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illumina cBot 2 System Manual

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cBot
2 System Guide
™
For Research Use Only. Not for use in diagnostic procedures.
ILLUMINA PROPRIETARY
Material # 20004364
Document # 15065681 v01
January 2016
Customize a short end-to-end work ow guide with the Custom Protocol Selector
support.illumina.com/custom-protocol-selector.html

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  • Page 1 2 System Guide ™ For Research Use Only. Not for use in diagnostic procedures. ILLUMINA PROPRIETARY Material # 20004364 Document # 15065681 v01 January 2016 Customize a short end-to-end work ow guide with the Custom Protocol Selector support.illumina.com/custom-protocol-selector.html...
  • Page 2 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 without the prior written consent of Illumina.

  • Page 3: Revision History

    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 Initial release. July 2015 cBot 2 System Guide...
  • Page 4 Material # 20004364 Document # 15065681 v01...

  • Page 5: Table Of Contents

    Chapter 1 Overview Introduction Additional Resources cBot 2 Components Illumina Consumables cBot Reagent Plates Chapter 2 Getting Started Start the cBot 2 Version Compatibility of Run Components User-Supplied Consumables Chapter 3 Preparing Reagents Introduction HiSeq X Flow Cell HiSeq 3000/4000 Flow Cell...
  • Page 6 Perform a Monthly Maintenance Wash Change the Adapter Plate Upgrade the Software Upgrade Recipes Shut Down the cBot 2 Appendix A Troubleshooting Pause or Abort a Run Troubleshoot Flow Check Failure Troubleshoot Run Problems Reset the External Barcode Scanner Edit Protocols...

  • Page 7: Chapter 1 Overview

      Chapter 1  Overview Overview Introduction Additional Resources cBot 2 Components Illumina Consumables cBot Reagent Plates cBot 2 System Guide...

  • Page 8: Introduction

    Illumina Consumables on page 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.

  • Page 9: Additional Resources

    PhiX control. This Guide (document # 15050107) 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. cBot 2 System Guide...

  • Page 10: Cbot 2 Components

    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.
  • Page 11 The left side of the template row is keyed to ensure the correct orientation of the 8-tube strip used with the sample tracking workflow. Figure 4 cBot 2 Reagent Stage Reagent plate lever Template row...
  • Page 12 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.

  • Page 13: Illumina Consumables

    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...
  • Page 14 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.

  • Page 15: Cbot Reagent Plates

    Personal injury can occur through inhalation, ingestion, skin contact, and eye contact. Dispose of containers and any unused contents in accordance with the governmental safety standards for your region. For more information, see the SDS for this kit at support.illumina.com/sds.html. cBot 2 System Guide...
  • Page 16 Material # 20004364 Document # 15065681 v01...

  • Page 17: Chapter 2 Getting Started

      Chapter 2  Getting Started Getting Started Start the cBot 2 Version Compatibility of Run Components User-Supplied Consumables cBot 2 System Guide...

  • Page 18: Start The Cbot 2

    Start the cBot 2 Start button Power switch Switch the power switch on the right side of the instrument to the ON position. 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.

  • Page 19: Version Compatibility Of Run Components

    PE_HiSeq_Cluster_Kit_v4_cBot_recipe_v9.0 TruSeq v3 Flow Cell SR_Amp_Lin_Block_TubeStripHyb_v8.0 PE_Amp_Lin_Block_TubeStripHyb_v8.0 SR_Amp_Lin_Block_Hyb_v8.0 PE_Amp_Lin_Block_Hyb_v8.0 HiSeq Rapid v2 Flow Cell RR_TemplateHyb_FirstExt_vR¹ TruSeq Rapid Flow Cell RR_TemplateHyb_FirstExt_vR¹ GAIIx v2 Flow Cell SR_Amp_Lin_Block_TubeStripHyb_v7.0² PE_Amp_Lin_Block_TubeStripHyb_v7.0² SR_Amp_Lin_Block_Hyb_v7.0² PE_Amp_Lin_Block_Hyb_v7.0² ¹ Used only with the Rapid Duo kits. cBot 2 System Guide...
  • Page 20 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. Material # 20004364 Document # 15065681 v01...

