ................................ 36
Unload the chips for sequencing ................................................. 39
■CHAPTER 5 Initialize the instrument ................................. 42
Ion GeneStudio™ S5 Food Protection System component positions .................... 42
Before you begin .............................................................. 43
When a manual cleaning of the instrument is required .............................. 43
Initialize the instrument ........................................................ 44
■CHAPTER 6 Start the sequencing run ................................ 46
Chip handling guidelines ........................................................ 46
Start the sequencing run ....................................................... 47
Maintain the instrument ........................................................ 48
Materials required ......................................................... 48
Clean or decontaminate the instrument ...................................... 48
Reagent consumables disposal .................................................. 48
CO2 scrubber removal and disposal .......................................... 49
Recycle Ion S5™ Wash Solution and Ion S5™ Cleaning Solution bottles ............ 49
■CHAPTER 7 Clean the Ion Chef™ Food Protection System .......... 50
About the cleaning protocol ..................................................... 50
Materials required ............................................................. 50
Clean the Ion Chef™ Food Protection Instrument ................................... 51
Remove and discard used consumables ...................................... 52
Inspect and clean the Recovery centrifuges and buckets ........................ 53
Start the cleaning ......................................................... 54
Contents
4
Ion 510
™
& Ion 520
™
& Ion 530
™
Food Protection Kit–Chef User Guide
■APPENDIX A Troubleshooting ......................................... 56
Ion Chef™ Food Protection System setup and operation ............................. 56
Ion GeneStudio™ S5 Food Protection System setup and operation .................... 59
Instrument alarms and events ............................................... 59
■APPENDIX B Supplemental procedures .............................. 60
Perform a manual cleaning of the instrument ...................................... 60
Perform an instrument reset run with an initialized, unused Ion S5™ Sequencing
Reagents cartridge ............................................................. 61
Maintain the Ion Chef™ Food Protection System .................................... 62
Install a firmware update ................................................... 62
Change the instrument name ............................................... 63
■APPENDIX C Safety ..................................................... 64
Symbols on this instrument ..................................................... 65
Conformity symbols ........................................................ 65
Location of safety labels on this instrument ....................................... 66
Safety information for instruments not manufactured by Thermo Fisher Scientific ..... 66
Instrument safety .............................................................. 66
General .................................................................. 66
Physical injury ............................................................ 66
Electrical safety ........................................................... 67
Cleaning and decontamination ............................................... 67
Ultraviolet (UV) Safety ...................................................... 67
Safety and electromagnetic compatibility (EMC) standards .......................... 67
Safety compliance ......................................................... 68
EMC ...................................................................... 68
Environmental design ...................................................... 68
Instrument safety — Ion GeneStudio™ S5 Food Protection Instrument ................ 69
Chemical safety ................................................................ 69
Biological hazard safety ......................................................... 70
■APPENDIX D Documentation and support ............................ 71
Food Safety support ............................................................ 71
Contents
Ion 510
™
& Ion 520
™
& Ion 530
™
Food Protection Kit–Chef User Guide
5
Product information
■Product description ................................................... 6
■Kit contents and storage ................................................ 7
■Related products ...................................................... 8
■Required materials not supplied ......................................... 9
■About the Ion Chef™ Food Protection System ............................ 10
■Workow ........................................................... 13
IMPORTANT! Before using this product, read and understand the information in the
“Safety” appendix in this document.
Product description
The Ion 510™ & Ion 520™ & Ion 530™ Food Protection Kit–Chef (Cat. Nos. A39476 and
A39477) includes reagents and materials to:
• Use the Ion Chef™ Food Protection Instrument to prepare template-positive Ion
Sphere™ Particles.
• Load them onto the Ion 510™ Food Protection Chip or Ion 520™ Food Protection
Chip.
• Sequence the loaded chips using the Ion GeneStudio™ S5 Food Protection
Instrument.
Library kit
Cat. No. A39476
(1 run per
initialization)
Cat. No. A39477
(2 runs per
initialization)
SGS All Species ID Meat DNA Analyser I ✓ ✓
SGS All Species ID Meat DNA Analyser II ✓ ✓
SGS All Species ID Fish DNA Analyser I ✓ ✓
SGS All Species ID Fish DNA Analyser II ✓ ✓
SGS All Species ID Plant DNA Analyser I ✓
SGS All Species ID Plant DNA Analyser II ✓
The Ion 510™ & Ion 520™ & Ion 530™ Food Protection Kit–Chef is compatible with
Torrent Suite™ Software 10 and later. Be sure to update your Torrent Server to the
latest available version of Torrent Suite™ Software before using this kit.
