illumina iSeq 100 Parts list manual

iSeq 100
Sequencing System Guide
Document # 1000000036024 v05
March 2019
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For Research Use Only. Not for use in diagnostic procedures.

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Document # 1000000036024 v05
For Research Use Only. Not for use in diagnostic procedures.
ii
iSeq 100 Sequencing System Guide

Revision History
Document Date Description of Change
Document #
1000000036024 v05
March
2019
Updated software descriptions to iSeq Control Software v1.4:
• Updated instructions on configuring system settings, including moving
and renaming some user interface elements.
• Added descriptions of %Clusters PF and %Occupancy metrics, which
appear on the Sequencing screen.
• Allowed mapped network drive locations for the sample sheets and
output folders.
• Indicated that the software automatically renames sample sheets to
SampleSheet.csv.
Added links to the following pages:
• The iSeq 100 System Sample Sheet Template for Manual Mode.
• The bcl2fast Conversion Software support pages.
Added volumes of 1 nM 100% PhiX and AmpliSeq Library PLUSfor
Illumina libraries to prepare.
Added instruction to move the reference genomes repository for Local
Run Manager toa location other than drive C when restoring to system
factory settings.
Increased the maximum recommended cycles for Index Read 1 and
Index Read 2 to 10 cycles each.
Increased the number of cycles the cartridge supports to 322.
Referenced the Cluster Density Optimization Guide (document #
1000000071511) for detailed information on optimizing loading
concentration.
Clarified that a cartridge being thawed in a water bath must be stored at
-25°C to -15°C for at least one day before thawing.
Corrected AmpliSeq for Illumina Library PLUSto AmpliSeq Library PLUS
for Illumina.
Document #
1000000036024 v04
October
2018
Added recommended loading concentrations and dilution instructions for
Nextera DNAFlex for Enrichment, TruSeq DNA Nano, and TruSeq DNA
PCR-Free libraries.
Added information on using a normalization method that does not result
in single-stranded libraries.
Added descriptions of the two run modes, Local Run Manager and
Manual.
Added a 5% PhiX spike-in option and defined the purpose of each spike-
in percentage.
Added the following steps:
• Switching to the sbsadmin operating system account when installing
the control software, analysis modules, and other software.
• Power cycling the instrument when restoring to factory settings.
Referenced Illumina Adapter Sequences (document # 1000000002694)
to determine Index 2 (i5)orientations for a sample sheet.
Clarified the following points:
• Cartridges must be used immediately after thawing.
• The loading concentrations listed for Nextera DNAFlex and Nextera
Flex for Enrichment libraries are not applicable to other Nextera library
types.
• SureCell WTA3′is not a compatible library.
Document # 1000000036024 v05
For Research Use Only. Not for use in diagnostic procedures.
iii
iSeq 100 Sequencing System Guide