  • Page 21: User-Supplied Consumables

    HiSeq X and HiSeq 3000/4000 kits. Make sure that you use the appropriate 8-tube strip for your workflow. The HiSeq X and HiSeq 3000/4000 kits introduce a denaturation step before clustering on the cBot 2. Using these kits, libraries are denatured in the 8-tube strip before adding the ExAmp reaction mix. Component...
  • Page 22 Material # 20004364 Document # 15065681 v01...

  • Page 23: Chapter 3 Preparing Reagents

      Chapter 3  Preparing Reagents Preparing Reagents Introduction HiSeq X Flow Cell HiSeq 3000/4000 Flow Cell HiSeq High Output Flow Cell HiSeq Rapid Flow Cell cBot 2 System Guide...

  • Page 24: Introduction

    Introduction Reagent preparation instructions depend on the reagent kit that you are using. Instructions are organized by flow cell type and include HiSeq X, HiSeq 3000/4000, HiSeq high output, and HiSeq rapid. For instructions on preparing reagents for a GAIIx flow cell, see the guide for your cluster kit: TruSeq PE Cluster Kit v2 Reagent Preparation Guide (part # 15019437) TruSeq SR Cluster Kit v2 Reagent Preparation Guide (part # 15019436)

  • Page 25: Hiseq X Flow Cell

    4 cBot instruments are available. Reagents cannot be stored after preparation. NOTE The reagent preparation instructions described in this guide do not apply to the automated workflow used for Illumina SeqLab. For Illumina SeqLab workflow instructions, see support.illumina.com/custom-protocol-selector.html. About Reagents ExAmp reagents are viscous, especially EPX2 and EPX3.
  • Page 26 Figure 6 Remove From Foil Packaging Open the clamshell package and remove the flow cell. Figure 7 Remove Flow Cell From Clamshell Package Clean the flow cell with a lint-free alcohol wipe. Dry with a lint-free tissue. Set aside at room temperature. Thaw the cBot Reagent Plate Remove the cBot reagent plate from -25°C to -15°C storage.
  • Page 27 TruSeq DNA PCR-Free libraries—Dilute to 1–2 nM in RSB. [Optional] Spike in 1% nondenatured Illumina PhiX control to nondenatured libraries: TruSeq Nano DNA libraries—Add 0.5 µl 2–3 nM PhiX to 50 µl 2–3 nM library. TruSeq DNA PCR-Free libraries—Add 0.5 µl 1–2 nM PhiX to 50 µl 1–2 nM library.
  • Page 28 Prepare the ExAmp Reaction Prepare the ExAmp reaction master mix immediately before use. Follow the appropriate instructions for the number of flow cells you are preparing. ExAmp Reaction for 1 Flow Cell (Single-Pack Kit) Invert EPX1 and EPX2 to mix. Briefly centrifuge EPX1, EPX2, and EPX3.

  • Page 29: Hiseq 3000/4000 Flow Cell

    Peel open the foil package from the end with the angled seal. Use the flow cell within 4 hours of opening the foil package. Figure 8 Open Flow Cell Package Remove the clamshell package from the foil packaging. cBot 2 System Guide...
  • Page 30 Figure 9 Remove From Foil Packaging Open the clamshell package and remove the flow cell. Figure 10 Remove Flow Cell From Clamshell Package Clean the flow cell with a lint-free alcohol wipe. Dry with a lint-free tissue. Set aside at room temperature. Thaw the cBot Reagent Plate Remove the cBot reagent plate from -25°C to -15°C storage.
  • Page 31 The library loading concentration depends on the libraries to be sequenced. The following instructions apply to supported Illumina libraries and assume an insert size typical for the associated library type. Make sure that you dilute to a concentration appropriate for the library type.
  • Page 32 Prepare the ExAmp Reaction Prepare the ExAmp reaction master mix immediately before use. Invert EPX1 and EPX2 to mix. Briefly centrifuge EPX1, EPX2, and EPX3. Prepare the ExAmp master mix in a 1.5 ml tube as follows. Add 210 µl EPX1. Add 30 µl EPX2.

