Thermo Scientific Ion Torrent Genexus Integrated Sequencer User manual

For Research Use Only. Not for use in diagnostic procedures.
Genexus™Integrated Sequencer
USER GUIDE
Catalog Number A45727
Publication Number MAN0017910
Revision A.0

Manufacturer:
Life Technologies Holdings Pte Ltd |
Block 33 |
Marsiling Industrial Estate Road 3 |
#07-06, Singapore 739256
Products:
Genexus™Integrated Sequencer
Genexus™Software
Manufacturer:
Life Technologies Corporation |
7335 Executive Way |
Frederick, MD 21704 | USA
Products:
GX5™Chip and Genexus™Coupler
Genexus™Library Strips 1 and 2‑AS
Genexus™Library Strips 1 and 2‑HD
Genexus™Templating Strips 3 and 4‑GX5™
Genexus™Barcodes 1–96 AS
Genexus™Barcodes 1–32 HD
Genexus™Primer Pool Tubes
Genexus™Pipette Tips
Genexus™Sequencing Kit
Genexus™Controls
Genexus™GX5™Starter Pack‑AS
Genexus™GX5™Starter Pack‑HD
Oncomine™GX assays
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. MAN0017910
Revision Date Description
A.0 13 November 2019 New user guide for the Genexus™Integrated Sequencer
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. Microsoft and Excel are
trademarks of Microsoft Corp. TaqMan is a registered trademark of Roche Molecular Systems, Inc., used under permission and license.
©2019 Thermo Fisher Scientific Inc. All rights reserved.