1
Library
compatibility
Software
compatibility
6
Ion 510
™
& Ion 520
™
& Ion 530
™
Food Protection Kit–Chef User Guide
Kit contents and storage
IMPORTANT! Do not substitute components from any other Ion sequencing kits. This
protocol has been veried using these specic materials. Substitution can adversely
aect system performance.
IMPORTANT! Store all consumables and cartridges under the recommended
conditions and in an upright position. Do NOT store the Ion S5™ Sequencing Reagents
(Cat. No. A27768) on dry ice or in a closed environment where dry ice is present.
The Ion 510™ & Ion 520™ & Ion 530™ Food Protection Kit–Chef (Cat. No. A39476)
contains all materials that are required to prepare and sequence 8 chips. The kit
supports 4 Ion Chef™ runs and 8 sequencer initializations, as required for
400-base-read libraries.
Cat. No. A39477 supports 4 Ion Chef™ runs and 4 sequencer initializations. Use
Cat. No. A39477 if you are preparing a single chip per Ion Chef™ run or when
performing two sequencing runs per initialization (for 200-base-read libraries).
On arrival, inspect all consumables and contact Technical Support if any of the
products have been damaged during shipping.
Component
Cat. No. A39476
(1 run per initialization)
Cat. No. A39477
(2 runs per initialization)
Part No. Quantity per
kit Part No. Quantity per
kit
Ion S5™ Chef Supplies A27755 4 boxes A27755 4 boxes
Ion S5™ Chef Solutions A27754 1 box A27754 1 box
Ion 510™ & Ion 520™ &
Ion 530™ Chef
Reagents
A34018 1 box A34018 1 box
Ion S5™ Sequencing
Solutions
A27767 2 boxes A27767 1 box
Ion S5™ Sequencing
Reagents
A27768 2 boxes A27768 1 box
Contents Amount / box Storage
Ion S5™ Chef Supplies (Part No. A27755)
Chip Adapter 2 15°C to 30°C
Enrichment Cartridge v2 1
Tip Cartridge v2 1
PCR Plate 1
Kit summary
Ion Chef™
reagents and
materials
Chapter 1 Product information
Kit contents and storage
1
Ion 510
™
& Ion 520
™
& Ion 530
™
Food Protection Kit–Chef User Guide
7
Contents Amount / box Storage
Frame Seal v2 15°C to 30°C1
Recovery Station Disposable Lid v2 2
Recovery Tube v2 12
Ion S5™ Chef Solutions (Part No. A27754)
Ion S5™ Chef Solutions 4 cartridges 15°C to 30°C
Ion 510™ & Ion 520™ & Ion 530™ Chef Reagents (Part No. A34018)
Ion 510™ & Ion 520™ & Ion 530™ Chef
Reagents
4 cartridges –30°C to –10°C
IMPORTANT! Do not store the Ion S5™ Sequencing Reagents (Part No. A27768) on
dry ice or in a closed environment containing dry ice.
Contents Amount / box Storage
Ion S5™ Sequencing Solutions (Part No. A27767)
Ion S5™ Wash Solution 4 × 1.5 L 15°C to 30°C
Ion S5™ Cleaning Solution 250 mL
Ion S5™ Sequencing Reagents (Part No. A27768)
Ion S5™ Sequencing Reagents
(Cartridges ship at 2°C to 8°C. Store as
indicated.)
4 cartridges –30°C to –10°C
do not store on dry ice
Related products
Description Source
Ion GeneStudio™ S5 Food Protection Instrument A37904
Ion Chef™ Food Protection Instrument 4484178
Description Catalog No. Quantity Storage
Ion 510™ Food Protection Chip Kit
(8 pack)
A27769 8 chips
15°C to 30°C
Ion 520™ Food Protection Chip Kit
(8 pack)
A39473 8 chips
Ion S5™ reagents
Instruments
Compatible Ion
Chip™ kits
Chapter 1 Product information
Related products
1
8
Ion 510
™
& Ion 520
™
& Ion 530
™
Food Protection Kit–Chef User Guide
The Ion S5™ Food Protection Controls Kit Plus (Cat. No. A39478) is ordered
separately. See the Ion S5™ Food Protection Controls Kit Plus Product Information Sheet
(Pub. No. MAN0017993) for details.
