Qiagen QIAcube HT User manual

QIAcube HT
User Manual
For use with the QIAcube HT Prep Manager Software
Sample to Insight
December 2017

2QIAcube HT User Manual 12/2017
Contents
1..............................................................................................................1-2 Introduction
......................................................................................................1-2
1.1 Provided user manuals
......................................................................................................1-2
1.2 About this user manual
......................................................................................................1-3
1.3 General information
1.3.1 .......................................................................................1-3 Technical assistance
1.3.2 .......................................................................................1-3 Policy statement
1.3.3 .......................................................................................1-3 Version management
......................................................................................................1-3
1.4 Intended use of the QIAcube HT
......................................................................................................1-4
1.5 Requirements for QIAcube HT users
......................................................................................................1-4
1.6 Requirements for some kits
2..............................................................................................................2-2 Safety information
......................................................................................................2-2
2.1 Proper use
......................................................................................................2-4
2.2 Electrical safety
......................................................................................................2-5
2.3 Biological safety
2.3.1 .......................................................................................2-5 Samples
......................................................................................................2-6
2.4 Chemicals
2.4.1 .......................................................................................2-6 Toxic fumes
......................................................................................................2-6
2.5 Waste disposal
......................................................................................................2-6
2.6 Mechanical hazards
......................................................................................................2-7
2.7 Maintenance safety
......................................................................................................2-10
2.8 Symbols on the QIAcube HT
3..............................................................................................................3-2 General description
......................................................................................................3-3
3.1 QIAcube HT instrument
3.1.1 .......................................................................................3-4 Lid
3.1.2 .......................................................................................3-4 Feet
3.1.3 .......................................................................................3-5 Tip chute

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3.1.4 .......................................................................................3-5 Tip disposal box
3.1.5 .......................................................................................3-6 HEPA filter
3.1.6 .......................................................................................3-6 UV lamp
3.1.7 .......................................................................................3-7 Pipettor head and robotic arm
3.1.8 .......................................................................................3-7 Worktable
3.1.9 .......................................................................................3-9 Accessory panel
3.1.10 .......................................................................................3-10 Vacuum chamber
3.1.11 .......................................................................................3-12 Vacuum control station and waste bottle
3.1.12 .......................................................................................3-14 Pinch valve
3.1.13 .......................................................................................3-16 Internal features of the QIAcube HT
......................................................................................................3-18
3.2 Computer
4..............................................................................................................4-2 Installation procedures
......................................................................................................4-2
4.1 System delivery
......................................................................................................4-3
4.2 Requirements
4.2.1 .......................................................................................4-3 Installation site
4.2.2 .......................................................................................4-4 Power requirements
4.2.3 .......................................................................................4-4 Grounding requirements
......................................................................................................4-5
4.3 Unpacking and installation
4.3.1 .......................................................................................4-5 Unpacking the QIAcube HT
.............................................................................4-6
Releasing transport locks
4.3.2 .......................................................................................4-7 Installation of vacuum control station
4.3.3 .......................................................................................4-11 Installation of pinch valve
4.3.4 .......................................................................................4-11 Installation of tip disposal box holder
4.3.5 .......................................................................................4-12 UV lamp
4.3.6 .......................................................................................4-12 Installation of AC power cord
4.3.7 .......................................................................................4-13 Connecting the computer to the QIAcube HT
......................................................................................................4-14
4.4 Software installation
4.4.1 .......................................................................................4-14 Installing QIAcube HT Prep Manager Software
4.4.2 .......................................................................................4-15 Uninstalling QIAcube HT Prep Manager Software
4.4.3 .......................................................................................4-16 Updating QIAcube HT Prep Manager Software