Contents
■CHAPTER 1 Product information ....................................... 8
Product description ............................................................. 8
Genexus™Integrated Sequencer .................................................. 9
Reagents and supplies—Ion AmpliSeq™library chemistry ........................... 10
Genexus™Library Strips 1 and 2‑AS .......................................... 10
Genexus™Barcodes AS ..................................................... 10
Genexus™GX5™Starter Pack‑AS ............................................. 11
Reagents and supplies—Ion AmpliSeq™HD library chemistry ....................... 12
Genexus™Library Strips 1 and 2‑HD .......................................... 12
Genexus™Barcodes 1–32 HD ................................................ 12
Genexus™GX5™Starter Pack‑HD ............................................ 13
Shared reagents and supplies ................................................... 14
Genexus™Templating Strips 3 and 4‑GX5™.................................... 14
Genexus™Primer Pool Tubes and Pipette Tips ................................. 14
GX5™Chip and Genexus™Coupler ............................................ 15
Genexus™Sequencing Kit ................................................... 15
Genexus™Controls ......................................................... 16
Genexus™Filter ........................................................... 16
Oncomine™GX assays .......................................................... 16
Required materials not supplied ................................................. 17
Recommended materials for nucleic acid isolation and quantification ................. 18
Genexus™Integrated Sequencer components ...................................... 19
Genexus™Integrated Sequencer deck stations ..................................... 20
Genexus™Integrated Sequencer input and output connections ....................... 21
Workflow ..................................................................... 22
Genexus
™
Integrated Sequencer User Guide
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■CHAPTER 2 Before you begin .......................................... 23
Precautions ................................................................... 23
Avoid nucleic acid contamination ............................................. 23
Avoid chip damage ......................................................... 23
Avoid strong electromagnetic radiation ....................................... 23
Protection by equipment .................................................... 23
Guidelines for Genexus™Integrated Sequencer operation ........................... 24
Power the Genexus™Integrated Sequencer on or off ............................... 25
Power on ................................................................. 25
Power off ................................................................. 26
Get started with Genexus™Software .............................................. 26
About the Genexus™Software user interface .................................. 26
User-access levels ......................................................... 27
System tracking ........................................................... 27
Request and sign in to a new account ......................................... 27
Sign in .................................................................... 28
■CHAPTER 3 Create and manage
assays (manager/administrator) ........................................ 29
About assays in Genexus™Software .............................................. 29
System-installed assays ........................................................ 30
Manage assays (manager/administrator) ......................................... 30
Create a new assay (manager/administrator) ...................................... 32
Copy an assay (manager/administrator) .......................................... 40
Import an assay (manager/administrator) ......................................... 41
■CHAPTER 4 Enter samples and libraries ............................. 42
Add a new sample .............................................................. 42
System-installed sample attributes .......................................... 43
Create a custom sample attribute (manager/administrator) ..................... 44
Import samples ............................................................... 45
Manage samples ............................................................... 46
Sort, search, and filter samples ............................................. 46
Export and print samples ................................................... 47
View notes or add a note to a sample ......................................... 48
Edit a sample (manager/administrator) ...................................... 48
Edit a sample and amend a report after a run (manager/administrator) .......... 49
Review sample edit history .................................................. 49
Delete samples ............................................................ 50
Prepare or import a library batch ................................................ 50
Prepare a library batch ..................................................... 50
Import a library batch ...................................................... 53
Contents
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■CHAPTER 5 Create and manage run plans .......................... 55
Create a run plan for a sample run ............................................... 56
Create a run plan for a library run ................................................ 63
■CHAPTER 6 Dilute the samples and load the sample plate ......... 68
Guidelines for nucleic acid isolation and quantification—sample runs ................. 68
Dilute the samples (if needed) and load the sample plate—sample run ............... 69
Guidelines for library quantification—library runs .................................. 71
Dilute and pool libraries, and load the sample plate—library run ..................... 71
■CHAPTER 7 Load the sequencer and start a run ..................... 72
Before you begin ............................................................... 72
Fill Genexus™Primer Pool Tubes
(custom assays only) ............................. 74
Load the sequencer and start a run ............................................... 75
Clear the instrument deck and perform a UV Clean ................................. 81
■CHAPTER 8 Monitor the run ........................................... 84
View run progress on the instrument ............................................. 84
■CHAPTER 9 Review data and results .................................. 85
Run Results screen ............................................................ 86
Lab Report .................................................................... 88
Download the Lab Report ................................................... 89
View sequencing results and run metrics ......................................... 89
Summary of the sample results ............................................. 91
Run metrics ............................................................... 92
QC results ................................................................ 94
SNV/INDEL results ......................................................... 95
Fusion results ............................................................. 97
CNV results ............................................................... 99
View annotation sources ................................................... 101
Create and assign variant classifications ..................................... 102
Filter results ............................................................. 102
View Oncomine™TCR Beta‑LR Assay GX run results ........................... 105
Sign off on the run results (manager/administrator) .............................. 107
Generate customized reports ................................................... 108
Results files .................................................................. 109
Review coverageAnalysis plugin results .......................................... 111
Contents
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5

Upload sample results files to Ion Reporter™Software ............................. 111
Verification runs .............................................................. 113
View and sign off on the verification run results (Field Service Engineer) ........ 114
■APPENDIX A Troubleshooting ........................................ 117
Genexus™Software ........................................................... 117
Genexus™Integrated Sequencer ................................................ 119
■APPENDIX B Touchscreen reference ................................ 120
Touchscreen icons ............................................................ 120
Settings ..................................................................... 121
Network Settings ......................................................... 122
Perform a Clean instrument operation ...................................... 124
System Tools ............................................................. 124
Data Management ........................................................ 129
Instrument settings ....................................................... 131
■APPENDIX C Supplemental information ............................ 134
Maintain the sequencer ........................................................ 134
Materials required ........................................................ 134
Clean or decontaminate the sequencer ...................................... 134
Replace the Genexus™Filter ............................................... 135
Quantify FFPE DNA with the Qubit™Fluorometer .................................. 135
Guidelines for using custom assays with the Genexus™Integrated Sequencer ........ 136
Planning sequencing runs for efficient use of consumables ........................ 138
Configure an Ion Reporter™Server account (administrator) ........................ 139
Tag an Ion Reporter™Software analysis workflow for use with the
IonReporterUploader plugin ............................................... 140
Configure Thermo Fisher (Connect) accounts (manager/administrator) .............. 141
■APPENDIX D coverageAnalysis plugin in Genexus™Software .... 143
Reads statistics .............................................................. 143
Example Coverage Analysis Report .............................................. 145
Example charts generated by the coverageAnalysis plugin ......................... 147
Output files generated by the coverageAnalysis plugin ............................. 148
■APPENDIX E Safety .................................................... 150
Symbols on this instrument .................................................... 150
Standard safety symbols ................................................... 150
Additional safety symbols .................................................. 152
Location of safety labels ................................................... 152
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Control and connection symbols ............................................ 153
Conformity symbols ....................................................... 153
Instrument safety ............................................................. 154
General ................................................................. 154
Physical injury ........................................................... 154
Electrical safety .......................................................... 155
Cleaning and decontamination ............................................. 156
Instrument component and accessory disposal ............................... 156
Safety and electromagnetic compatibility (EMC) standards ......................... 156
Safety standards .......................................................... 157
EMC standards ........................................................... 157
Environmental design standards ............................................ 158
Radio compliance standards ............................................... 158
Chemical safety ............................................................... 159
Biological hazard safety ........................................................ 161
■APPENDIX F Documentation and support .......................... 162
Related documentation ........................................................ 162
Customer and technical support ................................................ 162
Limited product warranty ...................................................... 162
Contents
Genexus
™
Integrated Sequencer User Guide
7