Contents Amount Storage
Human CEPH Genomic DNA Control (red cap) 30 µL −30°C to −10°C
Human CEPH Control 200 Library (yellow cap) 12 µL
E. coli
DH10B Control 400 Library (orange cap) 16 µL
Library kit Cat. No. Source
SGS All Species ID Meat DNA Analyser I A38452 Thermo Fisher
Scientific
microbiology
ordering process
SGS All Species ID Meat DNA Analyser II A38453
SGS All Species ID Fish DNA Analyser I A38454
SGS All Species ID Fish DNA Analyser II A38455
SGS All Species ID Plant DNA Analyser I A38456
SGS All Species ID Plant DNA Analyser II A38457
Required materials not supplied
Unless otherwise indicated, all materials are available through thermosher.com.
MLS: Fisher Scientic (sherscientic.com) or other major laboratory supplier.
Item Source
P2, P10, P20, P200, P1000 pipettor set and filtered tips MLS
Gloves, powder-free nitrile MLS
Ice buckets and ice —
Nuclease-free water, molecular biology grade MLS
Isopropanol, 70% solution MLS
Wipes, disposable lint-free MLS
(Optional)
Non-interruptible Power Supply (UPS) [1] MLS
[1] For laboratories that experience frequent power outages or line voltage fluctuations, we recommend that you
use a non-interruptible power supply that is compatible with 2500 W output or higher.
Ion S5™ Food
Protection
Controls Kit Plus
Compatible library
preparation kits
Chapter 1 Product information
Required materials not supplied
1
Ion 510
™
& Ion 520
™
& Ion 530
™
Food Protection Kit–Chef User Guide
9
About the Ion Chef™ Food Protection System
The Ion Chef™ Food Protection System provides automated, high-throughput
template preparation and chip loading for use with the Ion GeneStudio™ S5 Food
Protection Instrument. The system includes a complete set of cartridge-based
consumables and reagents that enable you to load two Ion 510™ Food Protection
Chips or Ion 520™ Food Protection Chips in approximately 13 hours with less than
15 minutes of hands-on time.
The Ion Chef™ Food Protection System features network integration with the Torrent
Suite™ Software to enable sample and reagent traceability throughout the chip
preparation workow.
The following gure illustrates the major external and internal features of the
Ion Chef™ Food Protection Instrument.
4
1 2 3
5 6 7
8
1Door—Provides access to the interior of
the instrument. The door is locked in the
closed position during operation.
2Micropipettor—A mechanical positive-
displacement pipettor that performs all
fluid transfers during sample and chip
preparation.
3Robotic arm—Performs fluid transfer
during chip loading. The arm also
contains an optical sensor that reads the
barcodes of instrument reagents and
consumables.
4Touchscreen—Provides access to all
instrument functions for operation,
maintenance, and troubleshooting.
5Power button—Power switch for the
Ion Chef™ Food Protection Instrument,
where the states are on (illuminated) and
off.
6Power port—A 100–240 VAC port that
provides power to the Ion Chef™ Food
Protection Instrument.
7Ethernet port—An RJ45 port that provides
Ethernet (100 Mbit) communication with
the Ion Chef™ Food Protection Instrument.
8USB port—Provides USB communication
with the Ion Chef™ Food Protection
Instrument. Used to update the
instrument firmware and to transfer data
during service or maintenance.
Ion Chef™ Food
Protection
Instrument
components
Chapter 1 Product information
About the Ion Chef
™
Food Protection System
1
10
Ion 510
™
& Ion 520
™
& Ion 530
™
Food Protection Kit–Chef User Guide
The following gure illustrates the interior of the Ion Chef™ Food Protection
Instrument and describes the stations that are involved in the preparation of chips for
sequencing on the Ion GeneStudio™ S5 Food Protection System.
A
B
C
D
E
F
G
H
1 2 3 4 56 7 8 9 10 11 12
5
3
8
12
6
4
7
530 CCBD02226
530 CCBD02226
9
1Waste pipette tip rack—The position of the rack containing waste (used) pipette tips.
2Automated heated cover—Transfers the plate cover to the PCR reaction plate within the
sample block. During thermal cycling, the heated cover applies compression to seal the
reaction plate and heats the cover to prevent condensation.
3New pipette tips—The position of the rack containing unused pipette tips.
4Thermal cycler sample block—Performs thermal cycling of the sequencing reactions on a
96-well PCR reaction plate.
