illumina MiniSeq Parts list manual

MiniSeq
System Guide
Document # 1000000002695 v02 Material # 20014309
March 2018
ILLUMINA PROPRIETARY
For Research Use Only. Not for use in diagnostic procedures.

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Document # 1000000002695 v02 Material # 20014309
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MiniSeq System Guide

Revision History
Document Date Description of Change
Material # 20014309
Document #
1000000002695 v02
March
2018
Added information about the Illumina Proactive monitoring service in
the Configure Analysis Settings section.
Removed the default user name and password required to log on to the
operating system. Illumina recommends using site-specific credentials.
Minor text edits.
Material # 20014309
Document #
1000000002695 v01
September
2016
Updated software descriptions to MiniSeq Control Software v1.1.8,
which includes Demo Mode.
Updated the automatic post-run wash duration to 60 minutes.
Added a server configuration step to the instructions for selecting
BaseSpace for analysis.
Noted that mapped drives are not supported by the Local Run
Manager software.
Material # 20002370
Document #
1000000002695 v00
January
2016
Initial release.
Document # 1000000002695 v02 Material # 20014309
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MiniSeq System Guide

Table of Contents
Chapter 1 Overview 1
Introduction 1
Additional Resources 1
Instrument Components 2
Sequencing Consumables Overview 5
Preinstalled Databases and Genomes 7
Chapter 2 Getting Started 8
Starting the Instrument 8
Customize System Settings 8
Configure Analysis Settings 10
User-Supplied Consumables and Equipment 13
Chapter 3 Sequencing 16
Introduction 16
Sequencing Workflow 17
Prepare Consumables 19
Prepare Libraries for Sequencing 20
Set Up a Sequencing Run 20
Monitor Run Progress 28
Automatic Post-Run Wash 30
Remove Used Reservoir from Position #9 30
Chapter 4 Maintenance 32
Introduction 32
Perform a Manual Instrument Wash 32
Software Updates 35
Appendix A Troubleshooting 38
Troubleshooting Files 38
Automatic Check Errors 39
RTA Errors 40
Rehybridization Workflow 41
System Check 42
Network Configuration Settings 45
Custom Genomes 46
Shut Down the Instrument 46
Appendix B Real-Time Analysis 48
Real-Time Analysis Overview 48
Input and Output Files 48
Real-Time Analysis Workflow 49
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Appendix C Output Files 52
Sequencing Output Files 52
Sequencing Output Folder Structure 52
Analysis Input File Requirements 53
Index 54
Technical Assistance 57
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Chapter 1 Overview
Introduction 1
Additional Resources 1
Instrument Components 2
Sequencing Consumables Overview 5
Preinstalled Databases and Genomes 7
Introduction
The Illumina®MiniSeq™ System provides high-quality, industry-standard Illumina sequencing technology with
the convenience of an easy-to-use cost-effective desktop system.
Features
uHigh-quality sequencing—The MiniSeq System enables small genome, amplicon, targeted enrichment,
and RNA sequencing using low library volumes.
uMiniSeq system software—The MiniSeq System includes a suite of integrated software that controls
instrument operations, processes images, and generates base calls. The suite includes on-instrument
data analysis software and data transfer tools for analysis using other options, such as BaseSpace.
uOn-instrument data analysis—The Local Run Manager software analyzes run data according to the
analysis module specified for the run. A suite of analysis modules are included in the software.
uBaseSpace®integration—The sequencing workflow is integrated with BaseSpace, the Illumina
genomics computing environment for run monitoring, data analysis, storage, and collaboration.
Output files are streamed in real time to BaseSpace or BaseSpace Onsite for analysis.
uConvenient consumable loading—A clamping mechanism positions the flow cell as it is loaded onto the
instrument. A single-use prefilled reagent cartridge provides reagents required for a run and subsequent
instrument wash. The flow cell and reagent cartridge include integrated identification to enable accurate
tracking.
Additional Resources
The MiniSeq System support pages on the Illumina website provide additional resources. These resources
include software, training, compatible products, and the following documentation. Always check support
pages for the latest versions.
Resource Description
Custom Protocol Selector A wizard for generating customized end-to-end documentation that is tailored to the
library prep method, run parameters, and analysis method used for the sequencing run.
MiniSeq System Site Prep
Guide (document #
1000000002696)
Provides specifications for laboratory space, electrical requirements, and environmental
considerations.
MiniSeq System Safety and
Compliance Guide
(document #
1000000002698)
Provides information about operational safety considerations, compliance statements,
and instrument labeling.