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4.4.4 .......................................................................................4-17 Upgrading from legacy QIAcube HT Software
4.4.5 .......................................................................................4-18 Installing additional kits
5..............................................................................................................5-2 Getting started
......................................................................................................5-2
5.1 Start the software
......................................................................................................5-3
5.2 Customizing global settings
......................................................................................................5-7
5.3 Customize user settings
......................................................................................................5-9
5.4 Managing users
5.4.1 .......................................................................................5-15 Changing password
......................................................................................................5-16
5.5 Managing labware
......................................................................................................5-18
5.6 Assembling the vacuum chamber
5.6.1 .......................................................................................5-19 Assembly for calibration
5.6.2 .......................................................................................5-21 Assembly for standard purification protocols
......................................................................................................5-23
5.7 Instrument calibration
5.7.1 .......................................................................................5-25 Calibrate volumes
5.7.2 .......................................................................................5-27 Calibration positioning buttons
5.7.3 .......................................................................................5-28 Calibrate tip racks
5.7.4 .......................................................................................5-30 Calibrate labware
.............................................................................5-30
Select labware to calibrate
.............................................................................5-34
Prepare worktable for labware calibration
.............................................................................5-36
Calibrate X- and Y-axis
.............................................................................5-38
Calibrate Z-axis
5.7.5 .......................................................................................5-40 Saving and importing calibration data
6..............................................................................................................6-2 Operating procedures
......................................................................................................6-2
6.1 Starting a run
6.1.1 .......................................................................................6-3 Setup step
6.1.2 .......................................................................................6-5 Labware selection step
.............................................................................6-8
Select other input labware
6.1.3 .......................................................................................6-11 Assignment
.............................................................................6-12
Assigning samples

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.............................................................................6-13
Removing assignment
.............................................................................6-13
Blocking output positions
6.1.4 .......................................................................................6-13 Worktable step
.............................................................................6-16
Preparing the worktable
.............................................................................6-17
Checking the waste bottle status
.............................................................................6-18
Preparing tip chute and tip disposal box
.............................................................................6-20
Preparing the vacuum chamber
.............................................................................6-20
Loading tips
.............................................................................6-23
Loading reagents and samples
.............................................................................6-24
Starting a run
6.1.5 .......................................................................................6-24 Run step
.............................................................................6-25
Open system test
.............................................................................6-25
Plate detection test
.............................................................................6-26
Pausing/Stopping a run
.............................................................................6-27
Vacuum performance check
.............................................................................6-29
Run completion
......................................................................................................6-30
6.2 Finishing work and shutting down
7..............................................................................................................7-2 QIAcube HT Prep Manager Software
......................................................................................................7-2
7.1 Basic concepts and general software usage
7.1.1 .......................................................................................7-2 Concepts
.............................................................................7-2
User roles concept
.............................................................................7-3
Experiments and templates
.............................................................................7-5
Protection of files
7.1.2 .......................................................................................7-5 General software usage
.............................................................................7-5
Controlling the mouse
.............................................................................7-6
Use of color
.............................................................................7-7
Displaying errors and warnings
.............................................................................7-8
Entering data
.............................................................................7-10
Working with tables
.............................................................................7-11
Selecting samples

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7.1.3 .......................................................................................7-13 General elements
.............................................................................7-13
Menu
.............................................................................7-16
Main toolbar
.............................................................................7-18
Button bar
.............................................................................7-18
Status bar
.............................................................................7-19
File dialog
.............................................................................7-23
Scan plate barcode dialog
7.1.4 .......................................................................................7-23 Environments
.............................................................................7-24
Home
.............................................................................7-25
Experiments
.............................................................................7-27
Service
.............................................................................7-28
Configuration
7.1.5 .......................................................................................7-29 Getting help
......................................................................................................7-31
7.2 Working with experiments
7.2.1 .......................................................................................7-31 Manage experiments and templates
.............................................................................7-31
Create a template
.............................................................................7-32
Manage favorite templates
.............................................................................7-34
View recent experiments
7.2.2 .......................................................................................7-35 Creating an experiment
.............................................................................7-36
Create an empty experiment
.............................................................................7-37
Create an experiment using a template
.............................................................................7-39
Create an experiment from an existing
experiment
......................................................................................................7-39
7.3 Report
......................................................................................................7-44
7.4 Administrative tasks
7.4.1 .......................................................................................7-44 Configuring QIAcube HT
7.4.2 .......................................................................................7-44 Viewing software version
7.4.3 .......................................................................................7-44 View system audit trail
8..............................................................................................................8-2 Maintenance procedures
......................................................................................................8-2
8.1 Cleaning agents

