Illumina CBot 2 Stücklistenhandbuch

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January 2016

Document # 15065681 v01

Material # 20004364

ILLUMINA PROPRIETARY

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

cBot 2 System Guide v

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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).

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