5Reagents station—The position on the instrument deck of the diluted libraries, NaOH, and
the Ion 510™ & Ion 520™ & Ion 530™ Chef Reagents cartridge.
6Solutions station—The position on the instrument deck of the Ion S5™ Chef Solutions
cartridge, which is maintained at room temperature.
7Recovery centrifuges—Twin stations that perform centrifugation of the ISPs during the
recovery phase of template preparation.
8Enrichment station—The position of the rack containing consumables for the enrichment
of the template-positive ISPs.
9Chip-loading centrifuge—Performs centrifugation of sequencing chips that have been
mounted to chip-loading adapters and loaded with template-positive ISPs.
Interior hardware
and consumables
Chapter 1 Product information
About the Ion Chef
™
Food Protection System
1
Ion 510
™
& Ion 520
™
& Ion 530
™
Food Protection Kit–Chef User Guide
11
The Ion Chef™ Food Protection System features a simple interface for loading chips,
cleaning the instrument, and performing system maintenance and conguration tasks.
2
1
3 4 5
1Set up run button – Set up the Ion Chef™ template preparation and chip-loading routine.
Choose Step by Step to have the instrument lead you stepwise through installation of
reagents and consumables, or choose Quick Start to proceed if you have already installed
the consumables.
2Open Door button.
3Notifications button – View notifications about instrument status during and between runs.
4Quick Start button – Proceed directly to the Quick Start instrument setup mode. User
verifies the loading of a new pipette tip cartridge and an empty pipette tip rack to hold
waste tips generated during the run, before proceeding to Deck Scan.
5Settings button – Advance to a screen providing the following options:
•Notifications: view notifications about instrument status during and between runs
•Instrument Settings: view current settings and network configuration, set instrument
name, adjust time zone
•Service tools: access screens for service-related maintenance and instrument
diagnostics
•Torrent Server: add and manage Torrent Server connections
•Clean Ion Chef: proceed directly to the instrument cleaning routine
•Check for updates: check availability of system software updates
About the Ion
Chef™ System
touchscreen
interface
Chapter 1 Product information
About the Ion Chef
™
Food Protection System
1
12
Ion 510
™
& Ion 520
™
& Ion 530
™
Food Protection Kit–Chef User Guide
Workflow
The following workow illustrates how to prepare and load samples using the Ion
510™ & Ion 520™ & Ion 530™ Food Protection Kit–Chef and Ion Chef™ Food Protection
System for sequencing on an Ion GeneStudio™ S5 Food Protection Instrument.
Create a Planned Run in Torrent Suite™ Software.
q
Dilute the library samples, and thaw the reagents.
q
Load the Ion Chef™ Food Protection Instrument.
q
Start the Ion Chef™ Food Protection Instrument.
q
Unload the Ion Chef™ Food Protection Instrument.
q
Load the prepared chip into the sequencer, then begin the sequencing
run.
Chapter 1 Product information
Workflow
1
Ion 510
™
& Ion 520
™
& Ion 530
™
Food Protection Kit–Chef User Guide
13
Before you begin
■Precautions .......................................................... 14
■Guidelines for using Ion Chef™ reagents and consumables ................ 14
■Prepare the instrument for use ......................................... 15
Precautions
IMPORTANT! A primary source of contamination is spurious DNA fragments from
previous sample processing steps. Do not introduce amplied DNA into the library
preparation laboratory or work area.
IMPORTANT! To avoid possible damage to the chip due to electrostatic discharge,
ground yourself before picking up a chip or placing a chip on a surface such as a lab
bench. For example, touch the metal trim on the chip compartment before inserting or
removing a chip from the chip clamp.
WARNING! The protection that is provided by the equipment can be impaired
if the instrument is operated outside the environment and use specications,
the user provides inadequate maintenance, or the equipment is used in a
manner that is not specied by the manufacturer (Thermo Fisher Scientic).
Guidelines for using Ion Chef™ reagents and consumables
To ensure the proper function of the Ion Chef™ Food Protection System, handle the
associated consumables and reagents according to the following guidelines:
• Store all consumables and cartridges under the recommended conditions and in
an upright position.
• Inspect all consumables and cartridges for damage on arrival and again before
use.
• Hold sequencing chips by gently gripping them by their edges.
• When the instrument is not in use, remove all consumables and reagents from the
deck and close the instrument door.
• Do not reuse any consumables or reagents. All components are single-use only.