7QIAcube HT User Manual 12/2017
......................................................................................................8-4
8.2 Servicing
......................................................................................................8-4
8.3 Regular maintenance
8.3.1 .......................................................................................8-4 Cleaning the instrument after completing a run
8.3.2 .......................................................................................8-5 Cleaning the instrument before shutting down
8.3.3 .......................................................................................8-7 Cleaning the lid
8.3.4 .......................................................................................8-7 Emptying the waste bottle
8.3.5 .......................................................................................8-8 Cleaning accessories
8.3.6 .......................................................................................8-10 Using UV lamp
......................................................................................................8-11
8.4 Periodic maintenance
8.4.1 .......................................................................................8-11 Maintenance of the QIAcube HT instrument
8.4.2 .......................................................................................8-12 Maintenance schedule
8.4.3 .......................................................................................8-15 Maintenance of the QIAcube HT pipettor
8.4.4 .......................................................................................8-15 Replacing the HEPA filters
8.4.5 .......................................................................................8-18 Replacing filters on vacuum station
9..............................................................................................................9-2 Troubleshooting
......................................................................................................9-3
9.1 Support packages
......................................................................................................9-6
9.2 System setup
......................................................................................................9-9
9.3 Operation
......................................................................................................9-11
9.4 Self-diagnostic tools
9.4.1 .......................................................................................9-12 Connection check
9.4.2 .......................................................................................9-12 Cycle pipettor head
9.4.3 .......................................................................................9-13 Check for loss of steps
9.4.4 .......................................................................................9-13 Check vacuum pressure
9.4.5 .......................................................................................9-14 Check for home-opto alignment
10 ..............................................................................................................10-2 Glossary
11 ..............................................................................................................11-2 Appendices
......................................................................................................11-2
11.1 Appendix A
11.1.1 .......................................................................................11-2 Technical data
11.1.2 .......................................................................................11-2 Environmental conditions

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.............................................................................11-3
Waste Electrical and Electronical Equipment
11.1.3 .......................................................................................11-4 FCC declaration
11.1.4 .......................................................................................11-4 Declaration of conformity
......................................................................................................11-5
11.2 Appendix B
11.2.1 .......................................................................................11-5 Liability clause
......................................................................................................11-5
11.3 Appendix C Consignes de sécurité
11.3.1 .......................................................................................11-6 Utilisation appropriée
11.3.2 .......................................................................................11-8 Sécurité électrique
11.3.3 .......................................................................................11-9 Sécurité biologique
.............................................................................11-9
Échantillons
11.3.4 .......................................................................................11-10 Produits chimiques
.............................................................................11-10
Vapeurs toxiques
11.3.5 .......................................................................................11-10 Traitement des déchets
11.3.6 .......................................................................................11-11 Dangers mécaniques
11.3.7 .......................................................................................11-12 Sécurité relative à la maintenance
11.3.8 .......................................................................................11-14 Symboles sur le QIAcube HT
......................................................................................................11-15
11.4 Appendix D Sicherheitshinweise
11.4.1 .......................................................................................11-15 Sachgemäße Handhabung
11.4.2 .......................................................................................11-17 Elektrische Sicherheit
11.4.3 .......................................................................................11-18 Biologische Sicherheit
.............................................................................11-18
Proben
11.4.4 .......................................................................................11-18 Chemikalien
.............................................................................11-19
Giftige Dämpfe
11.4.5 .......................................................................................11-19 Abfallentsorgung
11.4.6 .......................................................................................11-19 Gefahren durch mechanische Teile
11.4.7 .......................................................................................11-20 Sicherheitshinweise – Wartungsarbeiten
11.4.8 .......................................................................................11-23 Symbole auf dem QIAcube HT
......................................................................................................11-24
11.5 Appendix E
11.5.1 .......................................................................................11-24 QIAcube HT Accessories
......................................................................................................11-26
11.6 Appendix F

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11.6.1 .......................................................................................11-26 License Terms
11.6.2 .......................................................................................11-63 Copyright information

