WIXLIB

MiSeqSystem GuideDo c u m e n t # 15 0 2 76 17 v0 6 M a t e ria l # 2 0 0 0 0 2 6 2Ja n u a ry 2 0 2 1For Researc h Use Only. Not for use in diagnostic proc edures.ILLUM INA P ROP RIETA RY

M iSe q Syst e m Gu id eThis document and its contents are proprietary to Illumina, Inc. and its affiliates ("Illumina"), and are intended solely forthe contractual use of its customer in connection with the use of the product(s) described herein and for no otherpurpose. This document and its contents shall not be used or distributed for any other purpose and/ or otherwisecommunicated, disclosed, or reproduced in any way whatsoever without the prior written consent of Illumina. Illuminadoes not convey any license under its patent, trademark, copyright, or common-law rights nor similar rights of any thirdparties by this document.The instructions in this document must be strictly and explicitly followed by qualified and properly trained personnel inorder to ensure the proper and safe use of the product(s) described herein. All of the contents of this document must befully read and understood prior to using such product(s).FAILURE TO COMPLETELY READ AND EXPLICITLY FOLLOW ALL OF THE INSTRUCTIONS CONTAINED HEREIN MAYRESULT IN DAMAGE TO THE PRODUCT(S), INJURY TO PERSONS, INCLUDING TO USERS OR OTHERS, AND DAMAGETO OTHER PROPERTY, AND WILL VOID ANY WARRANTY APPLICABLE TO THE PRODUCT(S).ILLUMINA DOES NOT ASSUME ANY LIABILITY ARISING OUT OF THE IMPROPER USE OF THE PRODUCT(S)DESCRIBED HEREIN (INCLUDING PARTS THEREOF OR SOFTWARE). 2021 Illumina, Inc. All rights reserved.All trademarks are the property of Illumina, Inc. or their respective owners. For specific trademark information, seewww.illumina.com/ company/ legal.html.Do c u m e n t # 15 0 2 76 17 v0 6 M a t e ria l # 2 0 0 0 0 2 6 2For Researc h Use Only. Not for use in diagnostic proc edures.ii

Revision HistoryDocument #DateDescription of ChangeMaterial # 20000262Document # 15027617 v06January2021Updated to support MCS v4.0 and Local Run Manager v3.0upgrade.Updated to support system Windows 10 upgrade.Updated images and text to reflect UI changes.Updated maintenance wash information.Removed BaseSpace Onsite information as it is no longercompatible.Removed reference to Illumina Experiment Manager as it isno longer compatible.Removed references to MiSeq Reagent Kits v1 as thisversion is no longer supported.Material # 20000262Document # 15027617 v05June 2019Material # 20000262Document # 15027617 v04July2018Added new run configuration options for Local Run Manager,Sample Sheets, and Manual sequencing modes.Replaced references to MiSeq Reporter with Local RunManager.Added Resolve Chiller Temperature Ranges toTroubleshooting Appendix.Material # 20000262Document # 15027617 v03May2018Removed the default user name and password required tolog on to the operating system. Illumina recommends usingsite-specific credentials.Added information about the Illumina Proactive monitoringservice in the Customize System Settings section.Added note to Reagent Compartment regarding requiredchiller temperature range.Added back MiSeq Reporter and removed references toLocal Run Manager.Changed the name of the guide from the MiSeq SequencingSystem Guide to the MiSeq System Guide.Minor text edits.Material # 20000262Document # 15027617 v02January2018Added new run configuration options for Local Run Manager,Sample Sheets, and Manual sequencing modes.Replaced references to MiSeq Reporter with Local RunManager.Added Resolve Chiller Temperature Ranges toTroubleshooting Appendix.Added new instruction for collecting instrument performancedata in the Customize System Settings topic.Changed the name of the guide from the MiSeq SystemGuide to the MiSeq Sequencing System Guide.Updated index cycle information.Corrected material number.Do c u m e n t # 15 0 2 76 17 v0 6 M a t e ria l # 2 0 0 0 0 2 6 2For Researc h Use Only. Not for use in diagnostic proc edures.iii