Product information
■Product description .................................................... 8
■Genexus™ Integrated Sequencer ......................................... 9
■Reagents and supplies—Ion AmpliSeq™ library chemistry ................. 10
■Reagents and supplies—Ion AmpliSeq™ HD library chemistry ............. 12
■Shared reagents and supplies .......................................... 14
■Oncomine™ GX assays ................................................ 16
■Required materials not supplied ........................................ 17
■Recommended materials for nucleic acid isolation and quantication ....... 18
■Genexus™ Integrated Sequencer components ............................ 19
■Genexus™ Integrated Sequencer deck stations ............................ 20
■Genexus™ Integrated Sequencer input and output connections ............. 21
■Workow ........................................................... 22
Product description
The Ion Torrent™ Genexus™ Integrated Sequencer is a next-generation high-
throughput sequencing system that integrates library preparation, templating, and
sequencing into a single-day, single-instrument automated run. The instrument
supports both sample-to-results and library-to-results sequencing runs (up to 32 DNA
or RNA samples/run). Additional key features include:
• Sample to results in as lile as 14 hours (single lane run)
• Flexible and cost-eective run planning making use of multi-lane, multi-run
sequencing chips
• Automated library preparation for up to 400 base-read libraries using either
standard Ion AmpliSeq™ or Ion AmpliSeq™ HD library chemistry
• Automated Ion Sphere™ Particle (ISP)-loading and templating with on-chip
amplication
• Support for up to four compatible assays on a GX5™ Chip in a single run
• As lile as ve minutes total hands-on time required per run
• Real-time consumables tracking by the instrument to guide consumable loading
during run setup
• Consumables that are usable for up to 14 days after loading
• On-instrument sequencing data analysis requiring no external server
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Genexus™Integrated Sequencer
The Genexus™ Integrated Sequencer includes the following components.
Components Cat. No.
Genexus™Integrated Sequencer A45727
Genexus™Installation and Training Kit A40278[1]
[1] Not available for separate purchase.
The Ion Torrent™ Genexus™ Installation and Training Kit (Cat. No. A40278) is
available to rst-time owners of a Genexus™ Integrated Sequencer and is shipped with
the instrument. The kit contains the following reagents, supplies, and controls that are
used during the installation, training, and operation of the instrument.
Genexus™Installation and Training Kit
Contents Part No. Quantity Storage
Genexus™Controls A40267 1 −30°C to −10°C
Genexus™Strip 1 A40254 8 strips 2°C to 8°C
Genexus™Strip 2‑AS A40253 8 strips −30°C to −10°C
Genexus™Barcodes 1–32 AS A40258 1 plate 15°C to 30°C
Genexus™Strip 3‑GX5™A40265 8 strips 2°C to 8°C
Genexus™Strip 4 A40264 8 strips −30°C to −10°C
Genexus™Cartridge A40272 2 cartridges −30°C to −10°C
Genexus™Bottle 2 A40273 4 bottles
15°C to 30°C
Genexus™Bottles 1 and 3 A40274 2 bottles each
Genexus™Pipette Tips A40266 12 racks
Genexus™Conical Bottles A40275 2 sets of 5 bottles
Genexus™Filter A40302 1
Chapter 1 Product information
Genexus
™
Integrated Sequencer
1
Genexus
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Integrated Sequencer User Guide
9