  • Page 33: Hiseq High Output Flow Cell

    Prepare HP10 (TruSeq v3) Prepare HP10 for use on the cBot only when using Nextera libraries on a TruSeq v3 flow cell. HP10 is also compatible with other Illumina library types. Remove HP10 from -25°C to -15°C storage. Thaw in a beaker of room temperature deionized water for 20 minutes.

  • Page 34: Hiseq Rapid Flow Cell

    HiSeq Rapid Flow Cell To prepare reagents, thaw and inspect the reagent plate. The reagent plate takes approximately 30 minutes to thaw using a room temperature water bath. Alternatively, you can thaw reagents at 2°C to 8°C overnight, not to exceed 16 hours. About Reagents When vortexing or inverting the cBot reagent plate, keep a hand on top of the tubes.

  • Page 35: Chapter 4 Clustering With Sample Tracking

    Clustering With Sample Tracking Workflow Perform a Pre-Run Wash Load Consumables Load the Manifold Select a Protocol Scan Consumables Perform a Pre-Run Check Monitor the Run Unload Run Components Perform a Post-Run Wash Confirm Reagent Delivery (Optional) cBot 2 System Guide...

  • Page 36: Introduction

    Introduction Clustering with sample tracking is possible for all HiSeq flow cells except TruSeq Rapid (v1). All clustering steps are performed on the cBot except preparing libraries for sequencing and preparing reagents. Clustering steps for a HiSeq Rapid v2 flow cell consist only of template hybridization and first extension.

  • Page 37: Clustering With Sample Tracking Workflow

    Select a protocol and scan consumables. Select Pre-Run Check to initiate the automated pre-run check. Select Start. Monitor run progress from the Run Status screen. [Optional] Unload run components and confirm reagent delivery. Perform a post-run wash. cBot 2 System Guide...

  • Page 38: Perform A Pre-Run Wash

    Perform a Pre-Run Wash A wash is recommended before clustering on the cBot. Select User Name. Using the onscreen keyboard, type your name and then select Enter. Select Start. If the Manifold removed checkbox is not selected on the Wash screen, remove the manifold.

  • Page 39: Load Consumables

    HiSeq X and HiSeq 3000/4000 flow cells—The patterned flow cell is ready to use after flow cell preparation. Position the flow cell on the thermal stage with flow cell port holes facing upward. Lane 1 is on the right side with the keyed corner. cBot 2 System Guide...
  • Page 40 Load Templates Load the 8-tube strip containing libraries into the template row of the tube strip holder. Make sure that it is securely seated. Proceed as follows. If you are using additional primers, proceed to Load Primers. If you are not using additional primers, select the Consumables Loaded checkbox and proceed to Load the Manifold on page Load Primers...

  • Page 41: Load The Manifold

    Snap the outlet clamp closed to secure the outlet end of the manifold. Select the Outlet clamp closed checkbox. Align the sipper comb with the 2 metal guide pins on the front of the thermal stage. cBot 2 System Guide...
  • Page 42 Figure 15 Secure the Sipper Comb Metal Guide Pins Plastic Tabs Snap the sipper comb into place using the plastic tabs on either side of the comb. Make sure that the sippers are straight and perpendicular to the reagent plate, and that the Sipper comb in place checkbox is selected.

  • Page 43: Select A Protocol

    Select Experiment Name. Using the onscreen keyboard, type your experiment name and then select Enter. Select the appropriate recipe for your experiment from the list of protocols. Scroll through to see all available protocols. Select Next. cBot 2 System Guide...

  • Page 44: Scan Consumables

    Scan Consumables Internal barcode scanners scan and record all consumable IDs. The software guides you through each scan in a series of screens, starting at the Reagents screen. When a scan is successful, the consumable ID appears on the screen. Select Scan and then Next at each of the following screens: Reagents—Records the reagent kit ID.

  • Page 45: Perform A Pre-Run Check

    Flow Check Failure Flow check failure might be the result of an improperly loaded flow cell, a faulty manifold, or a clog in the lines. Before bypassing the flow check, see Troubleshoot Flow Check Failure on page cBot 2 System Guide...

  • Page 46: Monitor The Run

    After the run is complete, you can leave the flow cell on the instrument overnight. Otherwise, proceed to unloading run components. The cBot 2 holds the flow cell at 20°C. Run Data Report The run data report provides a summary of the run in progress. It lists the following...

