Axiom 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide—Applied Biosystems NIMBUS Target Preparation Instrument (Pub.No. MAN0017741 C.0)

Axiom 2.0 Assay

Thermo Fisher Scientific (13 December 2019)

Axiom 2.0 Assay 96-Array Format Automated Workflow

• IP address setup and quick start instructions To ensure successful performance of the Axiom™ 2.0 Assay on the NIMBUS™ Target Preparation Instrument, a Hamilton™ field service engineer must perform installation and testing of the NIMBUS™ Instrument system in the following order: 1. Uncrate, place, then level the NIMBUS™ Instrument.

Axiom™ 2.0 Assay 96-Array Format Automated Workflow

2021-04-28 — 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 ...

Axiom 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide—Applied Biosystems NIMBUS Target Preparation Instrum

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MAN0017741 Axiom 96F NIMBUS SPG

AxiomTM 2.0 Assay 96-Array Format Automated Workflow
SITE PREPARATION GUIDE
for use with: AxiomTM 2.0 Reagent Kit AxiomTM Array Plates Applied BiosystemsTM NIMBUSTM Target Preparation Instrument
Catalog Number 901758
Publication Number MAN0017741 Revision C.0
For Research Use Only. Not for use in diagnostic procedures.

Products: AxiomTM 2.0 Reagent Kit
Products: AxiomTM Array Plates AxiomTM myDesignTM Array Plates

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. MAN0017741

Revision C.0

Date 13 December 2019 Adding information for WindowsTM 10 users.

Description

B.0

26 November 2018 Corrected typos.

A.0

18 October 2018 Initial release in Thermo Fisher Scientific document control system.

Supersedes legacy Affymetrix publication number 703350.

Updated to the current document template, with associated updates to trademarks, logos, licensing, and

warranty.

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 either registered trademarks or trademarks of Microsoft Corporation in the United States and/or other countries. Vortex-Genie is a registered trademark of Scientific Industries, Inc. Jitterbug is a trademark of Boekel Scientific. Kimwipes is a trademark and brand of Kimberly-Clark Worldwide, Inc. Eppendorf and Mastercycler are registered trademarks of Eppendorf AG. SpectraMax is a registered trademark of Molecular Devices Corporation. Pipet-Lite and Green-Pak are trademarks of Rainin Instrument, LLC. Pipet-Aid is a registered trademark of Drummond Scientific Company. Bio-Rad, Microseal, DNA Engine Tetrad, and Hard-Shell are registered trademarks of Bio-Rad Laboratories, Inc. Microlab, NIMBUS, CO-RE, and Hamilton are owned and/or registered by Hamilton Company in the U.S. and/or other countries. Alpillo is a trademark and brand of Alpaqua Engineering, LLC.
©2019 Thermo Fisher Scientific Inc. All rights reserved.

Contents
CHAPTER 1 NIMBUSTM Target Preparation Instrument
configuration for WindowsTM 7 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Pre-installation information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 Site selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 Inventory of components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 Computer and software methods for WindowsTM 7 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 Power requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
HamiltonTM equipment and software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 Operation specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 Install and test the instrument for WindowsTM 7 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 Software installation requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
CHAPTER 2 NIMBUSTM Target Preparation Instrument
configuration for WindowsTM 10 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Pre-installation information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 Site selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 Inventory of components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 Computer and software methods for WindowsTM 10 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 Power requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
HamiltonTM equipment and software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 Operation specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 Install and test the instrument for WindowsTM 10 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 Software installation requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
CHAPTER 3 NIMBUSTM Target Preparation Instrument setup . . . . . . . 19
HamiltonTM equipment and software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 Setup INHECOTM devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 Pedestals, Thermoshake, and CPAC accessory tool kit . . . . . . . . . . . . . . . . . . . . . . . . . . 20 Assemble the trash chute . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 Set up the Thermoshake Deep-well Plate Adapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28 Assemble the AlpilloTM Plate Cushion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 Assemble the CPAC tube adapter and cover . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 O-ring care . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target 3
Preparation Instrument

Contents
CHAPTER 4 Assay equipment and supplies required . . . . . . . . . . . . . . . 35
Applied BiosystemsTM equipment, software, reagents, and arrays required . . . . . . . . . . . . 35 AxiomTM consumables kits for the NIMBUSTM Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37 AxiomTM Starter Kit for Applied BiosystemsTM NIMBUSTM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37 Labware and accessories required . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Deck accessories required . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 Pipette tips . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 Labware used on the deck . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39 Other equipment, consumables, and reagents required . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43 Preamplification area . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43 Oven requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44 Spectrophotome-ter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44 Thermal cycler recommendations and protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44 Shakers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45 Plate centrifuge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46 Other equipment, reagents, and supplies required . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
APPENDIX A Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Symbols on this instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49 Standard safety symbols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49 Location of safety labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 Control and connection symbols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52 Conformity symbols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Safety information for instruments not manufactured by Thermo Fisher Scientific . . . . . 53 Instrument safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
General . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53 Physical injury . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54 Electrical safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 Cleaning and decontamination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56 Instrument component and accessory disposal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56 Safety and electromagnetic compatibility (EMC) standards . . . . . . . . . . . . . . . . . . . . . . . . . . 57 Safety standards . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57 EMC standards . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57 Environmental design standards . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58 Chemical safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59 Biological hazard safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Documentation and support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Related documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62 Customer and technical support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63 Limited product warranty . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
4 AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target
Preparation Instrument

NIMBUSTM Target Preparation

Instrument configuration for

WindowsTM 7

The Applied BiosystemsTM NIMBUSTM Target Preparation Instrument is required to run this version of the AxiomTM 2.0 Assay with the automated target preparation. This
chapter contains information specific to the setup, maintenance, and safe use of the NIMBUSTM Instrument and equipment.

Pre-installation information

IMPORTANT! Read all of the information in this chapter before unpacking or moving the instrument.

Site selection

IMPORTANT! Determine the NIMBUSTM Instrument location carefully. Moving the instrument after installation requires recalibration.

Location considerations and requirements
· Keep the instrument away from direct sunlight, drafts, excessive vibrations, and widely fluctuating temperatures or humidity. This requirement is especially critical for low volume (<10 µL) applications that require highly accurate and precise pipetting.
· The instrument must be placed on a stable bench, table, or hood that can support up to 200 lbs (89.6 kg) without bowing or swaying.
· The instrument must be oriented so that when facing the instrument, the waste disposal station is on the left side of the instrument.
· Ensure that the bench/table surface is as level as possible and affords, at a minimum, the following dimensions: Width (front to rear) 20 inches (50.8 cm)
Length (left to right) 52.5 inches (133.4 cm)
Height 30 inches (76.2 cm)

AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target 5
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Chapter 1 NIMBUSTM Target Preparation Instrument configuration for WindowsTM 7 Pre-installation information

For optimum serviceability, it is best to position the NIMBUS Instrument on an island location in the laboratory. Ensure to plan additional space for:
· Computer, mouse, and other accessories such as a printer.
· Storage of manuals, tips, components, and labware.
· Integrated off-deck accessories and third-party devices.
The NIMBUSTM Instrument has a solid waste chute for collection of used tips which is mounted on the front left side of the instrument. The chute is designed with a slide such that the tips are directed off the bench/table into a waste collection bag or bin. Therefore, the front of the instrument must be approximately 1 inch (2.5 cm) from the front edge of the supporting table or bench.

Inventory of components

Find the NIMBUSTM Inventory List that is shipped with the unit. Use this list to check off each item as the components are unpacked. Components that are kits have their own inventory list inside the kit packaging.

Computer and software methods for WindowsTM 7

The NIMBUSTM Instrument includes a laptop running the WindowsTM 7 operating system. A Thermo Fisher Scientific field application scientist installs the AxiomTM 2.0
Software Methods for the instrument.

6 AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target
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Chapter 1 NIMBUSTM Target Preparation Instrument configuration for WindowsTM 7 HamiltonTM equipment and software

Power requirements

The input power (universal supply) is 100-24 VAC, 5060 Hz, 5/A. The power supply is a UL/CSA/CE-approved universal power supply with IEC connection. International power adapters must be supplied before installation.
A multi-port power strip is supplied with each instrument and can be plugged into a single outlet. If the power strip is not used, three power outlets are required: one for the NIMBUSTM Instrument, one for a laptop or PC, and one for the Multi TEC Controller integration. Uninterruptible power supply (UPS) backup for both the computer and NIMBUSTM Instrument is recommended, but not required.

HamiltonTM equipment and software

Operation specifications

IMPORTANT! The NIMBUSTM Target Preparation Instrument is for indoor operation and use only.

Table 1 Operation specifications for the NIMBUSTM Target Preparation Instrument, and the INHECOTM Thermoshake, and CPAC devices.