RFID Reader Compliance
Guide (document #
1000000002699)
Provides information about the RFID reader in the instrument, compliance certifications,
and safety considerations.
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Resource Description
MiniSeq System Denature
and Dilute Libraries Guide
(document #
1000000002697)
Provides instructions for denaturing and diluting prepared libraries for a sequencing run,
and preparing an optional PhiX control.
Local Run Manager
Software Guide (document
# 1000000002702)
Provides information about using the Local Run Manager software and available analysis
options.
Instrument Components
The MiniSeq System includes a touch screen monitor, a status bar, a flow cell compartment, and a reagent
compartment.
Figure 1 Instrument Components
ATouch screen monitor—Enables on-instrument configuration and setup using the control software interface.
BPower button–Turns on the integrated instrument computer and operating system.
CUSB ports—Convenient connections for peripheral components.
DFlow cell compartment—Holds the flow cell during a sequencing run.
EStatus bar—Indicates instrument status as processing (blue), requires attention (orange), ready to sequence
(green), or when a wash is due within the next 24 hours (yellow).
FReagent compartment—Holds the reagent cartridge and spent reagents bottle.
Flow Cell Compartment
The flow cell stage includes the flow cell latch, which secures the flow cell when it is closed. As the latch
closes, pins near the base of the latch align the flow cell ports with fluidics connections.
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Figure 2 Flow Cell Compartment
AFlow cell compartment door
BFlow cell latch
CFlow cell stage
DFlow cell
EFlow cell latch release button
The thermal station, located beneath the flow cell stage, controls changes in temperature required for cluster
generation and sequencing.
NOTE
Do not place objects on the instrument near the flow cell compartment.
Reagent Compartment
Setting up a sequencing run on the MiniSeq System requires access to the reagent compartment to load run
consumables and empty the spent reagents bottle.
Figure 3 Reagent Compartment
ASpent reagents bottle—Includes a threaded cap to prevent spills when carrying.
BReagent cartridge—Provides reagents in a single-use prefilled consumable.
CReagent compartment door—Provides access to the reagent compartment.
The reagent compartment door opens outward from hinges at the bottom edge of the instrument. To open
the door, gently pull forward from the side edges of the door.
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NOTE
Do not place objects on the reagent compartment door. The compartment door is not designed for use as a
shelf.
Power Button
The power button on the front of the instrument turns on power to the instrument and instrument computer.
The power button performs the following actions depending on the state of instrument power.
Power State Action
Instrument power is off Briefly press the button to turn on the power.
Instrument power is on Briefly press the button to turn off the power. A dialog box appears on the screen to
confirm a normal instrument shutdown.
Instrument power is on Press and hold the power button for 10 seconds to cause a hard shutdown of the
instrument and instrument computer.
Use this method to turn off the instrument only if the instrument is unresponsive.
NOTE
Under normal conditions, do not turn off the instrument power.
Turning off the instrument during a sequencing run ends the run immediately. Ending a run is final. Run
consumables cannot be reused and sequencing data are not saved.
System Software
The instrument software suite includes integrated applications that perform sequencing runs and on-
instrument analysis.
uMiniSeq Control Software—The control software guides you through the steps to set up a sequencing
run, controls instrument operations, and shows an overview of run statistics as the run progresses.
uReal-Time Analysis (RTA) software—RTA performs image analysis and base calling during the run. See
Real-Time Analysis Overview on page 48.
uLocal Run Manager—Before sequencing, use Local Run Manager to specify run parameters and the
analysis method. After sequencing, on-instrument data analysis begins automatically. For more
information, see the Local Run Manager Software Guide (document # 1000000002702) .
Status Icons
A status icon in the top-right corner of the control software interface screen indicates a change in condition
during run setup or during the run.
Status
Icon
Status
Name
Description
Status OK System is normal.
Processing System is processing.
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Status
Icon
Status
Name
Description
Attention Attention is required.
Warning A warning has occurred.
Warnings do not stop a run or require action before proceeding.
Error An error has occurred.
Errors require action before proceeding with the run.
When a change in condition occurs, the icon blinks to alert you. Select the icon to view a description of the
condition. Select Acknowledge to accept the message and Close to close the dialog box.
Sequencing Consumables Overview
Performing a sequencing run on the MiniSeq System requires a single-use MiniSeq Kit. Each kit includes a
flow cell and the reagents required for a sequencing run.
The flow cell and reagent cartridge use radio-frequency identification (RFID) for accurate consumable
tracking and to ensure compatibility with specified run parameters.
Flow Cell
The flow cell is a glass-based substrate on which clusters are generated and the sequencing reaction is
performed. The flow cell is encased in a flow cell cartridge.