Introduction
QIAcube HT User Manual 12/2017 1-1

QIAcube HT User Manual 12/2017 1-2
1Introduction
Thank you for choosing the QIAcube®HT. We are confident it will become an integral part of your laboratory.
Before using the QIAcube HT, it is essential that you read this user manual carefully and pay particular attention to the
safety information. The instructions and safety information in this user manual must be followed to ensure safe operation of
the instrument and to maintain the instrument in a safe condition.
1.1 Provided user manuals
This user manual is applicable to the QIAcube HT instruments using the QIAcube HT Prep Manager Software.
This user manual is also applicable to the QIAxtractor®instruments that have been upgraded to QIAcube HT using the
QIAcube HT Prep Manager Software.
1.2 About this user manual
This manual provides information about the QIAcube HT in the following sections:
1. Introduction
2. Safety information
3. General description
4. Installation procedures
5. Getting started
6. Operating procedures
7. QIAcube HT Prep Manager Software
8. Maintenance procedures
9. Troubleshooting
10.Glossary
11.Appendix
The Appendices contain the following:
Appendix A:
Technical data
Environmental conditions
Waste disposal
FCC declaration
Declaration of conformity
Appendix B: Liability clause
Appendix C: French (FR) translation of Safety Information

QIAcube HT User Manual 12/2017 1-3
Appendix D: German (DE) translation of Safety Information
Appendix E: QIAcube HT Accessories
Appendix F:
Copyright information
Licenses
1.3 General information
1.3.1 Technical assistance
At QIAGEN we pride ourselves on the quality and availability of our technical support. Our Technical Services
Departments are staffed by experienced scientists with extensive practical and theoretical expertise in sample and assay
technologies and the use of QIAGEN products. If you have any questions or experience any difficulties regarding the
QIAcube HT or QIAGEN products in general, do not hesitate to contact us.
QIAGEN customers are a major source of information regarding advanced or specialized uses of our products. This
information is helpful to other scientists as well as to the researchers at QIAGEN. We therefore encourage you to contact
us if you have any suggestions about product performance or new applications and techniques.
For technical assistance and more information, please see our Technical Support Center at www.support.qiagen.com.
1.3.2 Policy statement
It is the policy of QIAGEN to improve products as new techniques and components become available. QIAGEN reserves
the right to change specifications at any time.
In an effort to produce useful and appropriate documentation, we appreciate your comments on this user manual. Please
contact QIAGEN Technical Services.
1.3.3 Version management
This document is the QIAcube H T User M anual , version 3.0.
This user manual is for the operation of the QIAcube HT instrument with the QIAcube HT Prep Manager Software.
Check www.qiagen.com/QIAcubeHT for a newer version of the user manual.
1.4 Intended use of the QIAcube HT
The QIAcube HT is intended to perform automated, medium- to high-throughput purification of nucleic acids.
The QIAcube HT is intended for molecular biology applications. This product is not intended for the diagnosis, prevention
or treatment of a disease.
The QIAcube HT instrument is intended to be used only in combination with QIAcube HT Kits for applications described in
the respective kit handbooks.
The QIAcube HT instrument is intended for use by professional users trained in molecular biological techniques and the
operation of the QIAcube HT instrument.

QIAcube HT User Manual 12/2017 1-4
1.5 Requirements for QIAcube HT users
This table covers the general level of competence and training necessary for transportation, installation, use, maintenance
and servicing of the QIAcube HT.
Task
Personnel
Training and experience
Delivery
No special
requirements
No special requirements
Installation
Laboratory technicians
or equivalent
Appropriately trained and experienced personnel
familiar with use of computers and automation in
general
Routine use
(running experiments)
Laboratory technicians
or equivalent
Appropriately trained and experienced personnel
familiar with use of computers and automation in
general
Servicing and annual
preventive maintenance
QIAGEN Field Service
Specialists only
Regularly trained, certified and authorized by
QIAGEN
1.6 Requirements for some kits
For more information about available kits and protocols for the QIAcube HT, please visit www.qiagen.com/QIAcubeHT
or contact QIAGEN Technical Services.