Specification NIMBUSTM Target Preparation Instrument

Environmental conditions for operation: · Temperature · Relative humidity · Altitude

· 15°C to 35°C (59°F to 95°F) · 30% to 85% R.H. non-condensing · 2,000 m (1.2 miles) above sea level

INHECOTM Thermoshake device

Technical data: · Temperature range

· 4°C to 70°C (39.2°F to 158°F)

Environmental conditions for operation: · Temperature · Tolerable relative humidity
INHECOTM CPAC device Technical data:
· Temperature range

· 15°C to 32°C (59°F to 90°F) · 10-80% RH (non condensing) at 20°C
up to 30°C (68°F to 86°F)
· 4°C to 70°C (39.2°F to 158°F)

Environmental conditions for operation: · Temperature · Tolerable relative humidity

· 15°C to 32°C (59°F to 90°F) · 30-80% relative (non-condensing)

AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target 7
Preparation Instrument

Chapter 1 NIMBUSTM Target Preparation Instrument configuration for WindowsTM 7 HamiltonTM equipment and software

Components

WARNING! Condensate can prevent the Thermoshake and CPAC devices from operating properly and can damage the unit. Eliminate condensate daily, or if needed, especially in between heating and cooling cycles. On completion of a method run, click Finish in the final Cleanup window for that stage to prevent or minimize condensation.
The Applied BiosystemsTMNIMBUSTM Target Preparation Instrument (Cat. No. 00-0401) is used to run the AxiomTM 2.0 Assay with the automated target preparation. This workstation includes the accessories, software, and deck configuration listed in Table 2. In addition to this workstation, the components that are listed in the next chapter are required.
Table 2 NIMBUSTM Target Preparation Instrument components (Cat. No. 00-0401)
Item
Applied BiosystemsTM-specific Hamilton MicrolabTM NIMBUSTM 96 System: · 96-well CO-RETM pipetting head (1,000 µL) · 9+2 deck, +2 position at 48 mm · Labware Gripper Arm
Hamilton deck hardware: · 2 FTR Pedestals: (Hamilton, Cat. No. 61054-01) · One 1,000 µL Tip Isolator: (Hamilton, Cat. No. 64668-01) · 2 Precision DWP Pedestals: (Hamilton, Cat. No. 66591-01) · One 96 Tip Adapter pedestal: (Hamilton, Cat. No. 66450-01) · 3 DWP pedestals: (Hamilton, Cat. No. 61053-01)
INHECOTM devices: · INHECOTM Variomag Thermoshake with dock base (Hamilton, Cat. No. 59151-01) · INHECOTM CPAC with dock base (Hamilton, Cat. No. 59146-02) · INHECOTM Tube Rack 24 x 1.5 mL (INHECOTM, Cat. No. 7900029) · INHECOTM MultiTEC (INHECOTM, Cat. No. 8900030) · INHECOTM Slot Module Board 12V (INHECOTM, Cat. No. 2400128) · INHECOTM Slot Module Board 24V (INHECOTM, Cat. No. 2400125)

8 AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target
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Chapter 1 NIMBUSTM Target Preparation Instrument configuration for WindowsTM 7 HamiltonTM equipment and software

Item
Other items in the accessories kit include: · Custom solid waste chute · Solid waste chute components · Power cables (3) and power strip
Note: Supplied power cables are compatible with USA power outlets only. Compatible power cables for international power outlets are not included and must be obtained before installation. · Ethernet (Cat 5) cable · Integration hardware for the INHECOTM CPAC and Thermoshake devices · Laptop computer · IP address setup and quick start instructions

Install and test the instrument for WindowsTM 7

To ensure successful performance of the AxiomTM 2.0 Assay on the NIMBUSTM Target Preparation Instrument, a HamiltonTM field service engineer must perform installation and testing of the NIMBUSTM Instrument system in the following order:
1. Uncrate, place, then level the NIMBUSTM Instrument. · NIMBUSTM Instrument placed on designated bench or table · All required pedestals and labware have been received · Verify levelness and flatness of deck · Verify that the recess deck is at the 48 position · Verify that the integration plate is attached to INHECOTM Thermoshake · Verify that the integration plate is attached to INHECOTM CPAC (factory installed) · Attach INHECOTM tube rack to CPAC · Install CPAC and Thermoshake slot modules in MTEC · Connect power/communication cables from INHECOTM devices to MTEC Slot 1: CPAC Slot 2: Thermoshake · Connect USB cable to MTEC and laptop computer · Connect MTC power cord to outlet · Connect Ethernet Cat 5 cable to NIMBUSTM Instrument and laptop computer · Connect NIMBUSTM Instrument power cord · Connect laptop computer power cord · 96-head foam shipping block removed

2. Install the waste chute. · Ensure that the waste chute is installed and level to deck.

AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target 9
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Chapter 1 NIMBUSTM Target Preparation Instrument configuration for WindowsTM 7 HamiltonTM equipment and software

3. Prepare the laptop, then install NIMBUSTM Software v5.3.8.0 (for AxiomTM 2.0 Assay). Note: NVK can also be executed off the service engineer's laptop, in which case the customer's laptop can be configured with the appropriate version of NIMBUSTM Software for the application (v5.3.8.0 AxiomTM 2.0 Assay). · Verify that the computer has a 64-bit operating system · Language setting that is configured to English--United States · User Account Control set to "Never Notify" · Computer power setting that is changed to never sleep or hibernate · IP address set · NIMBUSTM Software installed: Phoenix version--4.3.0.7270 NIMBUSTM version--5.3.8.0 for AxiomTM 2.0 Assay · Checksum validation disabled · Set values in System Configuration Editor: Deck Configuration "9 +2, left recess at -48 mm" Gripper set to "Available" Pipette Head set to "CORE--96 Head, 1 mL" · Hamilton INHECOTM driver software installed v1.2 · Allow access of HxMTecServer through WindowsTM firewall if needed
4. Verify or load firmware to execute NVK.
5. Perform 96 head and gripper calibration.
6. Perform NVK positional and volume verifications.
7. Install INHECOTM devices.
8. Perform NVK INHECOTM device verifications.
9. If needed, load and install the final NIMBUSTM software and firmware.

10 AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target
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Chapter 1 NIMBUSTM Target Preparation Instrument configuration for WindowsTM 7 HamiltonTM equipment and software

10. Set up the AxiomTM 2.0 Assay NIMBUSTM Instrument Deck configuration (Figure 1).

Software installation requirements

Figure 1 Axiom 2.0 NIMBUSTM Instrument Deck configuration

1 Variomag Thermoshake with adapter
2 CPAC with reagent template
3 Precision DWP pedestal
4 DWP pedestal 5 35-mm pedestal with AlpilloTM Plate
Cushion

6 Tip adapter 7 Precision DWP pedestal 8 DWP pedestal 9 FTR pedestal 10 FTR pedestal 11 Tip isolator

Note: Positions 6, 9, 10, and 11 must be fastened onto the deck before use.

NIMBUSTM Software version for WindowsTM 7
· Phoenix version 4.3.0.7270 · NIMBUSTM version 5.3.8.0 (for AxiomTM 2.0 Assay)

NIMBUSTM firmware versions for WindowsTM 7

Component NIMBUSTM System Controller CORE 96 pipette head GripperGwz Dac2 (gw, y, x drives) Force monitor CPU status indicator IO board

Version 1.48 5.0S 1.32 1.20a 1.10 1.00 1.20

INHECOTM driver software for WindowsTM 7 HamiltonTM INHECOTM driver software v1.2.

AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target 11
Preparation Instrument

NIMBUSTM Target Preparation

Instrument configuration for

WindowsTM 10

Pre-installation information

IMPORTANT! Read all of the information in this chapter before unpacking or moving the instrument.

Site selection

IMPORTANT! Determine the NIMBUSTM Instrument location carefully. Moving the instrument after installation requires recalibration.

12 AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target
Preparation Instrument

Chapter 2 NIMBUSTM Target Preparation Instrument configuration for WindowsTM 10 Pre-installation information

Inventory of components

Computer and software methods for WindowsTM 10

The NIMBUSTM Instrument includes a laptop running the WindowsTM 10 operating system. A Thermo Fisher Scientific field application scientist installs the AxiomTM 2.0
Software Methods for the instrument.

AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target 13
Preparation Instrument

Chapter 2 NIMBUSTM Target Preparation Instrument configuration for WindowsTM 10 HamiltonTM equipment and software

Power requirements

HamiltonTM equipment and software

Operation specifications

IMPORTANT! The NIMBUSTM Target Preparation Instrument is for indoor operation and use only.

Table 3 Operation specifications for the NIMBUSTM Target Preparation Instrument, and the INHECOTM Thermoshake, and CPAC devices.

Specification NIMBUSTM Target Preparation Instrument

Environmental conditions for operation: · Temperature · Relative humidity · Altitude

· 15°C to 35°C (59°F to 95°F) · 30% to 85% R.H. non-condensing · 2,000 m (1.2 miles) above sea level

INHECOTM Thermoshake device

Technical data: · Temperature range

· 4°C to 70°C (39.2°F to 158°F)

Environmental conditions for operation: · Temperature · Tolerable relative humidity
INHECOTM CPAC device Technical data:
· Temperature range

· 15°C to 32°C (59°F to 90°F) · 10-80% RH (non condensing) at 20°C
up to 30°C (68°F to 86°F)
· 4°C to 70°C (39.2°F to 158°F)

Environmental conditions for operation: · Temperature · Tolerable relative humidity

· 15°C to 32°C (59°F to 90°F) · 30-80% relative (non-condensing)

14 AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target
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Components

Chapter 2 NIMBUSTM Target Preparation Instrument configuration for WindowsTM 10 HamiltonTM equipment and software