M iSe q Syst e m Gu id eDocument #DateDescription of ChangeMaterial # 20000262Document # 15027617 v01September2015Changed the name of the guide from the MiSeq System UserGuide to the MiSeq System Guide.New in MCS v2.6, added BaseSpace Onsite information.Rearranged guide information to center around tasks ratherthan screens.All references to the Welcome screen are changed to theHome screen.Added information that is in the MiSeq Reagent Kit ReagentPrep Guides, including flow cell types, reagent cartridgecontents, and directions for thawing the reagent cartridge.Visit the Illumina website for all other MiSeq Reagent Kitinformation atsupport.illumina.com/ sequencing/ sequencing kits/ miseqreagent kit.html.Corrected the expected wash volume of a maintenancewash from 17.25 ml to 51.75 ml.Updated the order of workflow steps to first prepare thereagent cartridge, and then if required, denature and dilutelibraries.Moved troubleshooting information to Appendix A.Moved output folder information and flow cell tile informationto Appendix B.Moved information on managing files to the Maintenancechapter.Moved the post-run wash instructions from the Maintenancechapter to the Sequencing chapter.The name of the Performing a Run chapter is nowSequencing.Changed references from primary analysis to analysis byRTA software.Updated the dilution directions for the post-run washprocedure with a template line wash from 6% NaOCl to 5%NaOCl.Added an NaOCl, 5% part number to the user-suppliedconsumables list.Part # 15027617 Rev. OSeptember2014Updated the following information: New in MCS v2.5, updated post-run wash option toinclude a template line wash Updated directions for a post-run wash with sodiumhypochlorite to the template line wash Added the expected wash volume for a post-run washesAdded VeriSeq PGS workflow information regardingadditional resources, run options, secondary analysisoptions, instrument washes, and flow cell cap color.Part # 15027617 Rev. NJune 2014Added information applicable to the VeriSeq PGS workflow.Updated run metrics information for cluster generation anddensity.Removed anti-virus software information. See MiSeq SystemSite Preparation Guide.Do c u m e n t # 15 0 2 76 17 v0 6 M a t e ria l # 2 0 0 0 0 2 6 2For Researc h Use Only. Not for use in diagnostic proc edures.iv

M iSe q Syst e m Gu id eDocument #DateDescription of ChangePart # 15027617 Rev. MJanuary2014Updated to change introduced in MCS v2.4:Added bundle logs feature for sending troubleshooting files.Part # 15027617 Rev. LOctober2013Added the reboot of system software as a pre-run step.Added microcentrifuge tubes to the list of user-suppliedconsumables.Eliminated MiSeq Software as a separate chapter anddistributed chapter contents throughout the guide.Removed information about folders for custom recipes.Removed information about recommended cluster densityranges for MiSeq reagent kits.Removed details about MiSeq reagent kits and added anoverview of reagent kit features. For detailed information, seethe reagent prep documentation for the kit you are using.Added content to the trademarks notice.Part # 15027617 Rev. KAugust2013Corrected formatting errors.Part # 15027617 Rev. JAugust2013Added run descriptions for MCS v2.3 and MiSeq Reagent Kitv3.Updated the following information: Reagent kit and version compatibility to include MiSeqReagent Kit v3 Custom Recipes folder description to include a v3subfolder Changed cluster density range for v2; added range for v3 Output path for image filesCorrected flow cell bar codes for nano flow cells (D) andmicro flow cells (G).Removed information about MiSeq Reagent Kit, includingcontents and flow cell types. For more information, seeMiSeq Reagent Preparation Guide (document # 15044983).Part # 15027617 Rev. HMarch2013Added section titled MiSeq Concepts that introduces theanalysis workflow, manifest file, and sample sheet.Removed information about FASTQ file generation, manifestfile formats, analysis workflow details, and sample sheetdetails. For information about these topics, see the MiSeqReporter User Guide, part # 15028784, or the MiSeq SampleSheet Quick Reference Guide, part # 15028392.Removed instructions for preparing custom primers. For moreinformation, see Using Custom Primers on the MiSeq, part #15041638.Do c u m e n t # 15 0 2 76 17 v0 6 M a t e ria l # 2 0 0 0 0 2 6 2For Researc h Use Only. Not for use in diagnostic proc edures.v