Note: Each new Tip Cartridge v2 is used by the instrument for multiple
pipeing steps, but after each run, the empty Tip Cartridge v2 is transferred to
the waste tip station.
2
Avoid nucleic acid
contamination
Avoid chip damage
Protection by
equipment
14
Ion 510
™
& Ion 520
™
& Ion 530
™
Food Protection Kit–Chef User Guide
• Use only specied kits and supplies with the Ion Chef™ Food Protection
Instrument. The use of third-party reagents and supplies can adversely aect the
performance of the instrument and chips.
• Remove and sequence chips within 1 hour after the instrument nishes loading
them. If you cannot sequence a loaded chip immediately, store it in a chip storage
container at 4°C until you are ready to run it (up to 6–8 hours maximum).
Note: If you choose to store a loaded chip, remove the chip from 4°C storage (but
keep it in the chip storage container) at least 20 minutes before running it,
allowing the chip to warm to room temperature.
Prepare the instrument for use
Before you use the Ion Chef™ Food Protection Instrument:
• Ensure that the instrument has been cleaned following the previous run. If not,
clean the instrument before loading it with consumables.
Note: For more information on the cleaning procedure, see Chapter 7, “Clean the
Ion Chef™ Food Protection System“.
• Inspect the empty compartments of the Reagents and Solutions stations for
condensation. Condensate can collect in these compartments, depending on
temperature and humidity conditions. Before loading consumables into the
instrument, wipe the compartments dry with a laboratory wipe or absorbent
cloth, if needed.
• Thaw the Ion 510™ & Ion 520™ & Ion 530™ Chef Reagents cartridge at room
temperature for 45 minutes before use.
• Ensure that the instrument has a connection to the Torrent Server. On the
instrument home touchscreen, touch Seings, then Torrent Server to view the
connection status.
Note: If the instrument is not connected, see Ion Chef™ and Torrent Server Network
Setup User Guide (MAN0013444) for instructions on how to congure a direct or
indirect network connection.
Chapter 2 Before you begin
Prepare the instrument for use
2
Ion 510
™
& Ion 520
™
& Ion 530
™
Food Protection Kit–Chef User Guide
15
Create a Planned Run
■About Planned Runs .................................................. 16
■Create an NGS Food Authenticity template .............................. 16
■Plan an NGS Food Authenticity run using the template ................... 19
■Planned Run wizard key elds ......................................... 21
About Planned Runs
Planned Runs are digital instructions that are created in Torrent Suite™ Software for
controlling the template preparation and sequencing instruments. Planned Runs
contain seings such as number of ows, kit types, barcodes, sample information, and
reference les (if any). Planned Runs are also used to track samples, chips, and
reagents throughout the workow, from template preparation on the Ion Chef™ Food
Protection Instrument through sequencing on an Ion GeneStudio™ S5 Food Protection
Instrument and subsequent data analysis. Each chip that is prepared in an Ion Chef™
run requires its own Planned Run.
IMPORTANT! For more information on creating a Planned Run in Torrent Suite™
Software, including a complete description of each eld in the Create Plan workow
bar, see the Torrent Suite™ Software Help, available by clicking the Help buon in the
software.
Create an NGS Food Authenticity template
Create one or more NGS Food Authenticity templates for your Planned Runs.
Detailed information on creating Planned Run templates is provided in the Torrent
Suite™ Software Help.
Dierent SGS All Species ID DNA Analyser library preparation kits require dierent
numbers of ows during sequencing, and the number of ows is controlled by the
Planned Run. Therefore, you may have to create dierent Planned Run templates,
depending on the library kits you are using. A single Planned Run template
containing 600 ows can be used for all SGS All Species ID DNA Analyser library
preparation kits. However, if using only the SGS All Species ID DNA Analyser library
3
16
Ion 510
™
& Ion 520
™
& Ion 530
™
Food Protection Kit–Chef User Guide
preparation kit for meat or for sh, an alternative Planned Run containing 500 ows
can be used to reduce the run time and enable two sequencing runs per initialization.
1. Sign in to Torrent Suite™ Software on the Torrent Server that is connected to your
Ion Chef™ Food Protection Instrument and Ion GeneStudio™ S5 Food Protection
Instrument.
Note: Your software account is set up on Torrent Server during system
installation.