  • Page 47: Unload Run Components

    Handle used reagents as chemical waste and discard in accordance with the governmental safety standards for your region. For environmental, health, and safety information, see the SDS for this kit at support.illumina.com/sds.html. Remove the 8-tube strip containing libraries. cBot 2 System Guide...
  • Page 48 Remove the 8-tube strip containing additional primers, if applicable. Select the checkbox to indicate that you have unloaded the reagents, templates, and primers. Choose a wash option: Select Wash to proceed to the post-run wash. Select Exit to bypass the post-run wash, if the bypass option is available. Material # 20004364 Document # 15065681 v01...

  • Page 49: Perform A Post-Run Wash

    Avoid the outlet ports to prevent fibers from entering the holes. Select the checkbox to indicate that the wash reservoir is dry, and then select Exit. The Start screen opens and your cBot 2 is ready for another run. cBot 2 System Guide...

  • Page 50: Confirm Reagent Delivery (Optional)

    Example of Successful Reagent Delivery (2-Lane Flow Cell) If reagent delivery was not successful and the foil seals on the reagent tubes are pierced, contact Illumina Technical Support. Inspect the 8-tube strip containing library template. If you used additional primers with your run, inspect the 8-tube strip containing primers.

  • Page 51: Chapter 5 Clustering Without Sample Tracking

    Clustering Without Sample Tracking Introduction Clustering Without Sample Tracking Workflow Perform a Pre-Run Wash Select a Protocol Load Consumables Perform a Pre-Run Check Monitor the Run Unload Run Components Perform a Post-Run Wash Confirm Reagent Delivery (Optional) cBot 2 System Guide...

  • Page 52: Introduction

    Introduction All clustering steps are performed on the cBot except for preparing libraries for sequencing and preparing the cBot reagent plate. Clustering steps for a rapid flow cell consist only of template hybridization and first extension. The remaining steps are performed on the sequencing instrument.

  • Page 53: Clustering Without Sample Tracking Workflow

    Select a protocol, scan and load consumables, and load tube strips containing prepared libraries. Select Pre-Run Check to initiate the automated pre-run check. Select Start. Monitor run progress from the Run Status screen. Unload run components and confirm reagent delivery. Perform a post-run wash. cBot 2 System Guide...

  • Page 54: Perform A Pre-Run Wash

    Perform a Pre-Run Wash A wash is recommended before clustering on the cBot. Select User Name. Using the onscreen keyboard, type your name and then select Enter. Select Start. If the Manifold removed checkbox is not selected on the Wash screen, remove the manifold.

  • Page 55: Select A Protocol

    Select Experiment Name. Using the onscreen keyboard, type your experiment name and then select Enter. Select the appropriate recipe for your experiment from the list of protocols. Scroll through to see all available protocols. Select Next. cBot 2 System Guide...

  • Page 56: Load Consumables

    Load Consumables The software guides you through the steps to load the cBot reagent plate, flow cell, cBot manifold, and the 8-tube strip containing prepared libraries. Depending on the clustering protocol selected, the software prompts you to load an 8-tube strip of additional primers. Load the Reagent Plate Remove the clear plastic lid from the cBot reagent plate.
  • Page 57 Figure 22 Close the Flow Cell Clamp Select the Flow cell clamp closed checkbox. Connect the outlet end of the manifold to the outlet port in the wash reservoir. Make sure that the outlet is evenly seated. cBot 2 System Guide...
  • Page 58 Figure 23 Secure Outlet End Outlet port Output clamp Snap the outlet clamp closed to secure the outlet end of the manifold. Select the Outlet clamp closed checkbox. Align the sipper comb with the 2 metal guide pins on the front of the thermal stage. Figure 24 Secure the Sipper Comb Metal guide pins...
  • Page 59 GAIIx flow cells—Tubes are numbered left to right. HiSeq X, HiSeq 3000/4000, HiSeq Rapid v2, TruSeq TruSeq v2 (GAIIx) HiSeq v4, and Rapid (HiSeq) TruSeq v3 (HiSeq) Select the checkbox to indicate that primers are loaded and close the instrument lid. Select Next. cBot 2 System Guide...