Reagents and supplies—Ion AmpliSeq™library chemistry
Genexus™ Integrated Sequencer reagents and supplies can be ordered in convenient
combo kits and starter packs, but most consumables can also be ordered individually
as your needs require. The following tables provide information on the various
ordering options that are available for Ion AmpliSeq™ library chemistry.
Note:
·Consumables that have catalog numbers are orderable. Components that have part
numbers cannot be ordered individually.
·Reagents that are specic to Ion AmpliSeq™ library chemistry have an AS sux.
Ion Torrent™ Genexus™ Library Strips 1 and 2-AS (Cat. No. A40252) for standard Ion
AmpliSeq™ library-based chemistry are ordered as kits with eight pairs of strips/kit.
Component Carrier color Part No. Quantity per
kit Storage
Genexus™Strip 1 Red A40254 8 strips 2°C to 8°C
Genexus™Strip 2‑AS Blue A40253 8 strips −30°C to
−10°C
Ion Torrent™ Genexus™ Barcodes AS are supplied in plates containing 32 dual
barcodes per plate. The barcodes can be ordered as a set of three plates (Cat. No.
A40257), or ordered individually.
Item Label color Cat. No. Quantity Storage
Genexus™Barcodes 1–96 AS Blue A40257 3 plates 15°C to 30°C
Genexus™Barcodes 1–32 AS Blue A40258 1 plate
Genexus™Barcodes 33–64 AS Blue A40259 1 plate
Genexus™Barcodes 65–96 AS Blue A40260 1 plate
Genexus™Library
Strips 1 and 2‑AS
Genexus™
Barcodes AS
Chapter 1 Product information
Reagents and supplies—Ion AmpliSeq
™
library chemistry
1
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Genexus
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Integrated Sequencer User Guide

Ion Torrent™ Genexus™ GX5™ Starter Pack-AS (Cat. No. A40279) supplies the
following components for Ion AmpliSeq™ library preparation and sequencing using a
Genexus™-ready assay.
Note: For custom assays, Genexus™ Primer Pool Tubes (Cat. No. A40262) must be
ordered separately.
Component Part or Cat. No. Quantity Storage
Genexus™Strip 1 A40254 8 strips 2°C to 8°C
Genexus™Strip 2‑AS A40253 8 strips −30°C to
−10°C
Genexus™Strip 3‑GX5™A40265 8 strips 2°C to 8°C
Genexus™Strip 4 A40264 8 strips −30°C to
−10°C
Genexus™Barcodes 1–32 AS A40258 1 plate 15°C to
30°C
Genexus™Pipette Tips A40266 12 racks
Genexus™Cartridge A40272 2 cartridges −30°C to
−10°C
Genexus™Bottle 2 A40273 4 bottles 15°C to
30°C
Genexus™Bottles 1 and 3 A40274 2 bottles
each
Genexus™GX5™
Starter Pack‑AS
Chapter 1 Product information
Reagents and supplies—Ion AmpliSeq
™
library chemistry
1
Genexus
™
Integrated Sequencer User Guide
11