Figure 4 Flow Cell Components
AImaging area
BFlow cell gasket
COutlet port
DInlet port
Reagents enter the flow cell through the inlet port, pass through the single-lane imaging area, and then exit
the flow cell through the outlet port.
The flow cell is shipped dry in a flow cell tube that is wrapped in a foil package. Store the flow cell in the
sealed foil package at 2°C to 8°C until use. For more information, see Prepare the Flow Cell on page 19.
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Reagent Cartridge Overview
The reagent cartridge is a single-use consumable with foil-sealed reservoirs that are prefilled with clustering,
sequencing, and wash reagents.
Figure 5 Reagent Cartridge
The reagent cartridge includes a designated reservoir for loading prepared libraries. After the run begins,
libraries are transferred automatically from the reagent cartridge to the flow cell.
WARNING
This set of reagents contains potentially hazardous chemicals. Personal injury can occur through inhalation,
ingestion, skin contact, and eye contact. Wear protective equipment, including eye protection, gloves, and
laboratory coat appropriate for risk of exposure. Handle used reagents as chemical waste and discard in
accordance with applicable regional, national, and local laws and regulations. For additional environmental,
health, and safety information, see the SDS at support.illumina.com/sds.html.
Store the reagent cartridge at -25°C to -15°C until use. For more information, see Prepare the Reagent
Cartridge on page 19.
Reserved Reservoirs
Figure 6 Numbered Reservoirs
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Position Description
13, 14, and 15 Reserved for optional custom primers
16 Load libraries
Removable Reservoir in Position #9
The prefilled reagent cartridge includes a denaturation reagent in position #9 that contains formamide. To
facilitate safe disposal of any unused reagent after the sequencing run, this reservoir is removable. For more
information, see Remove Used Reservoir from Position #9 on page 30.
Preinstalled Databases and Genomes
For most analysis methods, a reference is required to perform alignment. Several reference databases and
genomes are preinstalled on the instrument computer.
Preinstalled Description
Databases • miRbase for human
• dbSNP for human
• RefGene for human
Genomes
• Arabidopsis thaliana
• cow ( Bos taurus )
• E. coli strain DH10B
• E. coli strain MG1655
• fruit fly ( Drosophila melanogaster )
• human ( Homo sapiens ) build hg19
• mouse ( Mus musculus )
• PhiX
• rat ( Rattus norvegicus )
• Rhodobacter sphaeroides 2.4.1
• yeast ( Saccharomyces cerevisiae S288C)
• Staphylococcus aureus NCTC 8325
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Chapter 2 Getting Started
Starting the Instrument 8
Customize System Settings 8
Configure Analysis Settings 10
User-Supplied Consumables and Equipment 13
Starting the Instrument
Make sure that the instrument has been properly installed and initialized, and that instrument setup is
complete. Starting the instrument before it is ready can damage the system.
1 Turn on the power toggle switch to the I(on) position.
Figure 7 Power Switch Located on Back of Instrument
2 Press the power button above the reagent compartment.
The power button turns on the integrated instrument computer and operating system.
Figure 8 Power Button Located on Front of Instrument
3 Wait until the operating system has finished loading.
The MiniSeq Control Software launches and initializes the system automatically. The Home screen opens
after the initialization step is complete.
4 Wait for the system to load, and then log on to the operating system. If necessary, consult your facility
administrator for the user name and password.
Customize System Settings
The control software includes customizable settings for instrument identification and the following workflow
preferences:
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uPurging consumables at end of run.
uSkipping pre-run check confirmation to start the run automatically.
uUsing the on-screen keyboard for run setup steps.
uEnabling audio indicators.
uPerforming a simulated run.
Customize Instrument Identification
1 From the Manage Instrument screen, select System Customization.
2 To assign an avatar image for the instrument, select Browse and navigate to a preferred image.
3 In the Nick Name field, enter a preferred name for the instrument.
4 Select Save to save settings and advance the screen.
The image and name appear in the upper-left corner of each screen.
Set Automatic Purge Option
1 From the Manage Instrument screen, select System Customization.
2 Select the Purge consumables at end of run checkbox.
This setting purges unused reagents from the reagent cartridge to the spent reagents bottle automatically
after each run. If this setting is disabled, unused reagents remain in the reagent cartridge.
NOTE
Purging consumables automatically adds additional time to the workflow. For example, purging reagents
after a 300-cycle run (2×151), takes approximately 50 minutes.
3 Select Save to save settings and exit the screen.
Set Automatic Start Option
1 From the Manage Instrument screen, select System Customization.
2 Select the Skip pre-run check confirmation checkbox.
This setting starts the sequencing run automatically after a successful automatic check. If this setting is
disabled, start the run manually after the pre-run check.
