illumina cBot 2 System Manual

support.illumina.com/custom-protocol-selector.html For Research Use Only. Not for use in diagnostic procedures. January 2016 Document # 15065681 v01 Material # 20004364 ILLUMINA PROPRIETARY cBot™ 2 System Guide ...

Document # 15065681 v01 This document and its contents are proprietary to Illumina, Inc. and its affiliates ("Illumina"), and are intended solely for the contractual use of its customer in connection with the use of the product(s) described herein and for no other purpose. This document and its contents shall not be used or distributed for any other purpose and/or otherwise communicated, disclosed, or reproduced in any way whatsoever ...

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 ...

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 Ch ...

Document # 15065681 v01 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 ...

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

Document # 15065681 v01 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 use ...

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 ...

Document # 15065681 v01 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 ...

cBot 2 System Guide 5 Figure 3 Thermal Stage A Output clamp B Flow cell adapter plate and manifold C Flow cell clamp D Thermal stage E Sipper comb The manifold is a single-use component that delivers reagents from the reagent plate to the flow cell. The sippers on the sipper comb pierce the foil-sealed reagent tubes seated in the reagent plate. The outlet end of the manifold transfers waste to the waste container. The outlet clamp locks t ...

Document # 15065681 v01 cBot Software The cBot software interface provides prompts for setting up the instrument and monitoring clustering progress. During a cluster generation run, the following screens are used: Start screen, Run Setup screens, and the Run Status screen. Use the software interface to configure positive sample tracking, input requirements, wash preferences, email notifications, and remote monitoring. Sensor ...

7 Illumina Consumables cBot reagents are provided in a reagent plate that loads directly onto the instrument after thawing. cBot reagent plates are provided in the following Illumina kits. Descriptions of kit contents and other kit documentation is available on the cBot 2 support page on the Illumina website. For reagent preparation instructions, see Preparing Reagents on page 17. Cluster Kits for the HiSeq Each kit ...

Document # 15065681 v01 Kit Name Kit Catalog # TruSeq PE Cluster Kit v2 - GA (cBot) Catalog # PE-300-2001 TruSeq SR Cluster Kit v2 - GA (cBot) Catalog # GD-300-2001 Rehybridization Kits Use a cBot rehybridization kit to perform Read 1 primer rehybridization for run recovery or after extended flow cell storage. Kit Name Catalog # HiSeq X cBot Multi-Primer Rehybridization Kit v2 Catalog # GD-305-2001 HiSeq 3000/4000 cBot Multi ...

cBot 2 System Guide 9 cBot Reagent Plates The configuration of the reagent plate differs between kit types, including the number of rows that contain reagent. Each 8-tube strip is labeled with the reagent name followed by a number. The number indicates the row that it occupies on the reagent plate. If an 8-tube strip becomes dislodged, use the row number on the label to return the tube strip to the appropriate position. Flow Cell Type R ...

11   Chapter 2  Getting Started GettingStarted Start the cBot 2 12 Version Compatibility of Run Components 13 User-Supplied Consumables 15 ...

Document # 15065681 v01 Start the cBot 2 A Start button B Power switch 1 Switch the power switch on the right side of the instrument to the ON position. 2 Press the start button to the left of the waste bottle compartment to start the software. When the start-up routine is complete, the Start screen appears. ...

cBot 2 System Guide 13 Version Compatibility of Run Components For best performance and results, always use compatible versions of cBot software and kits. Kit Version Recipe Version Software Version HiSeq 3000/4000 Cluster Kit Version 1.0 recipes cBot v3.0.46, or later (SR kit) cBot v2.0.34, or later (PE kit) HiSeq X Ten Reagent Kit v2.5 Version 2.0 recipes cBot v2.0.29, or later HiSeq X Five Reagent Kit v2.5 Version ...

Document # 15065681 v01 ² To access v7 recipes, navigate to C:\Illumina\cBot\bin\Recipes\Hidden on the instrument drive. Copy recipes to C:\Illumina\cBot\bin\Recipes. ...