WARNING! Condensate can prevent the Thermoshake and CPAC devices from operating properly and can damage the unit. Eliminate condensate daily, or if needed, especially in between heating and cooling cycles. On completion of a method run, click Finish in the final Cleanup window for that stage to prevent or minimize condensation.
The Applied BiosystemsTMNIMBUSTM Target Preparation Instrument (Cat. No. 00-0401) is used to run the AxiomTM 2.0 Assay with the automated target preparation. This workstation includes the accessories, software, and deck configuration listed in Table 4. In addition to this workstation, the components that are listed in the next chapter are required.
Table 4 NIMBUSTM Target Preparation Instrument components (Cat. No. 00-0401)
Item
Applied BiosystemsTM-specific Hamilton MicrolabTM NIMBUSTM 96 System: · 96-well CO-RETM pipetting head (1,000 µL) · 9+2 deck, +2 position at 48 mm · Labware Gripper Arm
Hamilton deck hardware: · 2 FTR Pedestals: (Hamilton, Cat. No. 61054-01) · One 1,000 µL Tip Isolator: (Hamilton, Cat. No. 64668-01) · 2 Precision DWP Pedestals: (Hamilton, Cat. No. 66591-01) · One 96 Tip Adapter pedestal: (Hamilton, Cat. No. 66450-01) · 3 DWP pedestals: (Hamilton, Cat. No. 61053-01)
INHECOTM devices: · INHECOTM Variomag Thermoshake with dock base (Hamilton, Cat. No. 59151-01) · INHECOTM CPAC with dock base (Hamilton, Cat. No. 59146-02) · INHECOTM Tube Rack 24 x 1.5 mL (INHECOTM, Cat. No. 7900029) · INHECOTM MultiTEC (INHECOTM, Cat. No. 8900030) · INHECOTM Slot Module Board 12V (INHECOTM, Cat. No. 2400128) · INHECOTM Slot Module Board 24V (INHECOTM, Cat. No. 2400125)

AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target 15
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Chapter 2 NIMBUSTM Target Preparation Instrument configuration for WindowsTM 10 HamiltonTM equipment and software

Install and test the instrument for WindowsTM 10

To ensure successful performance of the AxiomTM 2.0 Assay on the NIMBUSTM Target Preparation Instrument, a HamiltonTM field service engineer must perform installation and testing of the NIMBUSTM Instrument system in the following order:
1. Uncrate, place, and level the NIMBUSTM Instrument. · NIMBUSTM Instrument placed on designated bench or table · All required pedestals and labware have been received · Verify levelness and flatness of deck · Verify that the recess deck is at the 48 position · Verify that the integration plate is attached to INHECOTM Thermoshake · Verify that the integration plate is attached to INHECOTM CPAC (factory installed) · Attach INHECOTM tube rack to CPAC · Install CPAC and Thermoshake slot modules in MTEC · Connect power/communication cables from INHECOTM devices to MTEC Slot 1: CPAC Slot 2: Thermoshake · Connect USB cable to MTEC and laptop computer · Connect MTC power cord to outlet · Connect Ethernet Cat 5 cable to NIMBUSTM Instrument and laptop computer · Connect NIMBUSTM Instrument power cord · Connect laptop computer power cord · 96-head foam shipping block removed

2. Install the waste chute. · Ensure that the waste chute is installed and level to deck.

16 AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target
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Chapter 2 NIMBUSTM Target Preparation Instrument configuration for WindowsTM 10 HamiltonTM equipment and software

3. Prepare the laptop and install NIMBUSTM Software v8.0.4.0 (for AxiomTM 2.0 Assay). · Verify that the computer has a WindowsTM 10 operating system installed · Language setting that is configured to English--United States · User Account Control set to "Never Notify" · Computer power setting that is changed to never sleep or hibernate · IP address set · NIMBUSTM Software installed: Phoenix version--4.5.0.7977 NIMBUSTM version--8.0.4.0 for AxiomTM 2.0 Assay · Checksum validation disabled · Set values in System Configuration Editor: Deck Configuration "9 +2, left recess at -48 mm" Gripper set to "Available" Pipette Head set to "CORE--96 Head, 1 mL" · Hamilton INHECOTM driver software installed v1.2.7.2 · Allow access of HxMTecServer through WindowsTM firewall if needed
4. Perform 96 head and gripper calibration.
5. Perform NVK positional and volume verifications.
6. Install INHECOTM devices.
7. Perform NVK INHECOTM device verifications.

AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target 17
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Chapter 2 NIMBUSTM Target Preparation Instrument configuration for WindowsTM 10 HamiltonTM equipment and software

8. Set up the AxiomTM 2.0 Assay NIMBUSTM Instrument Deck configuration (Figure 1).

Software installation requirements

Figure 2 Axiom 2.0 NIMBUSTM Instrument Deck configuration

1 Variomag Thermoshake with adapter
2 CPAC with reagent template
3 Precision DWP pedestal
4 DWP pedestal 5 35-mm pedestal with AlpilloTM Plate
Cushion

6 Tip adapter 7 Precision DWP pedestal 8 DWP pedestal 9 FTR pedestal 10 FTR pedestal 11 Tip isolator

Note: Positions 6, 9, 10, and 11 must be fastened onto the deck before use.

NIMBUSTM Software version for WindowsTM 10
· Phoenix version 4.5.0.7977 · NIMBUSTM version 8.0.4.0 (for AxiomTM 2.0 Assay)

NIMBUSTM firmware versions for WindowsTM 10

Component NIMBUSTM System Controller CORE 96 pipette head GripperGwz Dac2 (gw, y, x drives) Force monitor CPU status indicator IO board

Version 6.1.0.186
5.0S 1.32 1.41 1.15 1.00 1.23

INHECOTM driver software for WindowsTM 10 HamiltonTM INHECOTM driver software v1.2.7.2.

18 AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target
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NIMBUSTM Target Preparation

Instrument setup

HamiltonTM equipment and software

Setup INHECOTM devices

The INHECOTM Multi TEC (MTEC) Controller is used to operate the Thermoshake and the CPAC devices. There are two slot modules on the Multi TEC Controller where cables from each INHECOTM device must be attached into the assigned default slot locations:
· Slot 1: CPAC
· Slot 2: Thermoshake
The Thermoshake device must be set up with the adapter plate for the round deepwell plate to allow precise temperature control during fragmentation. The Hamilton field service engineer installs a 24-position tube rack into the CPAC device during system install. A cooling block template that is placed on top of the CPAC guides operators where reagents must be placed before the start of each run.

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Chapter 3 NIMBUSTM Target Preparation Instrument setup HamiltonTM equipment and software

Pedestals, Thermoshake, and CPAC accessory tool kit

The Applied BiosystemsTM NIMBUSTM Target Preparation Instrument comes with a
small accessory tool kit that includes a 2 mm, 2.5 mm, and a 3-mm hex wrench (also known as a hex key, Allen key, or Allen wrench). Also, the INHECOTM base plate kit
comes with a 1.5-mm hex wrench. These tools are required for fastening pedestals and devices to the NIMBUSTM Instrument deck. Save the small accessory tool kit for future
use.

Pedestals The pedestals in deck positions 6, 9, 10, and 11 are fastened to the NIMBUSTM Instrument deck by tightening the set screws, which are on the left and right side of each pedestal, with a 2-mm hex wrench. When fastening the pedestals to the deck, it is best to start with the pedestals in the back of the deck and work to the pedestals in the front to help the ease of access to set screws. Therefore, using a 2-mm hex wrench, ensure that the pedestals are placed and locked down in the following order:
1. Tip adapter at deck position 6 2. FTR pedestal at deck position 9 3. FTR pedestal at deck position 10 4. Tip isolator at deck position 11 See Figure 1 on page 11 for deck position locations. The remaining pedestals are easily positioned by placing them on the locator pins that are on the deck.
Secure pedestals to the deck When placing the pedestals on the deck, be aware of the correct orientation that is determined by the shape of the opening for the locator pins. The closed end must face left and the open end must face right.
X
20 AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target
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Chapter 3 NIMBUSTM Target Preparation Instrument setup HamiltonTM equipment and software

1. Place a pedestal on the deck, positioned using the two locator pins on the left and right side of the pedestal.

1
2
Figure 3 Pedestal placed on deck, positioned using locator pins (front view) 1 Locator pin. The locator pin that is shown is for a pedestal that is not yet placed on the deck. 2 Set screw that tightens the pedestal to the locator pin.
2. Tighten the set screws on the left and right side of the pedestal using a 2-mm hex wrench.

3. Using the locator pins on the deck, place, then fasten the remaining pedestals on deck in proper order, working from the back to the front of the deck. a. Deck position 6.
b. Deck position 9.
c. Deck position 10.

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Chapter 3 NIMBUSTM Target Preparation Instrument setup HamiltonTM equipment and software

d. Deck position 11.

IMPORTANT! Place a pedestal on the deck and secure by tightening the set screws. Fasten each pedestal that is placed onto the deck before moving on to placing and fastening the next pedestal. 4. Place the remaining pedestals onto the deck, positioning them using the locator pins on the left and right side of each pedestal. These remaining pedestals are not fastened to the deck with set screws. See Figure 1 on page 11 for deck configuration information.
Thermoshake and CPAC devices The Thermoshake and CPAC devices sit on the NIMBUSTM Target Preparation Instrument in deck positions 1 and 2. When fully assembled, they are found behind the trash chute attachment plate and trash chute mounting bracket. The Thermoshake and CPAC devices are fastened to the deck using a 1.5-mm hex wrench and set screws. The trash chute attachment plate and trash chute mounting bracket are fastened using a 2.5-mm hex wrench and M3 screws. The instructions that follow assume the first setup. If the set screws for the Thermoshake or CPAC device require tightening after the first installation, the trash chute attachment plate and the trash chute mounting bracket must be removed first to allow access to the device set screws.
22 AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target
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Fasten Thermoshake and CPAC devices to deck
1. Place the Thermoshake and CPAC devices in their proper locations onto the deck using the locator pins.

