Illumina MiSeq System Stücklistenhandbuch

MiSeq

System Guide

Document # 15027617 v04 Material # 20024228

July 2018

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For Research Use Only. Not for use in diagnostic procedures.

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Document # 15027617 v04 Material # 20024228

For Research Use Only. Not for use in diagnostic procedures.

MiSeq System Guide

Revision History

Document # Date Description of Change

Material # 20024228

Document # 15027617 v04

July

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.

Material # 20024228

Document # 15027617 v03

May

2018

Removed the default user name and password required to

log on to the operating system. Illumina recommends using

site-specific credentials.

Added information about the Illumina Proactive monitoring

service in the Customize System Settings section.

Added note to Reagent Compartment regarding required

chiller temperature range.

Added back MiSeq Reporter and removed references to

Local Run Manager.

Changed the name of the guide from the MiSeq Sequencing

System Guide to the MiSeq System Guide.

Minor text edits.

Material # 20024228

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.

Added new instruction for collecting instrument performance

data in the Customize System Settings topic.

Changed the name of the guide from the MiSeq System

Guide to the MiSeq Sequencing System Guide.

Document # 15027617 v04 Material # 20024228

For Research Use Only. Not for use in diagnostic procedures.

iii

Document # Date Description of Change

Material # 20000262

Document # 15027617 v01

September

2015

Changed the name of the guide from the MiSeq System User

Guide to the MiSeq System Guide.

New in MCS v2.6, added BaseSpace Onsite information.

Rearranged guide information to center around tasks rather

than screens.

All references to the Welcome screen are changed to the

Home screen.

Added information that is in the MiSeq Reagent Kit Reagent

Prep Guides, including flow cell types, reagent cartridge

contents, and directions for thawing the reagent cartridge.

Visit the Illumina website for all other MiSeq Reagent Kit

information at

support.illumina.com/sequencing/sequencing_kits/miseq_

reagent_kit.html.

Corrected the expected wash volume of a maintenance

wash from 17.25 ml to 51.75 ml.

Updated the order of workflow steps to first prepare the

reagent cartridge, and then if required, denature and dilute

libraries.

Moved troubleshooting information to Appendix A.

Moved output folder information and flow cell tile information

to Appendix B.

Moved information on managing files to the Maintenance

chapter.

Moved the post-run wash instructions from the Maintenance

chapter to the Sequencing chapter.

The name of the Performing a Run chapter is now

Sequencing.

Changed references from primary analysis to analysis by

RTA software.

Updated the dilution directions for the post-run wash

procedure with a template line wash from 6% NaOCl to 5%

NaOCl.

Added an NaOCl, 5% part number to the user-supplied

consumables list.

Part # 15027617 Rev. O September

2014

Updated the following information:

• New in MCS v2.5, updated post-run wash option to

include a template line wash

• Updated directions for a post-run wash with sodium

hypochlorite to the template line wash

• Added the expected wash volume for a post-run washes

Added VeriSeq PGS workflow information regarding

additional resources, run options, secondary analysis

options, instrument washes, and flow cell cap color.

Part # 15027617 Rev. N June 2014 Added information applicable to the VeriSeq PGS workflow.

Updated run metrics information for cluster generation and

density.

Removed anti-virus software information. See

MiSeq System

Site Preparation Guide

Document # 15027617 v04 Material # 20024228

For Research Use Only. Not for use in diagnostic procedures.

MiSeq System Guide

Document # Date Description of Change

Part # 15027617 Rev. M January

2014

Updated to change introduced in MCS v2.4:

Added bundle logs feature for sending troubleshooting files.

Part # 15027617 Rev. L October

2013

Added the reboot of system software as a pre-run step.

Added microcentrifuge tubes to the list of user-supplied

consumables.

Eliminated

MiSeq Software

as a separate chapter and

distributed chapter contents throughout the guide.

Removed information about folders for custom recipes.

Removed information about recommended cluster density

ranges for MiSeq reagent kits.

Removed details about MiSeq reagent kits and added an

overview of reagent kit features. For detailed information, see

the reagent prep documentation for the kit you are using.

Added content to the trademarks notice.

Part # 15027617 Rev. K August

2013

Corrected formatting errors.

Part # 15027617 Rev. J August

2013

Added run descriptions for MCS v2.3 and MiSeq Reagent Kit

v3.

Updated the following information:

• Reagent kit and version compatibility to include MiSeq

Reagent Kit v3

• Custom Recipes folder description to include a v3

subfolder

• Changed cluster density range for v2; added range for v3

• Output path for image files

Corrected flow cell bar codes for nano flow cells (D) and

micro flow cells (G).

Removed information about MiSeq Reagent Kit, including

contents and flow cell types. For more information, see

MiSeq Reagent Preparation Guide (document # 15044983)

Part # 15027617 Rev. H March

2013

Added section titled

MiSeq Concepts

that introduces the

analysis workflow, manifest file, and sample sheet.