Safety information
QIAcube HT User Manual 12/2017 2-1

QIAcube HT User Manual 12/2017 2-2
2Safety information
Before using the QIAcube HT, it is essential that you read this user manual carefully and pay particular attention to the
safety information. The instructions and safety information in the user manual must be followed to ensure safe operation of
the instrument and to maintain the instrument in a safe condition.
Note: Translations of the Safety Information are available in French and German in Appendix C and Appendix D,
respectively.
The following types of safety information appear throughout this manual:
WARNING
The term WARNING is used to inform you about situations that could result in
personal injury to you or other persons.
Details about these circumstances are given in a box like this one.
CAUTION
The term CAUTION is used to inform you about situations that could result in
damage to the instrument or other equipment.
Details about these circumstances are given in a box like this one.
The advice given in this manual is intended to supplement, not supersede, the normal safety requirements prevailing in the
user’s country.
2.1 Proper use
WARNING/
CAUTION
Risk of personal injury and material damage [W1]
Improper use of the QIAcube HT may cause personal injuries or damage to the instrument.
The QIAcube HT must only be operated by qualified personnel who have been
appropriately trained.
Servicing of the QIAcube HT must only be performed by QIAGEN Field Service
Specialists.
WARNING/
CAUTION
Risk of overheating [W2]
To ensure proper ventilation, maintain a minimum clearance of 10 cm at the sides and rear
of the QIAcube HT.
Slits and openings that ensure the ventilation of the QIAcube HT must not be covered.

QIAcube HT User Manual 12/2017 2-3
WARNING/
CAUTION
Risk of personal injury and material damage [W3]
The QIAcube HT is too heavy to be lifted by one person. To avoid personal injury or
damage to the instrument, do not lift the instrument alone.
WARNING/
CAUTION
Risk of personal injury and material damage [W4]
Do not attempt to move the QIAcube HT during operation.
WARNING
Explosive atmosphere [W5]
The QIAcube HT is not designed for use in an explosive atmosphere.
WARNING
Risk of explosion [W6]
The QIAcube HT is intended for use with reagents and substances supplied with QIAGEN
kits.
Use of other reagents and substances may lead to fire or explosion.
CAUTION
Damage to the instrument [C1]
Direct sunlight may bleach parts of the instrument and cause damage to plastic parts.
The QIAcube HT must be located out of direct sunlight.
CAUTION
Damage to the instrument [C2]
Avoid spilling water or chemicals onto the QIAcube HT. Damage caused by water or
chemical spillage will void your warranty.

QIAcube HT User Manual 12/2017 2-4
WARNING/
CAUTION
Risk of personal injury [W7]
The robotic arm moves during position calibration while the instrument lid is raised. Never
click any buttons while parts of your body are within the instrument workspace
In case of emergency, switch off the QIAcube HT at the power switch at the rear of the instrument and unplug the power
cord from the power outlet.
2.2 Electrical safety
Disconnect the line power cord from the power outlet before servicing.
WARNING
Electrical hazard [W8]
Any interruption of the protective conductor (earth/ground lead) inside or outside the
instrument or disconnection of the protective conductor terminal is likely to make the
instrument dangerous.
Intentional interruption is prohibited.
Lethal voltages inside the instrument
When the instrument is connected to line power, terminals may be live, and opening
covers or removing parts is likely to expose live parts.
WARNING
UV irradiation hazard [W9]
An electronic lid sensor ensures that the instrument lid must be closed for operation of the
UV lamp. Under no circumstances should this lid sensor be disabled.
If the lid sensor is not functioning correctly, contact QIAGEN Technical Services.
To ensure satisfactory and safe operation of the QIAcube HT:
Connect the line power cord to a line power outlet that has a protective conductor (earth/ground).
Do not adjust or replace internal parts of the instrument.
Do not operate the instrument with any covers or parts removed.
If liquid has spilled inside the instrument, switch off the instrument, disconnect it from the power outlet and contact
QIAGEN Technical Services.