1 Thermoshake in deck position 1 2 CPAC in deck position 2 3 Locator pin on deck

Figure 4 Each device has only 1 set screw

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Chapter 3 NIMBUSTM Target Preparation Instrument setup HamiltonTM equipment and software

2. Using a 1.5-mm hex wrench, tighten the set screws for each device to lock them into place on the NIMBUSTM Instrument deck.

3. After fastening the devices, place the trash chute attachment plate on the NIMBUSTM Instrument.

1 Slide the left side of the trash chute attachment plate horizontally into position. 2 Slide the right side down into place.

4. With the trash chute attachment plate in place, insert the trash chute mounting bracket into position on the right side.

24 AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target
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Chapter 3 NIMBUSTM Target Preparation Instrument setup HamiltonTM equipment and software

5. Using a 2.5-mm hex wrench and two M3 screws fasten the trash chute mounting bracket onto the NIMBUSTM Instrument.

6. Using a 2.5-mm hex wrench and two M3 screws fasten the left side of the trash chute attachment plate onto the NIMBUSTM Instrument.

7. Snap the end cover into place.
1 1 End cover
AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target 25
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Chapter 3 NIMBUSTM Target Preparation Instrument setup HamiltonTM equipment and software

Assemble the trash chute

This section provides instructions for the proper assembly of the trash chute and trash chute cover to the NIMBUSTM Instrument. Use these instructions to attach properly or remove the trash chute if needed for cleaning or other purposes. To remove the trash chute, follow these instructions in reverse.
1. Find the trash chute mounting bracket on the left side of the NIMBUSTM Instrument.

1 Trash chute mounting bracket
2. Hold trash chute with both hands, then align the two securing pins on the right side of the trash chute with the two holes in the trash chute mounting bracket.
1

1 Align the securing pins with holes in trash chute mounting bracket.
26 AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target
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Chapter 3 NIMBUSTM Target Preparation Instrument setup HamiltonTM equipment and software

3. Insert securing pins into the holes in the trash chute mounting bracket, then pull the trash chute forward toward the front of the NIMBUSTM Instrument. This
action holds the trash chute in place.

4. After successfully attaching the trash chute to the NIMBUSTM Instrument, turn the leveling foot, on the underside of the trash chute, to support, then level the trash chute.
1
1 Leveling foot
5. Ensure that the trash chute is level. IMPORTANT! Ensure that the trash chute is level. Trash chutes that are not level result in problems with disposal of tips, plates, or other materials from the deck.
AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target 27
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Chapter 3 NIMBUSTM Target Preparation Instrument setup HamiltonTM equipment and software

1 Example of a trash chute that is not level. 2 Example of a trash chute that is properly attached and leveled.

6. After the trash chute has been installed, then leveled, attach the trash chute cover.

Set up the Thermoshake Deep-well Plate Adapter

1. Gather materials that are needed for setting up the Thermoshake device with the adapter plate. · INHECOTM Thermoshake device · Thermoshake Deep-well Plate Adapter (INHECOTM, Cat. No. 203232) · 1/8 inch (4 mm) slotted screwdriver · No. 1 Phillips screwdriver · Three screws that are provided with the adapter plate

28 AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target
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2. Fasten the adapter plate onto the Thermoshake device using the three screws and the Phillips screwdriver.

1 1
1

1 Locations for the 3 screws to fasten the adapter plate to the Thermoshake device.
3. Using the slotted screwdriver, tighten the 8 grub screws, 2 at each corner, found at the top of the Thermoshake device (Figure 5). On the opposite side of each grub screw, there as a tab that protrudes towards adapter plate. As a grub screw is tightened, the tab becomes flush (Figure 6).

Figure 5 Grub screws on the Thermoshake device

AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target 29
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Chapter 3 NIMBUSTM Target Preparation Instrument setup HamiltonTM equipment and software

2
Figure 6 Image of a tab on the opposite side of a grub screw on the Thermoshake device before and after tightening.
1 Tab protruding 2 Tab flush after tightening

30 AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target
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Assemble the AlpilloTM Plate Cushion

Chapter 3 NIMBUSTM Target Preparation Instrument setup HamiltonTM equipment and software

The AlpilloTM Plate Cushion compensates for physical tolerances between labware and pipettor, and helps automated precision pipetting. The AlpilloTM Extension is used to increase the height of the plate cushion allowing it to be used for deeper plate nests. The AlpilloTM Plate Cushion and extension must be assembled before use on the NIMBUSTM Instrument deck.
1. Gather the necessary materials as listed in the following figure.
3

1 AlpilloTM Plate Cushion (Cat. No. A000007) 2 AlpilloTM Extension (Cat. No. K000018) with the 4 screws provided
3 No. 1 Phillips screwdriver

2. Position the plate cushion on top of the extension such that the 4 screw holes align.

3. Using the 4 screws, fasten the plate cushion to the extension.

Figure 7 Plate cushion and extension assembled

AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target 31
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Chapter 3 NIMBUSTM Target Preparation Instrument setup HamiltonTM equipment and software

Assemble the CPAC tube adapter and cover

If the CPAC tube adapter and tube adapter cover are not properly aligned when installed on the CPAC unit, you can experience difficulty inserting the reagent tubes into the block. Tubes that are not correctly inserted can cause reagent tube labels to peel off, or can generate an error during the run. A properly assembled tube adapter and cover helps ensure proper alignment of the holes and adapter plates.

1. Gather the necessary materials as listed in the following figure.

1 Fastening screw and hex wrench (also known as a hex key, Allen key, or Allen wrench) 2 Twenty-four 2-mL tubes 3 Twenty-four hole tube adapter 4 Twenty-four hole tube adapter cover

2. Place the 24-hole tube adapter over the CPAC unit, ensuring that it is in the proper orientation with the bottom side down.

1 Top side. This image shows the proper orientation.
2 Bottom side. Identify the bottom side of the 24-hole tube adapter by the ridge along the edge of the adapter.

32 AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target
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3. Place the 24-hole tube adaptor cover over the 24-hole tube adapter.

1 The 24-hole tube adapter that is placed on the CPAC unit 2 The 24-hole tube adapter cover in place

4. Insert 22 x 2-mL tubes into the cover with the upper left and lower right corner holes empty (Figure 8).

5. After inserting the tubes, inspect the alignment of the holes, then adjust the alignment if needed. Figure 8 shows examples of both improper and proper alignment.

Figure 8 Hole alignment between the tube adapter and cover
1 The holes that are not properly aligned between the 24-hole tube adapter and the cover
2 Proper aligned between the 24-hole tube adapter and the cover

6. Complete the assembly of the CPAC unit: a. Carefully insert two 2-mL tubes into the remaining empty holes.

b. Insert the fastening screw into the center hole.

c. Using the hex wrench, tighten the tube adapter and tube adapter cover to the CPAC unit.

7. Remove all the 2-mL tubes from the unit to complete the assembly.

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Chapter 3 NIMBUSTM Target Preparation Instrument setup HamiltonTM equipment and software

O-ring care

The o-rings on the head of the NIMBUSTM Target Preparation Instrument allow the instrument to pick up and manipulate the pipette tips that are loaded on the deck. When the head is left in a squeezed position for an extended amount of time, the orings wear out and the head is stressed.
WARNING! It is not recommended to leave tips on the head or leave the head in a squeezed position for extended lengths of time. This practice can lead to premature o-ring wear and poor system performance.
On successfully completing a method, the head is normally parked with the o-rings in a relaxed position. If a method is interrupted or stopped, it is possible that the head can stand still with the o-rings in the squeezed position (Figure 9). For instances when the o-rings remain in the squeezed position, try initializing the instrument.

Figure 9 O-rings shown in a squeezed and relaxed state
To help preserve the longevity of the o-rings, remember the following: · Never power off the instrument with any tips that are loaded on the head. · Never leave the instrument with the head in the squeezed position. · Initializing the instrument usually resolves the head remaining in the squeezed position leaving the head in a relaxed position.

34 AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target
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Assay equipment and supplies

required

This chapter includes the supplier and ordering information for the equipment,
software, reagents, arrays, labware, and other consumables that have been verified for use with the Applied BiosystemsTM AxiomTM 2.0 Assay 96-Array Format Automated
Workflow.

Applied BiosystemsTM equipment, software, reagents, and arrays required

Item

Equipment GeneTitanTM Multi-Channel Instrument[1]

Software GeneChipTM Command ConsoleTM (GCC) AxiomTM Analysis Suite
Reagents AxiomTM 2.0 Reagent Kit Sufficient to process one 96-array format plate. AxiomTM Reference Genomic DNA 103 (optional)
Arrays AxiomTM Array Plate AxiomTM Microbiome Array Plate (96-array format)

Source
Contact Thermo Fisher Scientific
version 4.3 or later version 4.0 or later
901758
951957
Varies by design 902904

AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target 35
Preparation Instrument

4 Chapter 4 Assay equipment and supplies required Applied BiosystemsTM equipment, software, reagents, and arrays required

Item

Source

Training Kits
AxiomTM 2.0 CEU Training Kit for Automated Target Preparation on Applied BiosystemsTM NIMBUSTM Instrument Each kit includes:
· Two AxiomTM CEU 96-Array Plates · Two AxiomTM 2.0 Reagent Kit (96 reactions per kit) · Two AxiomTM GeneTitanTM Consumables Kit · Two full plates of 96 HapMap DNA samples[2] · One GeneTitanTM ZeroStat AntiStatic Gun

902517

AxiomTM 2.0 CEU Training Kit for Automated Target Preparation on Applied BiosystemsTM NIMBUSTM Instrument for Agrigenomics Each kit includes:
· One AxiomTM CEU 96-Array Plate · Two AxiomTM 2.0 Reagent Kit (96 reactions per kit) · Two AxiomTM GeneTitanTM Consumables Kit
· One full plate of 96 HapMap DNA samples[2] · One GeneTitanTM ZeroStat AntiStatic Gun
· Please order an additional catalog array plate of your choosing for use with your samples.