Removed information about FASTQ file generation, manifest

file formats, analysis workflow details, and sample sheet

details. For information about these topics, see the

MiSeq

Reporter User Guide

, part # 15028784, or the

MiSeq Sample

Sheet Quick Reference Guide

, part # 15028392.

Removed instructions for preparing custom primers. For more

information, see

Using Custom Primers on the MiSeq

, part #

15041638.

Document # 15027617 v04 Material # 20024228

For Research Use Only. Not for use in diagnostic procedures.

MiSeq System Guide

Document # Date Description of Change

Part # 15027617 Rev. G January

2013

Removed instructions for denaturing and diluting DNA

libraries and preparing an Illumina PhiX control. See

Preparing 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 500

ml laboratory-grade water.

Part # 15027617 Rev. F November

2012

Added the following new information:

• Added kit descriptions for new MiSeq reagent kits: MiSeq

Reagent Nano Kit and MiSeq Reagent Micro Kit

• Added overview of flow cell types

• Added description of Enrichment analysis workflow

Updated the following information:

• New in MCS v2.1, updated Perform Wash screen to add a

post-run wash option and command to raise sippers

• Updated version compatibility table to include nano and

micro kit dependencies

• Updated version compatibility information to include new

reagent kits

Part # 15027617 Rev. E October

2012

Updated the following information:

• Corrected PhiX control preparation instructions and

expected cluster density of prepared PhiX control to 1000–

1200K/mm²

• Noted that the procedure for denaturing and diluting

libraries,

Preparing Your Libraries

, does not apply to

Nextera XT libraries as well as TruSeq Amplicon libraries

• Changed upgrade name from MiSeq Expansion Pack to

MiSeq hardware upgrade

• Add the

MiSeq Reporter User Guide

to Additional

Resources list.

Document # 15027617 v04 Material # 20024228

For Research Use Only. Not for use in diagnostic procedures.

MiSeq System Guide

Document # Date Description of Change

Part # 15027617 Rev. D July 2012 Updated software descriptions to MCS v2.0.

Added the following new information:

• Added a section titled

What's New in MCS

to describe new

software features, interface changes, and workflow

changes

• Added catalog number and description of the MiSeq

Reagent Kit v2, 500 Cycles

• Added Version Compatibility and Requirements section

• Added description of MiSeq Expansion Pack, which is

required 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 XT

libraries

• Added the use of 10% Tween 20 in wash procedures and

expected wash volumes

• Added the reagent cartridge version to the RFID read

failure procedure

Updated the following information:

• Changed reagent acronyms for IMF, CMF, and AMX to v2

reagent names IMS, CMS, and AMS, respectively

• Changed the PhiX concentration from 8 pM to 12.5 pM

• Changed the maximum recommended NaOH

concentration to 1 mM in final solution

• Noted that a maintenance wash is required to remove the

instrument from standby mode and begin the setup steps

for a subsequent run

• Removed Sample Sheet Parameters section and sample

sheet setup step in the workflow; Illumina recommends

creating the sample sheet prior to sample preparation (See

the

MiSeq Sample Sheet Quick Reference Guide

, part #

15028392 and the

Illumina Experiment Manager User

Guide

, part # 15031335).

Document # 15027617 v04 Material # 20024228

For Research Use Only. Not for use in diagnostic procedures.

vii

MiSeq System Guide

Document # Date Description of Change

Part # 15027617 Rev. C April 2012 Updated software descriptions to MCS v1.2

Added the following new procedures and sections:

BaseSpace overview, Using Custom Primers, Generating

FASTQ files, Troubleshooting Flow Rate Error, Performing a

Volume Test, Performing a Maintenance Wash, and Idling

the Instrument, which includes a standby wash.

Updated the following information:

• Updated name of Amplicon workflow to Custom Amplicon;

updated name of DenovoAssembly workflow to Assembly;

added GenerateFASTQ workflow

• Added descriptions of run folders and files; updated run

folder naming; added output file size

• Listed genome folder as required for amplicon sequencing

in Sample Sheet Parameters

• Added instructions for diluting NaOH to denature libraries

• Updated Resolving RFID Read Failure to include MiSeq

Self-Service instructions

• Listed files and folders used for troubleshooting run

performance

Part # 15027617 Rev. B December

2011

Updated software descriptions to MCS v1.1

Added information about anti-virus protection

Updated the following information:

• Instructions to resolve RFID failure

• Preparing libraries—Changed to 0.2 N NaOH

• Run folder naming convention

• Required disk space and storage capacity

• Run setup steps—Added more information to Setting Up

the Sample Sheet

• Run setup steps—Added note to dispose of remaining PR2

• Analysis duration—Added when analysis exceeds two

hours

• Analysis Input Requirements—Listed manifest files as

required for TruSeq Custom Amplicon libraries

• Corrected HT1 tube size in MiSeq Reagent Kit Contents

• Changed iCom references to MyIllumina

Part # 15027617 Rev. A September

2011

Initial release

Document # 15027617 v04 Material # 20024228

For Research Use Only. Not for use in diagnostic procedures.