QIAcube HT User Manual 12/2017 2-5
If the instrument becomes electrically unsafe, prevent other personnel from operating it, and contact QIAGEN Technical
Services. The instrument may be electrically unsafe when:
The line power cord appears to be damaged.
It has been stored for a prolonged period of time in conditions which are outside of the “Storage Conditions” outlined
in Appendix A.
It has been subjected to severe transport stresses.
2.3 Biological safety
Specimens and reagents containing materials from humans should be treated as potentially infectious. Use safe laboratory
procedures as outlined in publications such as Biosafety in Microbiological and Biomedical Laboratories, HHS (www.
cdc.gov/od/ohs/biosfty/biosfty.htm).
2.3.1 Samples
Samples may contain infectious agents. You should be aware of the health hazard presented by such agents and should
use, store, and dispose of such samples according to the required safety regulations.
WARNING
Samples containing infectious agents [W10]
Some samples used with this instrument may contain infectious agents. Handle such
samples with the greatest of care and in accordance with the required safety regulations.
Always wear safety glasses, 2 pairs of gloves, and a lab coat.
The responsible body (e.g., laboratory manager) must take the necessary precautions to
ensure that the surrounding workplace is safe and that the instrument operators are not
exposed to hazardous levels of infectious agents as defined in the applicable Safety Data
Sheets (SDSs) or OSHA,*ACGIH†or COSHH‡documents.
Venting for fumes and disposal of wastes must be in accordance with all national, state,
and local health and safety regulations and laws.
*OSHA: Occupational Safety and Health Administration (United States of America).
†ACGIH: American Conference of Government Industrial Hygienists (United States of America).
‡COSHH: Control of Substances Hazardous to Health (United Kingdom).

QIAcube HT User Manual 12/2017 2-6
2.4 Chemicals
WARNING
Hazardous chemicals [W11]
Some chemicals used with this instrument may be hazardous or may become hazardous
after completion of the protocol run.
Always wear safety glasses, gloves, and a lab coat.
The responsible body (e.g., laboratory manager) must take the necessary precautions to
ensure that the surrounding workplace is safe and that the instrument operators are not
exposed to hazardous levels of toxic substances (chemical or biological) as defined in the
applicable Safety Data Sheets (SDSs) or OSHA,*ACGIH†or COSHH‡documents.
Venting for fumes and disposal of wastes must be in accordance with all national, state,
and local health and safety regulations and laws.
*OSHA: Occupational Safety and Health Administration (United States of America).
†ACGIH: American Conference of Government Industrial Hygienists (United States of America).
‡COSHH: Control of Substances Hazardous to Health (United Kingdom).
2.4.1 Toxic fumes
If working with volatile solvents or toxic substances, you must provide an efficient laboratory ventilation system to remove
vapors that may be produced.
2.5 Waste disposal
Used plasticware and containers may contain hazardous chemicals or contagious/biohazardous materials. Such wastes
must be collected and disposed of properly according to local safety regulations.
For information on use of the tip disposal box, please see Tip disposal box.
For information about how to dispose of the QIAcube HT, see Appendix A.
2.6 Mechanical hazards
WARNING
Moving parts [W12]
Avoid contact with moving parts during operation of the QIAcube HT. Under no
circumstances should you place your hands under the pipetting arm when it is lowering.
Do not attempt to move any plates or tubes while the instrument is operating.

QIAcube HT User Manual 12/2017 2-7
WARNING
Moving parts [W15]
To avoid contact with moving parts during operation of the QIAcube HT, the instrument
must be operated with the lid closed.
If the lid sensor is not functioning correctly, contact QIAGEN Technical Services.
CAUTION
Damage to the instrument [C3]
Do not apply any manual force to the Y-arm (i.e., the pipetting head).
We strongly recommend restarting the system if the Y-arm was accidentally manually
moved.
To ensure satisfactory and safe operation of the QIAcube HT, follow the guidelines below:
Only use recommended tips and tip racks.
Keep the instrument lid closed whenever possible.
When calibrating with the lid open, always stand clear of the instrument when making adjustments. The lid sensor is
disabled during calibration. Therefore, do not click with the mouse or press any of the keys on the keyboard when
looking closely at calibrations. Wait until the robotic arm has completed its movements before moving any plates or
tubes.
Do not place any items onto the robotic arm.
During a run, click on the Pause button to pause the instrument before removing plates or tubes from the worktable. Wait
until the robotic arm has completed the current movement. This may take up to 10 seconds.
2.7 Maintenance safety
Perform the maintenance as described in Section Maintenance procedures. QIAGEN charges for repairs that are required
due to incorrect maintenance.
WARNING
Risk of personal injury and material damage [W13]
Only perform maintenance that is specifically described in this user manual.