  • Page 60: Perform A Pre-Run Check

    Perform a Pre-Run Check The pre-run check reads the instrument sensors to detect the correct installation of run components, and then performs a flow check using bubble sensors to detect air in the tubes. The pre-run check takes approximately 3 minutes. After successful completion of the pre-run check, select Start.

  • Page 61: Monitor The Run

    After the run is complete, you can leave the flow cell on the instrument overnight. Otherwise, proceed to unloading run components. The cBot 2 holds the flow cell at 20°C. Run Data Report The run data report provides a summary of the run in progress. It lists the following...

  • Page 62: Unload Run Components

    Handle used reagents as chemical waste and discard in accordance with the governmental safety standards for your region. For environmental, health, and safety information, see the SDS for this kit at support.illumina.com/sds.html. Remove the 8-tube strip containing libraries. Material # 20004364...
  • Page 63 Select the checkbox to indicate that you have unloaded the reagents, templates, and primers. Choose a wash option: Select Wash to proceed to the post-run wash. Select Exit to bypass the post-run wash, if the bypass option is available. cBot 2 System Guide...

  • Page 64: Perform A Post-Run Wash

    Avoid the outlet ports to prevent fibers from entering the holes. Select the checkbox to indicate that the wash reservoir is dry, and then select Exit. The Start screen opens and your cBot 2 is ready for another run. Material # 20004364...

  • Page 65: Confirm Reagent Delivery (Optional)

    Example of Successful Reagent Delivery (2-Lane Flow Cell) If reagent delivery was not successful and the foil seals on the reagent tubes are pierced, contact Illumina Technical Support. Inspect the 8-tube strip containing library template. If you used additional primers with your run, inspect the 8-tube strip containing primers.
  • Page 66 Material # 20004364 Document # 15065681 v01...

  • Page 67: Chapter 6 Maintenance

      Chapter 6  Maintenance Maintenance Perform Periodic Maintenance Perform a Monthly Maintenance Wash Change the Adapter Plate Upgrade the Software Upgrade Recipes Shut Down the cBot 2 cBot 2 System Guide...

  • Page 68: Perform Periodic Maintenance

    Illumina FAS or FSE. Preventive Maintenance Illumina recommends that you schedule a preventive maintenance service each year. If you are not under a service contract, contact your Territory Account Manager or Illumina Technical Support to arrange for a billable preventive maintenance service.

  • Page 69: Perform A Monthly Maintenance Wash

    Avoid the outlet ports. Water Wash (Final Rinse) Fill the wash reservoir with approximately 12 ml deionized water. Select Wash. After the wash is finished, blot water remaining in the wash reservoir with a low-lint tissue. Avoid the outlet ports. cBot 2 System Guide...
  • Page 70 Close the instrument lid. Empty the waste bottle. Your cBot is ready for the next cluster generation run. Material # 20004364 Document # 15065681 v01...

  • Page 71: Change The Adapter Plate

    GAIIx adapter plate HiSeq adapter plate Adapter plate sensor arm Tighten the 2 screws to secure the adapter plate. For optimal heat transfer, make sure that the adapter plate is sitting flat and the screws are tightened evenly. cBot 2 System Guide...
  • Page 72 Wipe the installed adapter plate with a lint-free cleaning tissue moistened with water. Dry with a clean tissue. Material # 20004364 Document # 15065681 v01...

  • Page 73: Upgrade The Software

    When the upgrade is complete and the instrument is restarting, remove the USB flash drive. If a BOOTMGR error appears, attach a keyboard and mouse to the cBot and press Ctrl+Alt+Del to restart the instrument. cBot 2 System Guide...

  • Page 74: Upgrade Recipes

    Upgrade Recipes Upgrade recipe versions independently of software upgrades using a USB flash drive containing the recipe installer. Insert the USB flash drive containing the new recipe installer into either of the USB ports on the front of the instrument. The installer must reside in the root directory of the USB flash drive, not in a folder.