Reagents and supplies—Ion AmpliSeq™HD library chemistry
Genexus™ Integrated Sequencer reagents and supplies can be ordered in convenient
combo kits and starter packs, but most consumables can also be ordered individually
as your needs require. The following tables provide information on the various
ordering options that are available for Ion AmpliSeq™ HD library chemistry.
Note:
·Consumables that have catalog numbers are orderable. Components that have part
numbers cannot be ordered individually.
·Reagents that are specic to Ion AmpliSeq™ HD library chemistry have an HD
sux.
Ion Torrent™ Genexus™ Library Strips 1 and 2-HD (Cat. No. A40255) for Ion
AmpliSeq™ HD library-based chemistry are ordered as kits with eight pairs of
strips/kit.
Component Carrier color Part No. Quantity per
kit Storage
Genexus™Strip 1 Red A40254 8 strips 2°C to 8°C
Genexus™Strip 2‑HD Purple A40256 8 strips −30°C to
−10°C
Ion Torrent™ Genexus™ Barcodes 1–32 HD are supplied in a plate containing 32 dual
barcodes.
Item Label color Cat. No. Quantity Storage
Genexus™Barcodes 1–32 HD Purple A40261 1 plate 15°C to 30°C
Genexus™Library
Strips 1 and 2‑HD
Genexus™
Barcodes 1–32 HD
Chapter 1 Product information
Reagents and supplies—Ion AmpliSeq
™
HD library chemistry
1
12
Genexus
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Integrated Sequencer User Guide

Ion Torrent™ Genexus™ GX5™ Starter Pack-HD (Cat. No. A40280) supplies the
following components for Ion AmpliSeq™ HD library preparation and sequencing
using a Genexus™-ready assay.
Note: For custom assays, Genexus™ Primer Pool Tubes (Cat. No. A40262) must be
ordered separately.
Component Part or Cat. No. Quantity Storage
Genexus™Strip 1 A40254 8 strips 2°C to 8°C
Genexus™Strip 2‑HD A40256 8 strips −30°C to
−10°C
Genexus™Strip 3‑GX5™A40265 8 strips 2°C to 8°C
Genexus™Strip 4 A40264 8 strips −30°C to
−10°C
Genexus™Barcodes 1–32 HD A40261 1 plate 15°C to
30°C
Genexus™Pipette Tips A40266 12 racks
Genexus™Cartridge A40272 2 cartridges −30°C to
−10°C
Genexus™Bottle 2 A40273 4 bottles 15°C to
30°C
Genexus™Bottles 1 and 3 A40274 2 bottles
each
Genexus™GX5™
Starter Pack‑HD
Chapter 1 Product information
Reagents and supplies—Ion AmpliSeq
™
HD library chemistry
1
Genexus
™
Integrated Sequencer User Guide
13

Shared reagents and supplies
The following reagents and supplies are used in both Ion AmpliSeq™ library
chemistry and Ion AmpliSeq™ HD library chemistry runs.
Note: Consumables that have catalog numbers are orderable. Components that have
part numbers cannot be ordered individually.
Ion Torrent™ Genexus™ Templating Strips 3 and 4-GX5™ (Cat. No. A40263) are
ordered as kits with eight pairs of strips/kit.
Component Carrier color Part No. Quantity per
kit Storage
Genexus™Strip 3‑GX5™Grey A40265 8 strips 2°C to 8°C
Genexus™Strip 4 Yellow A40264 8 strips −30°C to
−10°C
Genexus™ Primer Pool Tubes and Pipee Tips can be ordered individually. Genexus™
Primer Pool Tubes are required for custom assays.
Item Cat. No. Quantity Storage
Genexus™Primer Pool Tubes A40262 50 assemblies
(2 tubes/assembly)
Bag of 100 caps
15°C to 30°C
Genexus™Pipette Tips A40266 12 racks
Genexus™
Templating Strips
3 and 4‑GX5™
Genexus™Primer
Pool Tubes and
Pipette Tips
Chapter 1 Product information
Shared reagents and supplies
1
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Genexus
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Integrated Sequencer User Guide

The GX5™ Chip and Genexus™ Coupler (Cat. No. A40269) are ordered as a set that
contains two chips and two couplers, sucient for up to eight sequencing runs.
Component Part No. Quantity Storage
GX5™Chip 100081364 2 chips 15°C to 30°C
Genexus™Coupler 100081252 2 couplers
The Ion Torrent™ Genexus™ Sequencing Kit is ordered as a combo (Cat. No. A40271),
and components of the combo are also orderable as listed.
Component Cat. No. Quantity Storage
Genexus™Cartridge A40272 2 cartridges −30°C to −10°C
Genexus™Bottle 2 A40273 4 bottles 15°C to 30°C
Genexus™Bottles 1 and 3 A40274 2 bottles each
GX5™Chip and
Genexus™Coupler
Genexus™
Sequencing Kit
Chapter 1 Product information
Shared reagents and supplies
1
Genexus
™
Integrated Sequencer User Guide
15