902518

AxiomTM 2.0 Assay Training Module for Microbiome 96-Array Plates Each kit includes:
· One AxiomTM CEU 96-Array Plate · One AxiomTM Microbiome Array Plate (96-array format) · Two AxiomTM 2.0 Reagent Kit (96 reactions per kit) · Two AxiomTM GeneTitanTM Consumables Kit
· One full plate of 96 HapMap DNA samples[2] · One GeneTitanTM ZeroStat AntiStatic Gun

902988

GeneTitanTM consumables

AxiomTM GeneTitanTM Consumables Kit

901606

Sufficient to process one 96-format array plate. Consists of: · Five 96 layout GeneTitanTM stain trays with covers · One 96 layout GeneTitanTM hybridization tray · One 96 layout GeneTitanTM scan tray with cover and protective base
These trays are required for processing a CarrierScanTM Array Plate on the GeneTitanTM Multi-Channel Instrument[1].

[1] For a complete list of all equipment and supplies required for GeneTitanTM Multi-Channel Instrument installation and operation, consult the GeneTitanTM Multi-Channel Instrument Site Preparation Guide (Pub. No. 08-0305)
[2] Per agreement with Coriell, all residual HapMap DNA samples must be destroyed immediately following completion of training.

36 AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target
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4 Chapter 4 Assay equipment and supplies required
AxiomTM consumables kits for the NIMBUSTM Instrument

AxiomTM consumables kits for the NIMBUSTM Instrument

Table 5 AxiomTM 96 Consumables Kit for Applied BiosystemsTM NIMBUSTM 2.0 (Cat. No. 902907)

Component[1]

Part No. [2]

Number

Per run

Per kit[3]

96well full skirt plate

203023

96 halfskirt plate

203009

Square deepwell plate

203016

Round deepwell plate

203028

Square 1.2 mL plate

203031

4column reservoir

203056 or 203025

[1] This consumables kit does not include a 96well UV plate. This plate is in the AxiomTM 96 Consumables Kit for QC for Applied BiosystemsTM NIMBUSTM 2.0 (Cat. No. 902909).
[2] Plate part numbers are provided for identification purposes only. [3] The kit provides sufficient quantities of consumables for 4 runs of 96format array plates.

Table 6 AxiomTM 96 Consumables Kit for QC for Applied BiosystemsTM NIMBUSTM 2.0 (Cat. No. 902909)

Component 96-well UV plate

Part No. 202919

Number

Per run

Per kit

AxiomTM Starter Kit for Applied BiosystemsTM NIMBUSTM

Table 7 AxiomTM Starter Kit for Applied BiosystemsTM NIMBUSTM (Cat. No. 902365)

Component
96 Half-Skirt Plate Holder Thermoshake Deep-well Plate Adapter AlpilloTM Plate Cushion AlpilloTM Extension AxiomTM 2.0 Reagent Kit Template Pedestal, 35.48 mm Reservoir holder AxiomTM 96 Consumables Kit for Applied BiosystemsTM NIMBUSTM 2.0

Quantity/ run 1 1 1 1 1 1 2 1

AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target 37
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4 Chapter 4 Assay equipment and supplies required Labware and accessories required

Component AxiomTM 96 Consumables Kit for QC for Applied BiosystemsTM NIMBUSTM 2.0 2-mL tubes

Quantity/ run
1
25

Labware and accessories required

Deck accessories required

Table 8 Deck accessories required from other vendors

Item 24-Position Tube Rack Insert, 11 mm, for 1.5-mL Microfuge Tubes

Source
Beckman CoulterTM 373661 Beckman CoulterTM 373696

Quantity/ run
1
1

Pipette tips

The following table provides the pipette tip usage for one full run of the AxiomTM 2.0 Assay 96-Array Format Automated Workflow on the Applied BiosystemsTM NIMBUSTM Target Preparation Instrument workstation.

Step

CO-RETM Filter Tips 1,000 µL

CO-RETM Filter Tips 300 µL CO-RETM Filter Tips 50 µL

DNA amplification

24 tips

120 tips

Fragmentation

33 tips

114 tips

Resuspension

104 tips

Hybridization preparation

14 tips

105 tips

Sample QC

16 tips

192 tips

Hybridization transfer

96 tips

GeneTitanTM preparation 1

47 tips

7 tips

GeneTitanTM preparation 2

28 tips

1 tip

Totals

146 tips

563 tips

192 tips

38 AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target
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4 Chapter 4 Assay equipment and supplies required Labware and accessories required

Labware used on the deck

Unless otherwise indicated, all materials are available through thermofisher.com. MLS: Fisher Scientific (fisherscientific.com) or other major laboratory supplier.

Table 9 Labware images and ordering information

Labware
CO-RETM Filter Tips 1,000 µL
Conductive 1,000 L filter pipette tips in frames

Source HamiltonTM Robotics 235905

Image

CO-RETM Filter Tips 300 µL
Conductive 300 L filter pipette tips in frames

HamiltonTM Robotics 235903

CO-RETM Filter Tips 50 µL
Conductive 50 L filter pipette tips in frames

HamiltonTM Robotics 235948

96well full skirt plate

Available as a component of the AxiomTM 96 Consumables Kit for Applied BiosystemsTM
NIMBUSTM 2.0 Cat. No. 902907
Purchase separately: Fisher ScientificTM 14222326

96 halfskirt plate
also called Hard-ShellTM 96-Well PCR Plate, high profile, semi skirted

Available as a component of the AxiomTM 96 Consumables Kit for Applied BiosystemsTM
NIMBUSTM 2.0 Cat. No. 902907 Purchase separately: Bio-RadTM HSS9641

Square deepwell plate

Available as a component of the AxiomTM 96 Consumables Kit for Applied BiosystemsTM
NIMBUSTM 2.0 Cat. No. 902907
Purchase separately: Fisher ScientificTM AB0932

AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target 39
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4 Chapter 4 Assay equipment and supplies required Labware and accessories required

Labware Round deepwell plate

Source Available as a component of the AxiomTM 96 Consumables Kit for Applied BiosystemsTM
NIMBUSTM 2.0 Cat. No. 902907 Purchase separately: Axygen PDW20CS

Image

Square 1.2 mL plate

Available as a component of the AxiomTM 96 Consumables Kit for Applied BiosystemsTM
NIMBUSTM 2.0 Cat. No. 902907
Purchase separately: E&K Scientific OX1263

4-column reservoir with reservoir frame
96-well UV plate
AlpilloTM Plate Cushion and AlpilloTM Extension
Pedestal, 35.48 mm (designed specifically for the AxiomTM method to fasten the AlpilloTM Plate Cushion and extension on deck position 5)

4column reservoir: Available as a component of the AxiomTM 96 Consumables Kit for Applied BiosystemsTM NIMBUSTM 2.0
Cat. No. 902907

Purchase separately: E&K Scientific EK2119

Reservoir frame: Available as a component

of the AxiomTM Starter Kit for Applied Note: The 4-column reservoir must

BiosystemsTM NIMBUSTM (kit 902365) always be placed on a reservoir frame

Purchase separately: Fisher ScientificTM

when on the NIMBUSTM Instrument deck.

NC1353562

Available as a component of the AxiomTM 96 Consumables Kit for QC for Applied BiosystemsTM NIMBUSTM 2.0 Cat. No. 902909

Purchase separately: Fisher ScientificTM 07200623

Available as a component of the AxiomTM Starter Kit for Applied BiosystemsTM NIMBUSTM (kit 902365)

Purchase separately: ALPAQUA: plate cushion, A000007 extension, K000018

The image shown displays the plate cushion and extension
assembled.