3 Select Save.
Set Automatic Check for Software Updates
1 From the Manage Instrument screen, select System Customization.
2 Select the Automatically check for software updates on BaseSpace checkbox.
An internet connection is required.
3 Select Save to save settings and exit the screen.
Set On-Screen Keyboard Option
1 From the Manage Instrument screen, select System Customization.
2 Select the Use on-screen keyboard checkbox.
This setting enables the on-screen keyboard for input during run setup steps.
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3 Select Save.
Enable Audio Indicators
1 From the Manage Instrument screen, select System Customization.
2 Select the Play audio checkbox to turn on audio indicators for the following events.
uUpon instrument initialization
uWhen a run is started
uWhen errors occur
uWhen user interaction is required
uWhen a run has finished
3 Select Save.
Enable Demo Mode
Demo Mode simulates a sequencing run to provide a demonstration of instrument features and function. Use
Demo Mode to mimic run setup without reagents, a flow cell, or other consumables.
1 From the Manage Instrument screen, select System Customization.
2 Select the Enable Demo Mode checkbox.
3 Select Save.
4[Optional] Enter a 4-digit PIN.
When this field is blank, exiting Demo Mode does not require a PIN.
5 Select OK to restart the software in Demo Mode.
After restart, the MiniSeq Control Software banner reads Demonstration Only.
Exit Demo Mode
1 From the Manage Instrument screen, select System Customization.
2 Clear the Enable Demo Mode checkbox.
3 Select Save.
4 If a PIN is required, enter it when prompted.
5 Select OK to restart the software in the standard mode.
Configure Analysis Settings
The control software provides the following options for data transfer and subsequent analysis:
uBaseSpace—Sends data to Illumina BaseSpace for analysis on BaseSpace.
uBaseSpace Onsite—Sends data to the BaseSpace Onsite LTserver for analysis on the server.
uLocal Run Manager—Sends data to a specified output folder location for analysis using a Local Run
Manager module.
uStandalone—Saves data to a specified output folder location for later analysis.
Select BaseSpace
1 From the Manage Instrument screen, select System Configuration.
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2 Select Analysis Configuration.
3 Select BaseSpace.
4[Optional] Specify default BaseSpace login credentials as follows.
a Enter a User name and Password.
b Select the Save the credentials as the default checkbox.
c Select the Bypass Analysis Method login screen checkbox.
5 In the Server Name field, enter the full path to your BaseSpace server. For the EUserver, replace the
USserver name with https://api.euc1.sh.basespace.illumina.com.
The default US server is https://api.basespace.illumina.com.
6[Optional] Select the Output Folder checkbox, select Browse, and navigate to a preferred output folder
location.
This setting saves a copy of base call (BCL) files in the specified location.
7[Optional] Select Send instrument health information to Illumina to enable the Illumina Proactive monitoring
service. The name of the setting in the software interface might be different from the name in this guide,
depending on the version of MiniSeq Control Software in use.
With this setting turned on, instrument performance data are sent to Illumina. This data helps Illumina
troubleshoot more easily and detect potential failures, enabling proactive maintenance and maximizing
instrument uptime. For more information on the benefits of this service, see Illumina Proactive Technical
Note (document # 1000000052503) .
This service:
uDoes not send sequencing data.
uRequires that the instrument be connected to a network with internet access.
uIs turned on by default. To opt out of this service, disable the Send instrument health information to
Illumina setting.
8 Select Save.
Select BaseSpace Onsite
1 From the Manage Instrument screen, select System Configuration.
2 Select Analysis Configuration.
3 Select BaseSpace Onsite.
4[Optional] Specify default BaseSpace Onsite login credentials as follows.
a Enter a User name and Password.
b Select the Save the credentials as the default checkbox.
c Select the Bypass Analysis Method login screen checkbox.
5 In the Server Name field, enter the full path to your BaseSpace Onsite server.
6[Optional] Select the Output Folder checkbox, select Browse, and navigate to a preferred output folder
location.
This setting saves a copy of base call (BCL) files in the specified location.
7[Optional] Select Send instrument health information to Illumina to enable the Illumina Proactive monitoring
service. The name of the setting in the software interface might be different from the name in this guide,
depending on the version of MiniSeq Control Software in use.
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With this setting turned on, instrument performance data are sent to Illumina. This data helps Illumina
troubleshoot more easily and detect potential failures, enabling proactive maintenance and maximizing
instrument uptime. For more information on the benefits of this service, see Illumina Proactive Technical
Note (document # 1000000052503) .