The Genexus™ Controls kit (Cat. No. A40267) provides sucient Genexus™ Control
Library-AS to perform four library runs. The kit also provides sucient Genexus™
Control Panel-AS and Genexus™ DNA Control to perform eight sample runs.
Component Quantity Storage
Genexus™Control Library‑AS 1 tube −30°C to −10°C
Genexus™Control Panel‑AS 8 carriers (white)
Genexus™DNA Control 2 tubes
The Genexus™ Filter (Cat. No. A40302) is installed in the liquid waste disposal port on
the instrument deck to prevent liquid waste line blockage. For information on
installation, see “Replace the Genexus™ Filter“ on page 135.
Component Quantity Storage
Genexus™Filter 2 filters 15°C to 30°C
Oncomine™GX assays
Ion Torrent™ Oncomine™ GX assays are Genexus™-ready assays sufficient for 32
reactions, and are supplied in pre-measured ready-to-load Genexus™ Primer Pool
Tubes. Assays are provided with Genexus™ Library Strips 1 and 2-AS (Cat. No.
A40252) or Genexus™ Library Strips 1 and 2-HD (Cat. No. A40255) in the amount
listed.
Contents Carrier
color Pool Carriers/kit Part No. Storage
Oncomine™Comprehensive Assay v3 GX (Cat. No. A46296)
Oncomine™Comprehensive Assay v3 DNA GX Purple DNA Pool 1 4 A40281 −30°C to
−10°C
Teal DNA Pool 2 4
Oncomine™Comprehensive Assay v3 RNA GX Orange RNA Pool 1 4 A44351
Blue RNA Pool 2 4
Genexus™Strip 1 Red — 2 × 8 A40254 2°C to 8°C
Genexus™Strip 2‑AS Blue — 2 × 8 A40253 −30°C to
−10°C
Oncomine™Precision Assay GX (Cat. No. A46291)
Oncomine™Precision Assay GX (panel only) Purple OPA Pool 1
(FWD and REV
primers)
8 A44350 −30°C to
−10°C
Genexus™Strip 1 Red — 8 A40254 2°C to 8°C
Genexus™Strip 2‑HD Purple — 8 A40256 −30°C to
−10°C
Genexus™
Controls
Genexus™Filter
Chapter 1 Product information
Oncomine
™
GX assays
1
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Genexus
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Integrated Sequencer User Guide

Contents Carrier
color Pool Carriers/kit Part No. Storage
Oncomine™TCR Beta‑LR Assay GX (Cat. No. A46297)
Oncomine™TCR Beta‑LR Assay GX (panel
only)
Purple RNA Pool 1 8 A40282 −30°C to
−10°C
Genexus™Strip 1 Red — 8 A40254 2°C to 8°C
Genexus™Strip 2‑AS Blue — 8 A40253 −30°C to
−10°C
Note:
·Assays using Ion AmpliSeq™ chemistry have primer pools that are loaded in
capped tubes in position 1 of the primer pool tube carriers. Empty uncapped tubes
are loaded in position 2.
·Assays using Ion AmpliSeq™ HD chemistry have FWD and REV primer pools that
are loaded in capped tubes in both positions of the primer pool tube carrier.
Required materials 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.
Item Source
MicroAmp™EnduraPlate™Optical 96-Well Clear Reaction
Plates with Barcode
4483352, 4483354
Adhesive PCR Plate Foils AB0626
20‑, 200‑, and 1,000‑µL pipettes and appropriate filtered tips MLS
Microcentrifuge tubes, 1.5-mL or 1.7-mL (low retention for
nucleic acids)
MLS
Vortex mixer with a rubber platform MLS
Gloves, powder-free nitrile MLS
Ice buckets and ice —
Nuclease-free water, molecular biology grade MLS
Isopropyl alcohol, 70% solution MLS
Wipes, disposable lint-free MLS
(Optional) Uninterruptible Power Supply (UPS)[1] MLS
[1] 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.
Chapter 1 Product information
Required materials not supplied
1
Genexus
™
Integrated Sequencer User Guide
17