Available as a component of the AxiomTM Starter Kit for Applied BiosystemsTM NIMBUSTM (kit 902365)

40 AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target
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4 Chapter 4 Assay equipment and supplies required Labware and accessories required

Labware
96 Half-Skirt Plate Holder (used as holder for 96 halfskirt plate)

Source Available as a component of the AxiomTM
Starter Kit for Applied BiosystemsTM NIMBUSTM 902365
Purchase separately: Bio-RadTM TRC 9601

Thermoshake Deep-well Plate Adapter
(Adapter plate: Round deepwell plate, Axygen, Cat. No. PDW20CS)

Available as a component of the AxiomTM Starter Kit for Applied BiosystemsTM NIMBUSTM 902365
Purchase separately: INHECOTM 3200390

AxiomTM 2.0 Reagent Kit cooling block template
(designed specifically for use with the NIMBUSTM Instrument and the AxiomTM 2.0 Reagent Kit)

Available as a component of the AxiomTM Starter Kit for Applied BiosystemsTM NIMBUSTM 902365

Image

24-Position Tube Rack
(with one 11 mm tube insert in position D6)

Beckman CoulterTM 373661 Insert, 11 mm, for 1.5-mL Microfuge
Tubes, Beckman CoulterTM 373696

Plate collar

Included as part of the NIMBUSTM Instrument configuration

Tube collar

Included as part of the NIMBUSTM Instrument configuration

AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target 41
Preparation Instrument

4 Chapter 4 Assay equipment and supplies required Labware and accessories required

Labware Tip loading tool

Source Included as part of the NIMBUSTM
Instrument configuration
1

Image

GeneTitanTM ZeroStat AntiStatic Gun and Ion-Indicator Cap

74-0014

1 Tip loading tool attached to deck.

96-well Block
Cooling Chamber for 0.2 mL tubes, 96 holes (four for 1.5 mL and six for 0.5 mL tubes), Dim.: 6 1/8"L x 3 1/8"W x 1" H

Diversified Biotech CHAM1000

Adhesive film

Use one of the following: · MicroAmpTM Clear Adhesive Film, 4306311 · MicrosealTM 'B' PCR Plate Sealing Film, Bio-RadTM MSB1001

42 AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target
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4 Chapter 4 Assay equipment and supplies required Other equipment, consumables, and reagents required

Other equipment, consumables, and reagents required

Preamplification area

Precautions are required when manipulating genomic DNA to avoid contamination with foreign DNA amplified in other reactions and procedures. It is recommended that genomic DNA manipulations are performed in a dedicated preamplification room or area separate from the main laboratory.
This preamplification area must have a dedicated set of pipettes and plasticware. If no dedicated area is available, use of a dedicated bench or a dedicated biosafety hood and dedicated pipettes is suggested. If no dedicated bench or biosafety hood is available, a set of dedicated pipettes is recommended.

AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target 43
Preparation Instrument

4 Chapter 4 Assay equipment and supplies required Other equipment, consumables, and reagents required

Oven requirements
Spectrophotometer

We recommend using the BINDERTM ED 56 oven that is listed in the table below. If another oven is used, it must be able to maintain a constant temperature of 37°C for at least 24 hours, and have a temperature accuracy of ±1°C.
Unless otherwise indicated, all materials are available through thermofisher.com. MLS: Fisher Scientific (fisherscientific.com) or other major laboratory supplier.

Item

Source

Oven:
Required if processing more than 3 plates per week: · BINDERTM ED 56 drying and heating chamber ED056UL-120V Voltage: 120 V 1~60 Hz ED056-230V Voltage: 230 V 1~50/60 Hz

BINDERTM 9010-0334 BINDERTM 9010-0333

Optional--for low throughput of 3 or fewer array plates per week:
· GeneChipTM Hybridzation Oven 645[1]

00-0331

[1] The GeneChipTM Hybridzation Oven 640 is currently not supported with the AxiomTM 2.0 Assay. However, to use it in the workflow contact your field service engineer (FSE) or Thermo Fisher Scientific Technical Support regarding the compatibility of this oven with the AxiomTM 2.0 Assay.

We recommend using one of the following spectrophotometers, or equivalent. Unless otherwise indicated, all materials are available through thermofisher.com.

Item

Source

Thermo ScientificTM MultiskanTM Sky Microplate Spectrophotometer

Cat. No. 51119500

SpectraMax® Plus 384 Microplate Reader

Molecular Devices®, Cat. No. PLUS 384

DTX 880 Multimode Detector with genomic filter slide

Beckman CoulterTM

Thermal cycler recommendations and protocol

We have verified the performance of this assay using the following thermal cyclers. · Applied BiosystemsTM GeneAmpTM PCR System 9700 (with gold-plated or silver block) · Applied BiosystemsTM VeritiTM Thermal Cycler · Applied BiosystemsTM ProFlexTM PCR System · EppendorfTM MastercyclerTM pro S

IMPORTANT! Always use the heated lid option when programming protocols. See the appropriate thermal cycler user guide for programming information.

44 AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target
Preparation Instrument

Shakers

4 Chapter 4 Assay equipment and supplies required Other equipment, consumables, and reagents required

95°C 10 minutes

48°C 3 minutes

48°C Infinity

Figure 10 Axiom 2.0 Denature protocol (Stage 5)
WARNING! Evaporation during denaturation can negatively affect assay performance. Use the recommended thermal cycler consumables and sealing film to eliminate condensation and evaporation.

We recommend using one of the following shakers.
Unless otherwise indicated, all materials are available through thermofisher.com. MLS: Fisher Scientific (fisherscientific.com) or other major laboratory supplier.

Item

Source

Compact Digital Microplate Shaker The JitterbugTM

88880023 or 88880024 Boekel ScientificTM 130000 (115V) Boekel ScientificTM 130000-2 (230V)

AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target 45
Preparation Instrument

4 Chapter 4 Assay equipment and supplies required Other equipment, consumables, and reagents required

Plate centrifuge

One plate centrifuge is required for the AxiomTM 2.0 Assay. The plate centrifuges listed in Table 10 are recommended for the AxiomTM 2.0 Assay 96-Array Format Automated Workflow. When centrifuging and drying pellets, the centrifuge must be able to centrifuge plates at:
· Rcf: 3,200 × g with an appropriate rotor - bucket combination (4,000 rpm for the EppendorfTM Centrifuge 5810 R that is described in Table 10)
· Temperature: 4°C

Relative centrifugal force (rcf) is calculated using the following formula: rcf = (1.118 × 10-5) R S2

Where R is the radius of the rotor in centimeters, and S is the speed of the centrifuge in revolutions per minute.

In addition, the bottom of the rotor buckets must be soft rubber to ensure that the
deep well plates do not crack. Do not use buckets where the plates sit directly on a metal or hard plastic bottom. For the EppendorfTM Centrifuge 5810 R, do not use the
A-4-62 rotor with a WO-15 plate carrier (hard bottom).

Table 10 Plate centrifuge recommendations for the AxiomTM 2.0 Assay 96-Array Format Automated Workflow

Item

SorvallTM LegendTM XTR Centrifuge (refrigerated), with:

Supplier
Thermo Fisher Scientific

Cat. No.
75004520 (230 V, 50 Hz) 75004521 (120 V, 60 Hz) 75004523 (230 V, 5060 Hz,
USA and Canada)

TX-750 4 + 750mL Swinging Bucket Rotor

75003180 (rotor)

Microplate/Flask Carriers
Centrifuge 5810 R, with: Rotor A-4-81, with 4 MTP/Flex buckets
AllegraTM 25R Benchtop Centrifuge, Refrigerated, with:
S5700 Swinging-Bucket Rotor

EppendorfTM Beckman CoulterTM

75003795 (set of 2 carriers) 75003617 (set of 4 carriers)
022625551 (230 V, 5060 Hz) 022625501 (120 V, 5060 Hz, 15 A) 022625101 (120 V, 5060 Hz, 20 A)
022638807 (rotor)
369434 (280 V, 60 Hz) 369435 (200 V, 5060 Hz)
369436 (230 V, 50 Hz) 368954 (rotor)

46 AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target
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4 Chapter 4 Assay equipment and supplies required Other equipment, consumables, and reagents required

Other equipment, reagents, and supplies required

Unless otherwise indicated, all materials are available through thermofisher.com. MLS: Fisher Scientific (fisherscientific.com) or other major laboratory supplier.

Item

Source

Common laboratory equipment

Freezer, 20°C

MLS

Refrigerator, 2°C to 8°C Vortex-GenieTM 2 (for plates and microtubes)[1]
Mini microcentrifuge, for 2-mL tubes[1] Bel-ArtTM SP Scienceware® Cryo-SafeTM Mini Quick-Freeze Microcentrifuge Tube Cooler, 15°C[1]

MLS
Fisher ScientificTM 50728002 (120 V/60 Hz) 50728004 (230 V/50 Hz)
MLS
Fisher ScientificTM 03-410-497

Ice bucket, 49 liters Pipet-AidTM GeneTitanTM ZeroStat AntiStatic Gun

MLS MLS 74-0014

Reagents

2-Propanol, anhydrous, 99.5% (isopropanol) Low EDTA TE Buffer (10 mM Tris-HCl pH 8.0, 0.1 mM EDTA) Quant-iTTM PicoGreenTM dsDNA Assay Kit

Sigma-Aldrich 278475 Fisher ScientificTM AAJ75793AE
P7589

Materials, reagents, and gels required to run QC steps Mother E-BaseTM Device Daughter E-BaseTM Device EGelTM 48 Agarose Gels, 4% TrackItTM 25 bp DNA Ladder, or equivalent (Follow the product instructions for dilution method.) TrackItTM Cyan/Orange Loading Buffer EGelTM 48 Agarose Gel, 1% EGelTM 48 Agarose Gels, 2% EGelTM 96 High Range DNA Marker
Water, Nuclease-free, Molecular Biology Grade, Ultrapure

EBM03 EBD03 G800804 10488022
10482028 G800801 G800802 12352019 Fisher ScientificTM 71786

Pipettes and tips recommended for performing the gel QC steps Pipet-LiteTM Magnetic Assist Pipet, single channel P20 Pipet-LiteTM Magnetic Assist Pipet, single channel P200

RaininTM L-20 RaininTM L-200

AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target 47
Preparation Instrument

4 Chapter 4 Assay equipment and supplies required Other equipment, consumables, and reagents required

Item

Pipet-LiteTM Magnetic Assist Pipet, single channel P1000

Pipette 12-channel P20

Pipette 12-channel P50 (optional)

Pipette 12-channel P200

Pipette 12-channel P1200 Pipette tips Green-PakTM 10 µL refill Pipette tips Green-PakTM 200 µL refill Pipette tips Green-PakTM 1,000 µL refill

Pipette tips RT 10 µL (racked tips)

Pipette tips RT 200 µL (racked tips)

Pipette tips RT 1,000 µL (racked tips)

Other laboratory supplies

Adhesive film for 96-well platesuse one of the following: · MicroAmpTM Clear Adhesive Film · MicrosealTM 'B' PCR Plate Sealing Film

KimwipesTM laboratory tissue

Markers, permanent, fine point
[1] Equivalent item from other manufacturer is acceptable.

