illumina cBot 2 Parts list manual

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January 2016
Document # 15065681 v01
Material # 20004364
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cBot™2 System Guide

ii Material # 20004364
Document # 15065681 v01
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Revision History
Document Date Description of Change
Material # 20004364
Document # 15065681
v01
January
2016
Updated software descriptions to cBot software v3.0, which supports
the HiSeq 3000/4000 SR ClusterKit.
Added the following information:
•Recipe and clustering duration for the HiSeq 3000/4000 SR flow
cell.
•PhiX and library volumes to the PhiX spike-in procedure for
libraries clustered on a HiSeq 3000/4000 flow cell.
•Recommendation for annual preventive maintenance service.
Updated instructions for unloading run components to include flow
cell storage options.
Moved troubleshooting information to Appendix A.
Simplified software descriptions at the beginning of the guide.
Listed the cBot System Configuration Guide (document #
1000000005301) in Additional Resources.
Part # 15065681 Rev. A July
2015
Initial release.
cBot 2 System Guide iii

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Table of Contents
Revision History iii
Table of Contents v
Chapter 1 Overview 1
Introduction 2
Additional Resources 3
cBot 2 Components 4
Illumina Consumables 7
cBot Reagent Plates 9
Chapter 2 Getting Started 11
Start the cBot 2 12
Version Compatibility of Run Components 13
User-Supplied Consumables 15
Chapter 3 Preparing Reagents 17
Introduction 18
HiSeq X Flow Cell 19
HiSeq 3000/4000 Flow Cell 23
HiSeq High Output Flow Cell 27
HiSeq Rapid Flow Cell 28
Chapter 4 Clustering With Sample Tracking 29
Introduction 30
Clustering With Sample Tracking Workflow 31
Perform a Pre-Run Wash 32
Load Consumables 33
Load the Manifold 35
Select a Protocol 37
Scan Consumables 38
Perform a Pre-Run Check 39
Monitor the Run 40
Unload Run Components 41
Perform a Post-Run Wash 43
Confirm Reagent Delivery (Optional) 44
Chapter 5 Clustering Without Sample Tracking 45
Introduction 46
Clustering Without Sample Tracking Workflow 47
Perform a Pre-Run Wash 48
Select a Protocol 49
Load Consumables 50
Perform a Pre-Run Check 54
Monitor the Run 55
Unload Run Components 56
Perform a Post-Run Wash 58
Confirm Reagent Delivery (Optional) 59
Chapter 6 Maintenance 61
Perform Periodic Maintenance 62
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Perform a Monthly Maintenance Wash 63
Change the Adapter Plate 65
Upgrade the Software 67
Upgrade Recipes 68
Shut Down the cBot 2 69
Appendix A Troubleshooting 71
Pause or Abort a Run 72
Troubleshoot Flow Check Failure 73
Troubleshoot Run Problems 75
Reset the External Barcode Scanner 76
Edit Protocols 77
Index 79
Technical Assistance 83

Chapter 1
cBot 2 System Guide 1
Chapter 1 Overview
Overview
Introduction 2
Additional Resources 3
cBot 2 Components 4
Illumina Consumables 7
cBot Reagent Plates 9

Overview
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Introduction
The cBot 2 uses amplification to create hundreds of millions of single-molecule DNA
templates simultaneously.
The cBot software dispenses reagents and controls reaction times, flow rates, and
temperatures. Setup and operation are performed on-instrument from the software interface
using the touch screen monitor. On-instrument barcode readers record the reagents, flow
cell, and template used for each experiment.
A positive sample tracking option provides internal barcode scanning for enhanced control
of libraries to be sequenced on the HiSeq. Consumables are loaded and the instrument lid
is closed. Internal scanners then record the IDof the reagent plate, flow cell, and 8-tube
strip.
Figure 1 cBot 2
Several cluster kits are available for use on the cBot. Use a kit that is compatible with the
sequencing instrument and type of sequencing run to be performed. For a list of available
kits, see Illumina Consumables on page 7.
Workflow Differences for Illumina SeqLab
If you are using the cBot 2 as a component of Illumina SeqLab, your workflow differs from
the workflow described in this guide. Differences introduced by Clarity LIMS X Edition
affect all steps from library prep through sequencing. Visit the Illumina SeqLab support
page on the Illumina website to generate a custom workflow guide for your experiment.

Additional Resources
cBot 2 System Guide 3
Additional Resources
The following documentation is available for download from the Illumina website.
Resource Description
cBot System Site Prep Guide
(document # 15053710)
Provides specifications for laboratory space, electrical
requirements, and environmental considerations and
instructions for configuring the instrument.
cBot 2 System Safety and
Compliance Guide (document #
15065643)
Provides information about instrument labeling, compliance
certifications, and safety considerations.
HiSeq and GAIIx Systems
Denature and Dilute Libraries
Guide (document # 15050107)
Provides instructions for denaturing and diluting prepared
libraries before sequencing, and preparing a PhiX control. This
step applies to most library types and flow cells.
Visit the cBot 2 support page on the Illumina website for access to documentation, software
downloads, online training, and frequently asked questions.

Overview
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cBot 2 Components
The cBot 2 uses sensors to detect the presence of run components, and provides prompts
when a component is missing or installed incorrectly. The thermal stage and reagent stage
are located under the instrument lid. A magnetic switch keeps the lid closed, and a sensor
detects when it is opened. For safety, the software prompts you to close the lid before
proceeding with the run.
Figure 2 cBot 2 Components
AThermal stage—Holds the flow cell and controls the flow cell temperature throughout the
run.
BReagent stage—Holds the cBot reagent plate, library templates, and specialty primers. For
runs with sample tracking, a barcode scanner located behind the reagent stage records the ID
of the reagent plate and the 8-tube strip containing template.
CWaste bottle compartment—Holds a sensor-controlled waste bottle that collects spent
reagents.
DExternal barcode scanner—Records the unique ID of the reagent plate and flow cell used
with each run that does not include sample tracking.
EPower switch—Turns on the instrument. The start button, located to the left of the waste
bottle compartment, starts the instrument software.
FTouch screen monitor—Provides on-instrument run setup and visual status of the cluster
generation process.
GFlow cell barcode scanner—Records the unique ID of the flow cell used with each sample
tracked run.
Thermal Stage
The thermal stage holds the flow cell and manifold, which is seated over the flow cell. The
flow cell clamp locks the flow cell and manifold into place.
WARNING
Do not touch the aluminum thermal block on the thermal stage. The heater poses a serious
burn hazard during operation. For more safety information, see the cBot 2 System Safety and
Compliance Guide (document # 15065643).