  • Page 75: Shut Down The Cbot 2

    Shut Down the cBot 2 The cBot 2 is designed to run in an idle state from the Start screen, so shutting it down between runs is not necessary. Select Menu in the upper-left corner of the Start screen, and then select Configure.
  • Page 76 Material # 20004364 Document # 15065681 v01...

  • Page 77: Appendix A Troubleshooting

    Appendix A  Troubleshooting Troubleshooting Pause or Abort a Run Troubleshoot Flow Check Failure Troubleshoot Run Problems Reset the External Barcode Scanner Edit Protocols cBot 2 System Guide...

  • Page 78: Pause Or Abort A Run

    Pause or Abort a Run Use commands on the Run Status screen to pause or abort a run. Pause—Completes the current command in the protocol, and then pauses the run. Allow a few minutes before the run pauses. When the run is paused, the sippers lift from the reagent tubes, the reagent stage returns the home position, and the Pause button changes to the Resume button.

  • Page 79: Troubleshoot Flow Check Failure

    Follow the software prompts to reload run components and set up your run. If the flow check fails a third time, you can safely bypass the flow check: Select Bypass Flow Check to proceed with the run. After the run, check reagent delivery from all tubes. cBot 2 System Guide...
  • Page 80 Troubleshooting Flowchart The following flowchart illustrates the troubleshooting procedure. Steps to repeat the flow check include a number to indicate how many of the allowed flow checks have been performed at that point in the procedure. Figure 35 Troubleshooting Flowchart Material # 20004364 Document # 15065681 v01...

  • Page 81: Troubleshoot Run Problems

    (part # 1003709) to the coolant reservoir. Coolant is not flowing and Potential coolant pump failure. Email Illumina Technical coolant level is not low Support. Instrument is in a locked Potential software error. Email Illumina Technical state Support. cBot 2 System Guide...

  • Page 82: Reset The External Barcode Scanner

    Reset the External Barcode Scanner The external barcode scanner is ready for use when you receive your cBot. If the scanner is reset to an incorrect configuration, use the following instructions to restore it to the default configuration. Print the barcode. Figure 36 Restore Defaults Barcode From the start screen, select Menu and then Manual Commands.

  • Page 83: Edit Protocols

    Selections to change to the number of cycles for the selected chemistry definition appear in the right-hand panel. Use the Protocol Editor icons to the right of the step name to rearrange, delete, or copy steps and commands. Figure 38 Protocol Editor, Expanded Steps cBot 2 System Guide...
  • Page 84 Chemistry section Expanded chemistry section Protocol section Protocol Editor Icons Icon Description Moves the highlighted step below the following step in the protocol. Moves the highlighted step above the preceding step in the protocol. Deletes the highlighted step. Repeats the highlighted step. Saves your changes to the protocol library.

  • Page 85: Index

    21, 25 diluting 30, 46 documentation 3, 83 libraries denaturing 21, 25 diluting 21, 25 ending a run 72 loading 34, 52 error messages 75 loading concentration 21, 25 ExAmp master mix 26 loading libraries 34 cBot 2 System Guide...
  • Page 86 reagents barcode scanning 38 reagents, preparing maintenance 43, 58, 63 GAIIx flow cell 18 periodic care 62 high output 27 maintenance wash duration 63 HiSeq 3000/4000 23 maintenance, preventive 62 HiSeq X flow cell 19 manifold rapid 28 outlet clamp 35, 52 recipes sipper comb 4, 35, 52 list of 13...
  • Page 87 13 software 13 wash reservoir 32, 48 washes 32, 48 frequency 62 washing adapter plates 33, 50 washing the instrument 43, 58 waste bottle 62 cBot 2 System Guide...
  • Page 88 Material # 20004364 Document # 15065681 v01...

  • Page 89: Technical Assistance

    Other countries +44.1799.534000 Italy 800.874909 Safety data sheets (SDSs)—Available on the Illumina website at support.illumina.com/sds.html. Product documentation—Available for download in PDF from the Illumina website. Go to support.illumina.com, select a product, then select Documentation & Literature. cBot 2 System Guide...
  • Page 90 Illumina 5200 Illumina Way San Diego, California 92122 U.S.A. +1.800.809.ILMN (4566) +1.858.202.4566 (outside North America) techsupport@illumina.com www.illumina.com...

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