M iSe q Syst e m Gu id eDocument #DateDescription of ChangePart # 15027617 Rev. GJanuary2013Removed instructions for denaturing and diluting DNAlibraries and preparing an Illumina PhiX control. SeePreparing DNA Libraries for Sequencing on the MiSeq, part #15039740.Updated instrument wash instructions to add 25 ml 10%Tween 20 to 475 ml laboratory-grade water, instead of 500ml laboratory-grade water.Part # 15027617 Rev. FNovember2012Added the following new information: Added kit descriptions for new MiSeq reagent kits: MiSeqReagent Nano Kit and MiSeq Reagent Micro Kit Added overview of flow cell types Added description of Enrichment analysis workflowUpdated the following information: New in MCS v2.1, updated Perform Wash screen to add apost-run wash option and command to raise sippers Updated version compatibility table to include nano andmicro kit dependencies Updated version compatibility information to include newreagent kitsPart # 15027617 Rev. EOctober2012Updated the following information: Corrected PhiX control preparation instructions andexpected cluster density of prepared PhiX control to 1000–1200 K/ mm² Noted that the procedure for denaturing and dilutinglibraries, Preparing Your Libraries, does not apply toNextera XT libraries as well as TruSeq Amplicon libraries Changed upgrade name from MiSeq Expansion Pack toMiSeq hardware upgrade Add the MiSeq Reporter User Guide to AdditionalResources list.Do c u m e n t # 15 0 2 76 17 v0 6 M a t e ria l # 2 0 0 0 0 2 6 2For Researc h Use Only. Not for use in diagnostic proc edures.vi

M iSe q Syst e m Gu id eDocument #Part # 15027617 Rev. DDateJuly 2012Description of ChangeUpdated software descriptions to MCS v2.0.Added the following new information: Added a section titled What' s New in MCS to describe newsoftware features, interface changes, and workflowchanges Added catalog number and description of the MiSeqReagent Kit v2, 500 Cycles Added Version Compatibility and Requirements section Added description of MiSeq Expansion Pack, which isrequired for 14-tile dual-surface flow cell imaging Added description of dual-surface flow cell tile numbering Added the PCR Amplicon analysis workflow for Nextera XTlibraries Added the use of 10% Tween 20 in wash procedures andexpected wash volumes Added the reagent cartridge version to the RFID readfailure procedureUpdated the following information: Changed reagent acronyms for IMF, CMF, and AMX to v2reagent names IMS, CMS, and AMS, respectively Changed the PhiX concentration from 8 pM to 12.5 pM Changed the maximum recommended NaOHconcentration to 1 mM in final solution Noted that a maintenance wash is required to remove theinstrument from standby mode and begin the setup stepsfor a subsequent run Removed Sample Sheet Parameters section and samplesheet setup step in the workflow; Illumina recommendscreating the sample sheet prior to sample preparation (Seethe MiSeq Sample Sheet Quick Reference Guide, part #15028392 and the Illumina Experiment Manager UserGuide, part # 15031335).Do c u m e n t # 15 0 2 76 17 v0 6 M a t e ria l # 2 0 0 0 0 2 6 2For Researc h Use Only. Not for use in diagnostic proc edures.vii

M iSe q Syst e m Gu id eDocument #DateDescription of ChangePart # 15027617 Rev. CApril 2012Updated software descriptions to MCS v1.2Added the following new procedures and sections:BaseSpace overview, Using Custom Primers, GeneratingFASTQ files, Troubleshooting Flow Rate Error, Performing a

System Guide to the MiSeq System Guide. Minor text edits. Material # 20000262 Document # 15027617 v02 January 2018 Added new run configuration options for Local Run Manager, Sample Sheets, and Manual sequencing modes. Replaced references to MiSeq Reporter with Local Run Manager. Added Resolve Chiller Temperature Ranges to Troubleshooting Appendix.