viii

MiSeq System Guide

Table of Contents

Chapter 1 Overview 1

Introduction 1

Additional Resources 1

Components 2

MiSeq Concepts 4

System Software 5

Secondary Analysis Options 6

Sequencing Analysis Viewer 8

Required Disk Space 8

MiSeq Reagent Kit Overview 8

Chapter 2 Getting Started 11

Start the MiSeq 11

Customize System Settings 11

Configure Notifications of BaseSpace Updates 12

Set Email Preferences 12

Set Default Folder Locations 12

User-Supplied Consumables 13

Chapter 3 Sequencing 15

Introduction 15

Run Duration 15

MiSeq Workflow 17

Thaw Reagent Cartridge 18

Inspect the Reagent Cartridge 19

Denature and Dilute Libraries 19

Load Sample Libraries 19

Set Up a Run Using MCS 20

Clean the Flow Cell 21

Load the Flow Cell 23

Load Reagents 24

Start the Run 26

Monitor the Run 27

Perform a Post-Run Wash 29

Chapter 4 Maintenance 33

Maintenance Frequency 33

Maintenance Frequency for the VeriSeq PGS Workflow 33

Perform a Maintenance Wash 34

Perform a Standby Wash 36

Manage Files 38

Software Updates 39

Shut Down the Instrument 39

Document # 15027617 v04 Material # 20024228

For Research Use Only. Not for use in diagnostic procedures.

Appendix A Troubleshooting 41

Introduction 41

Bundle Logs for Troubleshooting 41

Perform a System Check 42

Pause or Stop a Run 42

Raise Reagent Cartridge Sippers Manually 44

Resolve Run Setup Errors 44

Resolve RFID Read Failure 44

Perform a Volume Test 45

Measure Expected Wash Volumes 46

Resolve Reagent Chiller Temperature Errors 46

Resolve Local Run Manager Analysis Errors 46

Configure System Settings 46

Appendix B Output Files and Folders 47

Run Folders 47

MiSeqOutput Folder Contents 47

RTA Folders and Files 49

Index 51

Technical Assistance 55

Document # 15027617 v04 Material # 20024228

For Research Use Only. Not for use in diagnostic procedures.

MiSeq System Guide

Andere Handbücher für MiSeq System

Inhaltsverzeichnis

Andere illumina Laborausrüstung Handbücher

illumina

illumina NovaSeq 6000 Bedienungsanleitung

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illumina NextSeq 550Dx Bedienungsanleitung

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illumina MiSeqDx Bedienungsanleitung

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illumina NextSeq 550Dx Bedienungsanleitung

illumina

illumina cBot 2 Stücklistenhandbuch

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illumina MiniSeq Stücklistenhandbuch

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illumina Infinium HD Super Assay Bedienungsanleitung

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illumina NextSeq 500 Stücklistenhandbuch

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illumina NeoPrep Library Prep System Installations- und Betriebsanleitung

illumina

illumina HiSeq X Bedienungsanleitung

illumina

illumina MiSeqDx Instrument Installations- und Betriebsanleitung

illumina

illumina Infinium LiHa Bedienungsanleitung

Beliebte Laborausrüstung Handbücher anderer Marken

Qiagen

Qiagen DML 3000 Bedienungsanleitung

Queensgate

Queensgate NANOSCAN OP400 Programmierhandbuch

Conviron

Conviron GEN1000-GE Bedienungsanleitung

Parr Instrument

Parr Instrument 4560 Bedienungsanleitung

IKA

IKA IC control Bedienungsanleitung

Integra

Integra DOSE IT Bedienungsanleitung

Agilent Technologies

Agilent Technologies 5800 ICP-OES Bedienungsanleitung

Endress+Hauser

Endress+Hauser Cleanfit CPA875 Bedienungsanleitung

NI PXI-5422 Handbuch

Collomix

Collomix Aqix Bedienungsanleitung

SPEX SamplePrep

SPEX SamplePrep 6875 Freezer/Mill Series Bedienungsanleitung

Ocean Insight

Ocean Insight FLAME-NIR+ Bedienungsanleitung

Parker

Parker ALIGN-MG-NA Bedienungsanleitung

BD 644787 Bedienungsanleitung

DENTAURUM

DENTAURUM Compact Megaplus Bedienungsanleitung

Biuged Laboratory Instruments

Biuged Laboratory Instruments BGD 626 Bedienungsanleitung

VWR

VWR SAS Super IAQ Bedienungsanleitung

Yamato

Yamato BM510 Bedienungsanleitung

illumina MiSeq System Stücklistenhandbuch

Beliebte Laborausrüstung Handbücher anderer Marken