Recommended materials for nucleic acid isolation and quantification
Unless otherwise indicated, all materials are available through thermosher.com.
MLS: Fisher Scientic (sherscientic.com) or other major laboratory supplier.
Item Source
Nucleic acid isolation
Ion AmpliSeq™Direct FFPE DNA Kit A31133, A31136
RecoverAll™Total Nucleic Acid Isolation Kit for FFPE AM1975
RecoverAll™Multi-Sample RNA/DNA Workflow A26069
MagMAX™FFPE Total Nucleic Acid Isolation Kit 4463365
MagMAX™FFPE DNA/RNA Ultra Kit A31881
PureLink™Genomic DNA Mini Kit K1820-00
MagMAX™Cell‑Free DNA Isolation Kit A29319
MagMAX™Cell-Free Total Nucleic Acid Isolation Kit A36716
RNase Zap
™RNase Decontamination Solution AM9780, AM9782, AM9784
Nucleic acid quantification
TaqMan™RNase P Detection Reagents Kit (Recommended
for DNA only)
4316831
Qubit™4 Fluorometer[1] Q33226
One or more of the following kits for use with the Qubit™4
Fluorometer:
• Qubit™dsDNA HS Assay Kit (High-sensitivity DNA)
• Qubit™dsDNA BR Assay Kit (Broad range DNA)
• Qubit™RNA HS Assay Kit (High-sensitivity RNA)
• Qubit™RNA BR Assay Kit (Broad range RNA )
Q32851, Q32854, Q32850,
Q32853
Q32852, Q32855, Q10210,
Q10211
Library quantification (Library Runs only)
Ion Library TaqMan™Quantitation Kit 4468802
[1] Qubit™2.0 Fluorometer and later are supported.
Chapter 1 Product information
Recommended materials for nucleic acid isolation and quantification
1
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Genexus™Integrated Sequencer components
2
10
1
3
4
7
8
9
5 6
4
11 11
Major features and components of the exterior and sequencing reagents bay of the Genexus™Integrated Sequencer
1Door to deck chamber. The door is locked in the closed
position during an instrument run.
2Power button
3Genexus™Bottle 1 (Chemical Waste)
4Genexus™Conical Bottles (Reusable conical bottles for
Genexus™Cartridge reagent dilution—do not remove or
replace unless advised by Thermo Fisher Scientific
support representative.)
5Genexus™Bottle 2 (Sequencing Solution)
6Genexus™Bottle 3 (Cleaning Solution)
7Waste Carboy
8Waste pipette tip bin
9Genexus™Cartridge
10 Touchscreen
11 Sequencing reagents bay door. Doors are locked in the
closed position during an instrument run.
Chapter 1 Product information
Genexus
™
Integrated Sequencer components
1
Genexus
™
Integrated Sequencer User Guide
19

Genexus™Integrated Sequencer deck stations
3
13
7
1
6
2
4
5
15
14
16
12
8
11
9 10
6
Interior Genexus™Integrated Sequencer deck components and stations
1PCR amplification station
2Microcentrifuge
3Genexus™Barcodes station
4Genexus™Primer Pool Tube station
5Genexus™Coupler station
6Chip install station
7Zone 1 station (Genexus™Strip 1)
8Zone 2 station (Genexus™Strip 2‑AS or Genexus™
Strip 2‑HD, depending on your assay,)
9Zone 3 station (Genexus™Strip 3‑GX5™)
10 Zone 4 station (Genexus™Strip 4)
11 Enrichment plate station
12 Liquid waste disposal port
13 Waste pipette tip disposal port
14 Sample plate station
15 Genexus™Pipette Tips station
16 Robotic pipettor
Chapter 1 Product information
Genexus
™
Integrated Sequencer deck stations
1
20
Genexus
™
Integrated Sequencer User Guide