Source RaininTM L-1000 RaininTM L12-20 RaininTM L12-50 RaininTM L12-200 RaininTM L12-1200 RaininTM 30389274 RaininTM 30389276 RaininTM 30389272 RaininTM 30389225 RaininTM 30389239 RaininTM 30389212
4306311 Bio-RadTM MSB1001
MLS MLS

48 AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target
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Safety

WARNING! GENERAL SAFETY. Using this product in a manner not specified in the user documentation may result in personal injury or damage to the instrument or device. Ensure that anyone using this product has received instructions in general safety practices for laboratories and the safety information provided in this document.
· Before using an instrument or device, read and understand the safety
information provided in the user documentation provided by the manufacturer of the instrument or device.
· Before handling chemicals, read and understand all applicable Safety Data
Sheets (SDSs) and use appropriate personal protective equipment (gloves, gowns, eye protection, and so on). To obtain SDSs, see the "Documentation and Support" section in this document.

Symbols on this instrument

In this document, the hazard symbol is used along with one of the following user attention words.
· CAUTION!--Indicates a potentially hazardous situation that, if not avoided, may result in minor or moderate injury. It may also be used to alert against unsafe practices.
· WARNING!--Indicates a potentially hazardous situation that, if not avoided, could result in death or serious injury.
· DANGER!--Indicates an imminently hazardous situation that, if not avoided, will result in death or serious injury.

Standard safety symbols

Symbol and description

CAUTION! Risk of danger. Consult the manual for further safety information.

CAUTION! Risk of electrical shock.

CAUTION! Hot surface.

AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target 49
Preparation Instrument

A Appendix A Safety Symbols on this instrument Symbol and description CAUTION! Potential biohazard. CAUTION! Ultraviolet light. Symbole et description MISE EN GARDE ! Risque de danger. Consulter le manuel pour d'autres renseignements de sécurité. MISE EN GARDE ! Risque de choc électrique. MISE EN GARDE ! Surface chaude. MISE EN GARDE ! Danger biologique potentiel. MISE EN GARDE ! Rayonnement ultraviolet.
50 AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target
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Location of safety labels

Label and location

A Appendix A Safety
Symbols on this instrument

Figure 11 Warning label on the right side of the unit to the left of the power switch

Figure 12 Pinch points
1 Gantry arm 2 NIMBUSTM Instrument head

AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target 51
Preparation Instrument

A Appendix A Safety Symbols on this instrument

Control and connection symbols

Symbols and descriptions

On (Power)

Off (Power)

Earth (ground) terminal

Protective conductor terminal (main ground)

Direct current

Alternating current

Both direct and alternating current

Conformity symbols

Conformity mark

Description

Indicates conformity with safety requirements for Canada and U.S.A.

Indicates conformity with China RoHS requirements.
Indicates conformity with European Union requirements.
Indicates conformity with the WEEE Directive 2012/19/EU.
CAUTION! To minimize negative environmental impact from disposal of electronic waste, do not dispose of electronic waste in unsorted municipal waste. Follow local municipal waste ordinances for proper disposal provision and contact customer service for information about responsible disposal options.

52 AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target
Preparation Instrument

A Appendix A Safety
Safety information for instruments not manufactured by Thermo Fisher Scientific

Safety information for instruments not manufactured by Thermo Fisher Scientific
Some of the accessories provided as part of the instrument system are not designed or built by Thermo Fisher Scientific. Consult the manufacturer's documentation for the information needed for the safe use of these products.

Instrument safety

General

CAUTION! Do not remove instrument protective covers. If you remove the protective instrument panels or disable interlock devices, you may be exposed to serious hazards including, but not limited to, severe electrical shock, laser exposure, crushing, or chemical exposure.

CAUTION! Solvents and Pressurized fluids. Wear eye protection when working with any pressurized fluids. Use caution when working with any polymeric tubing that is under pressure:
· Extinguish any nearby flames if you use flammable solvents. · Do not use polymeric tubing that has been severely stressed or kinked. · Do not use polymeric tubing with tetrahydrofuran or nitric and sulfuric
acids.
· Be aware that methylene chloride and dimethyl sulfoxide cause polymeric
tubing to swell and greatly reduce the rupture pressure of the tubing.
· Be aware that high solvent flow rates (~40mL/min) may cause a static charge
to build up on the surface of the tubing and electrical sparks may result.

AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target 53
Preparation Instrument

A Appendix A Safety Instrument safety
Physical injury

CAUTION! Moving and Lifting Injury. The instrument is to be moved and positioned only by the personnel or vendor specified in the applicable site preparation guide. Improper lifting can cause painful and permanent back injury.
Things to consider before lifting or moving the instrument or accessories:
· Depending on the weight, moving or lifting may require two or more
persons.
· If you decide to lift or move the instrument after it has been installed, do not
attempt to do so without the assistance of others, the use of appropriate moving equipment, and proper lifting techniques.
· Ensure you have a secure, comfortable grip on the instrument or accessory. · Make sure that the path from where the object is to where it is being moved
is clear of obstructions.
· Do not lift an object and twist your torso at the same time. Keep your spine
in a good neutral position while lifting with your legs.
· Participants should coordinate lift and move intentions with each other
before lifting and carrying.
· For smaller packages, rather than lifting the object from the packing box,
carefully tilt the box on its side and hold it stationary while someone else slides the contents out of the box.
CAUTION! Moving Parts. Moving parts can crush, pinch and cut. Keep hands clear of moving parts while operating the instrument. Disconnect power before servicing.

54 AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target
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Electrical safety

A Appendix A Safety Instrument safety
WARNING! Fuse Installation. Before installing the instrument, verify that the fuses are properly installed and the fuse voltage matches the supply voltage. Replace fuses only with the type and rating specified for the unit. Improper fuses can damage the instrument wiring system and cause a fire.
AVERTISSEMENT ! Installation des fusibles. Avant d'installer l'instrument, vérifier que les fusibles sont correctement insérés et que leur tension correspond à celle fournie par le circuit d'alimentation. Ne remplacer les fusibles que par des modèles du type et de la puissance spécifiés pour l'appareil. L'utilisation de fusibles inadaptés peut endommager le circuit électrique de l'instrument et provoquer un incendie.
WARNING! Voltage Selector Switch. Before installing the instrument, verify that the voltage selector switch is set for the supply voltage. This will prevent damage to the instrument, reduce risk of fire, and enable proper operation.
AVERTISSEMENT ! Sélecteur de tension. Avant d'installer l'instrument, vérifier que le sélecteur de tension est adapté à la tension d'alimentation. Cela permet d'éviter d'endommager l'instrument, de réduire le risque d'incendie et d'assurer son bon fonctionnement.
WARNING! Ensure appropriate electrical supply. For safe operation of the instrument:
· Plug the system into a properly grounded receptacle with adequate current
capacity.
· Ensure the electrical supply is of suitable voltage. · Never operate the instrument with the ground disconnected. Grounding
continuity is required for safe operation of the instrument.
AVERTISSEMENT ! Veiller à utiliser une alimentation électrique appropriée. Pour garantir le fonctionnement de l'instrument en toute sécurité :
· Brancher le système sur une prise électrique correctement mise à la terre et
de puissance adéquate.
· S'assurer que la tension électrique est convenable. · Ne jamais utiliser l'instrument alors que le dispositif de mise à la terre est
déconnecté. La continuité de la mise à la terre est impérative pour le fonctionnement de l'instrument en toute sécurité.
WARNING! Power Supply Line Cords. Use properly configured and approved line cords for the power supply in your facility.
AVERTISSEMENT ! Cordons d'alimentation électrique. Utiliser des cordons d'alimentation adaptés et approuvés pour raccorder l'instrument au circuit électrique du site.

AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target 55
Preparation Instrument

A Appendix A Safety Instrument safety

Cleaning and decontamination
Instrument component and accessory disposal

WARNING! Disconnecting Power. To fully disconnect power either detach or unplug the power cord, positioning the instrument such that the power cord is accessible.
AVERTISSEMENT ! Déconnecter l'alimentation. Pour déconnecter entièrement l'alimentation, détacher ou débrancher le cordon d'alimentation. Placer l'instrument de manière à ce que le cordon d'alimentation soit accessible.
CAUTION! Cleaning and Decontamination. Use only the cleaning and decontamination methods specified in the manufacturer's user documentation. It is the responsibility of the operator (or other responsible person) to ensure the following requirements are met:
· No decontamination or cleaning agents are used that could cause a
HAZARD as a result of a reaction with parts of the equipment or with material contained in the equipment.
· The instrument is properly decontaminated a) if hazardous material is
spilled onto or into the equipment, and/or b) prior to having the instrument serviced at your facility or sending the instrument for repair, maintenance, trade-in, disposal, or termination of a loan (decontamination forms may be requested from customer service).
· Before using any cleaning or decontamination methods (except those
recommended by the manufacturer), users should confirm with the manufacturer that the proposed method will not damage the equipment.
MISE EN GARDE ! Nettoyage et décontamination. Utiliser uniquement les méthodes de nettoyage et de décontamination indiquées dans la documentation du fabricant destinée aux utilisateurs. L'opérateur (ou toute autre personne responsable) est tenu d'assurer le respect des exigences suivantes:
· Ne pas utiliser d'agents de nettoyage ou de décontamination susceptibles de
réagir avec certaines parties de l'appareil ou avec les matières qu'il contient et de constituer, de ce fait, un DANGER.
· L'instrument doit être correctement décontaminé a) si des substances
dangereuses sont renversées sur ou à l'intérieur de l'équipement, et/ou b) avant de le faire réviser sur site ou de l'envoyer à des fins de réparation, de maintenance, de revente, d'élimination ou à l'expiration d'une période de prêt (des informations sur les formes de décontamination peuvent être demandées auprès du Service clientèle).
· Avant d'utiliser une méthode de nettoyage ou de décontamination (autre que
celles recommandées par le fabricant), les utilisateurs doivent vérifier auprès de celui-ci qu'elle ne risque pas d'endommager l'appareil.
To minimize negative environmental impact from disposal of electronic waste, do not dispose of electronic waste in unsorted municipal waste. Follow local municipal waste ordinances for proper disposal provision and contact customer service for information about responsible disposal options.