2. Click the Plan tab, then click Templates.
3. Select Generic Sequencing4Add New Template
4. Select parameters for the template based on the types of samples to be analyzed.
Meat and/or fish
analysis parameter Selection
Ion Reporter
Ion Reporter
Account
None
Sample Grouping Other
Research Application
Research
Application
DNA
Target Technique Other
Kits
Instrument Select Ion GeneStudio™ S5 Food Protection Instrument
Sample
Preparation Kit
Library Kit Type
Template Kit Select Ion 510™ & Ion 520™ & Ion 530™ Food Protection Kit–
Chef
Advanced settings Use recommended defaults for meat or fish samples
Sequencing Kit Select Ion S5 Sequencing Kit
Note: The sequencing kit name is generic for this application.
Chip Type Select the chip type that you are using
Chapter 3 Create a Planned Run
Create an NGS Food Authenticity template
3
Ion 510
™
& Ion 520
™
& Ion 530
™
Food Protection Kit–Chef User Guide
17
Meat and/or fish
analysis parameter Selection
Control sequence
Barcode Set
Flows Select 500 for meat or fish samples
Advanced settings Use the recommended defaults
Plugins
Plugins FileExporter™ plugin
Note: To configure the FileExporter™ settings, click
Settings4Plugins4FileExporter settings4Configure . In the
dialog, include FastQ files and do not include other file types,
then save the configuration.
Projects
Projects
Save
Template Name Type a name for the template
Analysis
Parameters
Default
Plant analysis
parameter Selection
Ion Reporter
Ion Reporter
Account
None
Sample Grouping Other
Research Application
Research
Application
DNA
Target Technique Other
Kits
Instrument Select Ion GeneStudio™ S5 Food Protection Instrument
Sample
Preparation Kit
Library Kit Type
Template Kit Select Ion 510™ & Ion 520™ & Ion 530™ Food Protection Kit–
Chef
Advanced settings Select Customize4Chef Protocol4400 bp for plant samples,
and do not change any other settings.
Sequencing Kit Select Ion S5 Sequencing Kit
Note: The sequencing kit name is generic for this application.
Chapter 3 Create a Planned Run
Create an NGS Food Authenticity template
3
18
Ion 510
™
& Ion 520
™
& Ion 530
™
Food Protection Kit–Chef User Guide
Plant analysis
parameter Selection
Chip Type Select the chip type that you are using
Control sequence
Barcode Set
Flows Select 600 for plant samples
Advanced settings Use the recommended defaults
Plugins
Plugins FileExporter™ plugin
Note: To configure the FileExporter™ settings, click
Settings4Plugins4FileExporter settings4Configure . In the
dialog, include FastQ files and do not include other file types,
then save the configuration.
Projects
Projects
Save
Template Name Type a name for the template
Analysis
Parameters
Default
5. Save the template.
Plan an NGS Food Authenticity run using the template
1. Sign in to Torrent Suite™ Software on the Torrent Server that is connected to your
Ion Chef™ Food Protection Instrument and Ion GeneStudio™ S5 Food Protection
Instrument.
Note: Your software account is set up on Torrent Server during system
installation.
2. On the Plan tab, click Templates, then select Generic Sequencing.
3. For the template that you will use for the run, on the far right click the Seings
buon, then select Plan Run.
4. In the Planned Run wizard, review the tabs (IonReporter, Research Application,
Kits, Plugins, Projects) and make selections appropriate for your run (see
“Planned Run wizard key elds“ on page 21).
5. Complete the Plan tab.
a. Enter a name for the planned run.
b. For Analysis Parameters, make sure that Default (Recommended) is
selected.
Chapter 3 Create a Planned Run
Plan an NGS Food Authenticity run using the template
3
Ion 510
™
& Ion 520
™
& Ion 530
™
Food Protection Kit–Chef User Guide
19
c. Enter the number of chips to create for the Planned Runs. To specify two
sample names, in Number of chips, enter 2, then click the check mark
buon on the right.
d. In the Sample elds appropriate for each plan, enter a sample name
(Library pool name).
e. In Sample Tube Label, enter or scan the barcode of the Ion Chef™ Library
Sample Tube.
IMPORTANT! You must enter or scan the barcode of each Ion Chef™ Library
Sample Tube.
f. When you have completed your selections, click Plan Run to save the run.
The run is listed on the Planned Runs page with the specied name and is
automatically used by the Ion Chef™ Food Protection Instrument when the
sample is loaded.
Chapter 3 Create a Planned Run
Plan an NGS Food Authenticity run using the template
3
20
Ion 510
™
& Ion 520
™
& Ion 530
™
Food Protection Kit–Chef User Guide
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