Document Date Description of Change
Document #
1000000036024 v03
August
2018
Updated software descriptions to iSeq Control Software v1.3:
• Added configuration instructions for Universal Copy Service.
• Renamed the Network Configuration tab to Network Access.
• Added instructions on opening Local Run Manager from the control
software.
Updated the default output folder location to D:\SequencingRuns.
Added instructions on connecting the system to a proxy server.
Added requirement to specify a UNCpath for output folder and sample
sheet locations on the network.
Indicated the unique requirements for configuring an output folder
location on an internal drive, external drive, or network location.
Made instructions on creating a sample sheet for Manual mode the first
step of run setup.
Corrected instructions on using the system suite installation wizard.
Corrected the description of output thumbnail files.
Document #
1000000036024 v02
June
2018
Updated tubes used for diluting libraries to Fisher Scientific catalog #
14-222-158 or equivalent low-bind tubes.
Added a section describing the regional availability of Advanced
Exchange.
Clarified that libraries diluted to the loading concentration must be
sequenced that day.
Clarified that the reagent cartridge must be removed from the box for
thawing.
Document #
1000000036024 v01
May
2018
Updated software descriptions to iSeq Control Software v1.2:
• Added option to browse to a downloaded software installer from the
control software.
• Added instructions for saving thumbnails.
• Moved network settings to the Network Configuration tab.
• Increased maximum uses of reusable test components to 36 and noted
that the remaining number of uses appear onscreen.
Updated Local Run Manager information:
• Added steps for opening Local Run Manager and setting up the run.
• Added RNAAmplicon as a preinstalled analysis module, and
DNAEnrichment and Resequencing as other supported modules.
• Updated documentation references to Local Run Manager Software
Guide (document #1000000002702) .
Updated cartridge thawing instructions:
• Added a room-temperature thawing option.
• Provided more detailed water bath instructions, including storing before
thawing.
Updated instructions on preparing libraries for sequencing:
• Updated the Nextera DNAFlex loading concentration to 200 pM.
• Added starting loading concentration for unlisted library types.
• Added information on the %Occupied metric.
• Increased volume of 1 nM PhiX for a spike-in to 50 µl.
Updated Illumina catalog numbers for:
• iSeq 100 Spare Drip Tray Pad to 20023927.
• iSeq 100 Spare Air Filter to 20023928.
Updated pipette and pipette tip recommendations.
Document # 1000000036024 v05
For Research Use Only. Not for use in diagnostic procedures.
iv
iSeq 100 Sequencing System Guide

Document Date Description of Change
Document #
1000000036024 v01
May
2018
Added the following miscellaneous instructions:
• Performing validation runs.
• Creating a sample sheet when sequencing in Manual mode.
• Minimizing the control software to access other applications.
Added the following steps to the system check procedure:
• Unloading and storing reusable test components.
• Cleaning visible debris from the reusable test flow cell.
Reorganized the following content to improve continuity:
• Merged instructions for performing a PhiX-only run with the standard
sequencing instructions.
• Merged flow cell preparation instructions with library dilution
instructions.
• Consolidated PhiX spike-in instructions.
• Moved information on number of cycles in a read.
• Moved Real-Time Analysis and renamed to Sequencing Output .
Simplified the error messages workflow diagram.
Removed information on Tablet and Desktop modes. The operating
system runs in Desktop mode by default and Tablet mode is not
necessary.
Removed requirement to complete and return a decontamination
certificate for advanced exchange.
Corrected average run size to 2 GB.
Document #
1000000036024 v00
February
2018
Initial release.
Document # 1000000036024 v05
For Research Use Only. Not for use in diagnostic procedures.
v
iSeq 100 Sequencing System Guide

Table of Contents
Chapter 1 Overview 1
Introduction 1
Additional Resources 2
Instrument Components 3
iSeq 100 i1 Reagent 7
Chapter 2 Getting Started 11
First Time Setup 11
Minimize the Control Software 11
Run Settings 12
Instrument Customization 14
Network Setup 15
User-Supplied Consumables and Equipment 17
Chapter 3 Sequencing 19
Introduction 19
Thaw the Bagged Cartridge 20
Prepare the Flow Cell and Libraries 21
Load Consumables Into the Cartridge 23
Set Up a Sequencing Run (Local Run Manager) 24
Set Up a Sequencing Run (Manual Mode) 27
Chapter 4 Maintenance 31
Clear Hard Drive Space 31
Software Updates 31
Replace the Air Filter 32
Relocate the Instrument 34
Software Restriction Policies 35
Appendix A Sequencing Output 38
Real-Time Analysis Overview 38
Real-Time Analysis Workflow 40
Appendix B Troubleshooting 44
Error Message Resolution 44
Cancel a Started Run 45
Power Cycle the Instrument 45
Perform a System Check 46
Leak Mitigation 48
Restore to Factory Settings 50
Appendix C Advanced Exchange 52
Document # 1000000036024 v05
For Research Use Only. Not for use in diagnostic procedures.
vi