56 AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target
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A Appendix A Safety
Safety and electromagnetic compatibility (EMC) standards

Safety and electromagnetic compatibility (EMC) standards
The instrument design and manufacture complies with the following standards and requirements for safety and electromagnetic compatibility.
Safety standards

Reference
EU Directive 2014/35/EU
IEC 61010-1 EN 61010-1 UL 61010-1 CAN/CSA C22.2 No. 61010-1
IEC 61010-2-081 EN 61010-2-081

Description European Union "Low Voltage Directive" Safety requirements for electrical equipment for measurement, control, and laboratory use Part 1: General requirements
Safety requirements for electrical equipment for measurement, control and laboratory use Part 2-081: Particular requirements for automatic and semi-automatic laboratory equipment for analysis and other purposes

EMC standards

Reference EU Directive 2014/30/EU EN 61326-1 IEC 61326-1

Description
European Union "EMC Directive"
Electrical Equipment for Measurement, Control and Laboratory Use EMC Requirements Part 1: General Requirements

AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target 57
Preparation Instrument

A Appendix A Safety Safety and electromagnetic compatibility (EMC) standards

Reference FCC Part 15 Subpart B (47 CFR)

Description
U.S. Standard Radio Frequency Devices
This equipment has been tested and found to comply with the limits for a Class B digital device, pursuant to part 15 of the FCC Rules. These limits are designed to provide reasonable protection against harmful interference in a residential installation. This equipment generates, uses and can radiate radio frequency energy and, if not installed and used in accordance with the instructions, may cause harmful interference to radio communications. However, there is no guarantee that interference will not occur in a particular installation. If this equipment does cause harmful interference to radio or television reception, which can be determined by turning the equipment off and on, the user is encouraged to try to correct the interference by one or more of the following measures:
· Reorient or relocate the receiving antenna.
· Increase the separation between the equipment and receiver.
· Connect the equipment into an outlet on a circuit different from that to which the receiver is connected.
· Consult the dealer or an experienced radio/TV technician for help.

Environmental design standards

Reference Directive 2012/19/EU Directive 2011/65/EU
SJ/T 11364-2014

Description
European Union "WEEE Directive"--Waste electrical and electronic equipment
European Union "RoHS Directive"--Restriction of hazardous substances in electrical and electronic equipment
"China RoHS" Standard--Marking for the Restricted Use of Hazardous Substances in Electronic and Electrical Products

58 AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target
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A Appendix A Safety Chemical safety

Chemical safety

WARNING! GENERAL CHEMICAL HANDLING. To minimize hazards, ensure laboratory personnel read and practice the general safety guidelines for chemical usage, storage, and waste provided below. Consult the relevant SDS for specific precautions and instructions:
· Read and understand the Safety Data Sheets (SDSs) provided by the
chemical manufacturer before you store, handle, or work with any chemicals or hazardous materials. To obtain SDSs, see the "Documentation and Support" section in this document.
· Minimize contact with chemicals. Wear appropriate personal protective
equipment when handling chemicals (for example, safety glasses, gloves, or protective clothing).
· Minimize the inhalation of chemicals. Do not leave chemical containers open.
Use only with adequate ventilation (for example, fume hood).
· Check regularly for chemical leaks or spills. If a leak or spill occurs, follow
the manufacturer's cleanup procedures as recommended in the SDS.
· Handle chemical wastes in a fume hood. · Ensure use of primary and secondary waste containers. (A primary waste
container holds the immediate waste. A secondary container contains spills or leaks from the primary container. Both containers must be compatible with the waste material and meet federal, state, and local requirements for container storage.)
· After emptying a waste container, seal it with the cap provided. · Characterize (by analysis if necessary) the waste generated by the particular
applications, reagents, and substrates used in your laboratory.
· Ensure that the waste is stored, transferred, transported, and disposed of
according to all local, state/provincial, and/or national regulations.
· IMPORTANT! Radioactive or biohazardous materials may require special
handling, and disposal limitations may apply.
AVERTISSEMENT ! PRÉCAUTIONS GÉNÉRALES EN CAS DE MANIPULATION DE PRODUITS CHIMIQUES. Pour minimiser les risques, veiller à ce que le personnel du laboratoire lise attentivement et mette en oeuvre les consignes de sécurité générales relatives à l'utilisation et au stockage des produits chimiques et à la gestion des déchets qui en découlent, décrites cidessous. Consulter également la FDS appropriée pour connaître les précautions et instructions particulières à respecter :
· Lire et comprendre les fiches de données de sécurité (FDS) fournies par le
fabricant avant de stocker, de manipuler ou d'utiliser les matériaux dangereux ou les produits chimiques. Pour obtenir les FDS, se reporter à la section « Documentation et support » du présent document.
· Limiter les contacts avec les produits chimiques. Porter des équipements de
protection appropriés lors de la manipulation des produits chimiques (par exemple : lunettes de sûreté, gants ou vêtements de protection).
· Limiter l'inhalation des produits chimiques. Ne pas laisser les récipients de
produits chimiques ouverts. Ils ne doivent être utilisés qu'avec une ventilation adéquate (par exemple, sorbonne).

AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target 59
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A Appendix A Safety Chemical safety

· Vérifier régulièrement l'absence de fuite ou d'écoulement des produits
chimiques. En cas de fuite ou d'écoulement d'un produit, respecter les directives de nettoyage du fabricant recommandées dans la FDS.
· Manipuler les déchets chimiques dans une sorbonne. · Veiller à utiliser des récipients à déchets primaire et secondaire. (Le récipient
primaire contient les déchets immédiats, le récipient secondaire contient les fuites et les écoulements du récipient primaire. Les deux récipients doivent être compatibles avec les matériaux mis au rebut et conformes aux exigences locales, nationales et communautaires en matière de confinement des récipients.)
· Une fois le récipient à déchets vidé, il doit être refermé hermétiquement avec
le couvercle fourni.
· Caractériser (par une analyse si nécessaire) les déchets générés par les
applications, les réactifs et les substrats particuliers utilisés dans le laboratoire.
· Vérifier que les déchets sont convenablement stockés, transférés, transportés
et éliminés en respectant toutes les réglementations locales, nationales et/ou communautaires en vigueur.
· IMPORTANT ! Les matériaux représentant un danger biologique ou
radioactif exigent parfois une manipulation spéciale, et des limitations peuvent s'appliquer à leur élimination.
WARNING! HAZARDOUS WASTE (from instruments). Waste produced by the instrument is potentially hazardous. Follow the guidelines noted in the preceding General Chemical Handling warning.
WARNING! 4L Reagent and Waste Bottle Safety. Four-liter reagent and waste bottles can crack and leak. Each 4-liter bottle should be secured in a low-density polyethylene safety container with the cover fastened and the handles locked in the upright position.

60 AxiomTM 2.0 Assay 96-Array Format Automated Workflow Site Preparation Guide--Applied BiosystemsTM NIMBUSTM Target
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A Appendix A Safety
Biological hazard safety
Biological hazard safety
WARNING! Potential Biohazard. Depending on the samples used on this instrument, the surface may be considered a biohazard. Use appropriate decontamination methods when working with biohazards. WARNING! BIOHAZARD. Biological samples such as tissues, body fluids, infectious agents, and blood of humans and other animals have the potential to transmit infectious diseases. Conduct all work in properly equipped facilities with the appropriate safety equipment (for example, physical containment devices). Safety equipment can also include items for personal protection, such as gloves, coats, gowns, shoe covers, boots, respirators, face shields, safety glasses, or goggles. Individuals should be trained according to applicable regulatory and company/ institution requirements before working with potentially biohazardous materials. Follow all applicable local, state/provincial, and/or national regulations. The following references provide general guidelines when handling biological samples in laboratory environment.
· U.S. Department of Health and Human Services, Biosafety in Microbiological
and Biomedical Laboratories (BMBL), 5th Edition, HHS Publication No. (CDC) 21-1112, Revised December 2009; found at: https://www.cdc.gov/labs/pdf/ CDC-BiosafetymicrobiologicalBiomedicalLaboratories-2009-P.pdf
· World Health Organization, Laboratory Biosafety Manual, 3rd Edition,
WHO/CDS/CSR/LYO/2004.11; found at: www.who.int/csr/resources/publications/biosafety/Biosafety7.pdf
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