This service:
uDoes not send sequencing data.
uRequires that the instrument be connected to a network with internet access.
uIs turned on by default. To opt out of this service, disable the Send instrument health information to
Illumina setting.
8 Select Save.
Select Local Run Manager
1 From the Manage Instrument screen, select System Configuration.
2 Select Analysis Configuration.
3 Select Local Run Manager.
4[Optional] Specify default Local Run Manager login credentials as follows.
a Enter a User name and Password.
b Select the Save credentials as the default checkbox.
c Select the Bypass Analysis Method login screen checkbox.
5[Optional] Select Use Run Monitoring to monitor the contents using visualization tools on BaseSpace. A
BaseSpace login and internet connection are required.
6[Optional] Specify default BaseSpace login credentials as follows.
a Enter a User name and Password.
b Select the Save credentials as the default checkbox.
7 Select Browse and navigate to a preferred output folder location.
8 In the Contents pane of the output folder location, create a folder named Runs.
NOTE
Local Run Manager does not support mapped drives.
9[Optional] Select Send instrument health information to Illumina to enable the Illumina Proactive monitoring
service. The name of the setting in the software interface might be different from the name in this guide,
depending on the version of MiniSeq Control Software in use.
With this setting turned on, instrument performance data are sent to Illumina. This data helps Illumina
troubleshoot more easily and detect potential failures, enabling proactive maintenance and maximizing
instrument uptime. For more information on the benefits of this service, see Illumina Proactive Technical
Note (document # 1000000052503) .
This service:
uDoes not send sequencing data.
uRequires that the instrument be connected to a network with internet access.
uIs turned on by default. To opt out of this service, disable the Send instrument health information to
Illumina setting.
10 Select Save.
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Select Standalone
1 From the Manage Instrument screen, select System Configuration.
2 Select Analysis Configuration.
3 Select Standalone.
4[Optional] Select Use Run Monitoring to monitor the run using visualization tools on BaseSpace. A
BaseSpace login and internet connection are required.
5[Optional] Specify default BaseSpace login credentials as follows.
a Enter a User name and Password.
b Select the Save credentials as the default checkbox.
6 Select Browse and navigate to a preferred output folder location.
7[Optional] Select Send instrument health information to Illumina to enable the Illumina Proactive monitoring
service. The name of the setting in the software interface might be different from the name in this guide,
depending on the version of MiniSeq Control Software in use.
With this setting turned on, instrument performance data are sent to Illumina. This data helps Illumina
troubleshoot more easily and detect potential failures, enabling proactive maintenance and maximizing
instrument uptime. For more information on the benefits of this service, see Illumina Proactive Technical
Note (document # 1000000052503) .
This service:
uDoes not send sequencing data.
uRequires that the instrument be connected to a network with internet access.
uIs turned on by default. To opt out of this service, disable the Send instrument health information to
Illumina setting.
8 Select Save.
User-Supplied Consumables and Equipment
The following consumables and equipment are used for sequencing and system maintenance.
User-Supplied Consumables for Sequencing Runs
Consumable Supplier Purpose
1 N NaOH
(sodium hydroxide)
General lab supplier Library denaturation, diluted to 0.1N
200 mM Tris-HCl, pH7 General lab supplier Library neutralization after denaturation
Isopropyl alcohol wipes, 70%
or
Ethanol, 70%
VWR, catalog#95041-714
(or equivalent)
General lab supplier
Flow cell cleaning and general purpose
Disposable gloves, powder-free General lab supplier General purpose
Lab tissue, low-lint VWR, catalog#21905-026
(or equivalent)
Flow cell cleaning
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User-Supplied Consumables for Instrument Maintenance
Consumable Supplier Purpose
NaOCl, 5%
(sodium hypochlorite)
Sigma-Aldrich, catalog # 239305
(or laboratory-grade equivalent)
Performing a manual post-run wash;
diluted to 0.12%
Tween 20 Sigma-Aldrich, catalog # P7949 Performing a manual instrument wash;
diluted to 0.05%
Water, laboratory-grade General lab supplier Performing a manual instrument wash
Guidelines for Laboratory-Grade Water
Always use laboratory-grade water or deionized water to perform instrument procedures. Never use tap
water. Use only the following grades of water or equivalents:
uDeionized water
uIllumina PW1
u18Megohms (MΩ) water
uMilli-Q water
uSuper-Q water
uMolecular biology grade water
User-Supplied Equipment
Item Source
Freezer, -25°C to -15°C, frost-free General lab supplier
Ice bucket General lab supplier
Refrigerator, 2°C to 8°C General lab supplier
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