Exchanging the iSeq 100 System 52
Receive a Replacement System 52
Prepare the Original System for Return 52
Return the Original System 55
Index 59
Technical Assistance 65
Document # 1000000036024 v05
For Research Use Only. Not for use in diagnostic procedures.
vii
iSeq 100 Sequencing System Guide

Chapter 1 Overview
Introduction 1
Additional Resources 2
Instrument Components 3
iSeq 100 i1 Reagent 7
Introduction
The Illumina®iSeq™ 100 Sequencing System provides a targeted approach to next-generation sequencing
(NGS). This applications-focused system packages Illumina sequencing technology into a cost-effective
desktop instrument.
Features
uAccessibility and reliability—The iSeq 100 System has a small footprint and is easy to install and use.
Fluidics and imaging components are built into the consumable, simplifying instrument maintenance.
uSingle-step consumable loading—A single-use cartridge is prefilled with all reagents required for a run.
Library and a sensor-equipped flow cell load directly into the cartridge, which is then loaded onto the
instrument. Integrated identification enables accurate tracking.
uiSeq 100 System software—A suite of integrated software controls instrument operations, processes
images, and generates base calls. This suite features on-instrument data analysis and data transfer tools
for external analysis.
uOn-instrument analysis—Local Run Manager inputs sample information and then analyzes run data
using the analysis module specified for the run. The software includes a suite of analysis modules.
uCloud-based analysis—The sequencing workflow is integrated with BaseSpace Sequence Hub, the
Illumina cloud computing environment for run monitoring, data analysis, storage, and collaboration.
Output files are streamed in real time to BaseSpace Sequence Hub for analysis.
Sample to Analysis
The following diagram illustrates the complete sequencing workflow, from experimental design to analyzing
data. Tools and documentation are included with each step. This guide covers the sequence libraries step.
For other documentation, visit support.illumina.com.
Document # 1000000036024 v05
For Research Use Only. Not for use in diagnostic procedures.
1

Figure 1 Sample to Analysis Workflow
Additional Resources
The iSeq 100 Sequencing System support pages on the Illumina website provide additional system
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 tool for generating end-to-end instructions tailored to your library prep method, run
parameters, and analysis method, with options to refine the level of detail.
iSeq 100 Sequencing System
Setup Poster (document #
1000000035963)
Provides instructions for instrument installation and initiating first time setup.
iSeq 100 Sequencing System Site
Prep Guide (document #
1000000035337)
Provides specifications for laboratory space, electrical requirements, and environmental
and network considerations.
iSeq 100 Sequencing System
Safety and Compliance Guide
(document # 1000000035336)
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, including compliance
certifications and safety considerations.
Document # 1000000036024 v05
For Research Use Only. Not for use in diagnostic procedures.
2
iSeq 100 Sequencing System Guide

Instrument Components
iSeq 100 Sequencing System comprises a power button, monitor, status bar, consumables compartment,
and drip tray.
Figure 2 External System Components
APower button—Controls instrument power and indicates whether the system is on (glows), off (dark), or off
but with ACpower (pulses).
BTouch-screen monitor—Enables on-instrument configuration and setup using the control software interface.
CStatus bar—Indicates system status as ready to sequence (green), processing (blue), or needs attention
(orange).
DConsumables compartment—Contains consumables during a run.
EDrip tray door—Provides access to the drip tray, which catches leaked fluids.
Power and Auxiliary Connections
You can move the instrument to access USBports and other rear panel components.
The back of the instrument has the switch and inlet that controls power to the instrument, and an Ethernet
port for an optional Ethernet connection. Two USBports provide the option to connect a mouse and
keyboard, or to upload and download data using a portable device.
NOTE
Connecting the system to a keyboard and mouse overrides the onscreen keyboard.
Document # 1000000036024 v05
For Research Use Only. Not for use in diagnostic procedures.
3
iSeq 100 Sequencing System Guide