Illumina NextSeq 550Dx Manuel utilisateur

NextSeq 550Dx Research Mode

Instrument Reference Guide

Document # 1000000041922 v01

March 2018

ILLUMINA PROPRIETARY

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

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. Illumina

does not convey any license under its patent, trademark, copyright, or common-law rights nor similar rights of any third

parties by this document.

The instructions in this document must be strictly and explicitly followed by qualified and properly trained personnel in

order to ensure the proper and safe use of the product(s) described herein. All of the contents of this document must

be fully read and understood prior to using such product(s).

FAILURE TO COMPLETELY READ AND EXPLICITLY FOLLOW ALL OF THE INSTRUCTIONS CONTAINED HEREIN

MAY RESULT IN DAMAGE TO THE PRODUCT(S), INJURY TO PERSONS, INCLUDING TO USERS OR OTHERS,

AND DAMAGE TO 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).

All trademarks are the property of Illumina, Inc. or their respective owners. For specific trademark information, see

www.illumina.com/company/legal.html.

Document # 1000000041922 v01

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

NextSeq 550Dx Research Mode Instrument Reference Guide

Revision History

Document Date Description of Change

Document #

1000000041922 v01

March

2018

Added information about the Illumina Proactive monitoring service in

the Customize System Settings section.

Document #

1000000041922 v00

November

2017

Initial release.

Document # 1000000041922 v01

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

iii

NextSeq 550Dx Research Mode Instrument Reference Guide

Table of Contents

Chapter 1 Overview 1

About this Guide 1

Introduction 1

Additional Resources 2

Instrument Components 2

Sequencing Consumables Overview 6

Chapter 2 Getting Started 11

Starting the Instrument 11

Customize System Settings 12

User-Supplied Consumables and Equipment 13

Chapter 3 Sequencing 15

Introduction 15

Sequencing Workflow 16

Prepare the Reagent Cartridge 16

Prepare the Flow Cell 17

Prepare Libraries for Sequencing 17

Set Up a Sequencing Run 18

Monitor Run Progress 24

Automatic Post-Run Wash 26

Chapter 4 Scanning 27

Introduction 27

Scanning Workflow 28

Download the DMAP Folder 28

Load the BeadChip Onto the Adapter 29

Set Up a Scan 30

Monitor Scan Progress 32

Chapter 5 Maintenance 35

Introduction 35

Perform a Manual Wash 35

Replace Air Filter 38

Software Updates 39

Reboot and Shut Down Options 40

Appendix A Troubleshooting 43

Introduction 43

Troubleshooting Files 43

Resolve Automatic Check Errors 44

Spent Reagents Container is Full 45

Rehybridization Workflow 46

Document # 1000000041922 v01

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

BeadChip and Scan Errors 48

Custom Recipes and Recipe Folders 49

RAID Error Message 49

Configure System Settings 50

Appendix B Real-Time Analysis 53

Real-Time Analysis Overview 53

Real-Time Analysis Workflow 54

Appendix C Output Files and Folders 59

Sequencing Output Files 59

Sequencing Output Folder Structure 61

Scanning Output Files 62

Scanning Output Folder Structure 63

Index 65

Technical Assistance 69

Document # 1000000041922 v01

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

NextSeq 550Dx Research Mode Instrument Reference Guide

Chapter 1 Overview

About this Guide 1

Introduction 1

Additional Resources 2

Instrument Components 2

Sequencing Consumables Overview 6

About this Guide

This instrument reference guide provides instructions on the use of the NextSeq 550Dx instrument in

research (RUO) mode.

Introduction

The Illumina®NextSeq™550Dx instrument is a single solution that provides a seamless transition

between high-throughput sequencing and array scanning.

Sequencing Features

uHigh-throughput sequencing—The NextSeq™550 instrument enables sequencing of exomes, whole

genomes, and transcriptomes and supports TruSeq™and Nextera™libraries.

uFlow cell types—Flow cells are available in configurations for high output and mid output. Each flow

cell type is kitted with a compatible prefilled reagent cartridge.

uReal-Time Analysis (RTA)—Integrated analysis software performs on-instrument data analysis,

which includes image analysis and base calling. The NextSeq 550Dx uses an implementation of

RTA called RTA v2, which includes important architecture and feature differences. For more

information, see

Real-Time Analysis

on page 53.

uBaseSpace®integration—The sequencing workflow is integrated with BaseSpace, the Illumina

genomics computing environment for data analysis, storage, and collaboration. For instruments

configured for BaseSpace, library information and run parameters are specified on the BaseSpace

Prep tab. Runs that were set up in BaseSpace appear on the instrument interface during run setup.

As the run progresses, output files are streamed in real time to BaseSpace or BaseSpace Onsite.

Array Scanning Features

uIntegrated array scanning in control software—The NextSeq 550Dx instrument allows you to

transition between array scanning and high-throughput sequencing on the same instrument using the

same control software.

uExtended imaging capability—The imaging system in the NextSeq 550Dx instrument includes

software and stage modifications that enable imaging of a larger surface area to accommodate

BeadChip scanning.

uBeadChip types—Compatible BeadChip types include CytoSNP-12, CytoSNP-850K, and Karyomap-

12.

uBeadChip adapter—A reusable BeadChip adapter enables easy loading of a BeadChip onto the

instrument.

uData Analysis—Use the BlueFuse®Multi software to analyze array data.

Document # 1000000041922 v01

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

Additional Resources

The following documentation is available for download from the Illumina website.

Resource Description

NextSeq 550Dx Instrument

Reference Guide (document #

1000000009513)

When in diagnostic mode, provides instructions for operating the instrument and

troubleshooting procedures.

NextSeq 550Dx Instrument

Site Prep Guide (document #

1000000009869)

Provides specifications for laboratory space, electrical requirements, and

environmental considerations.

NextSeq 550Dx Instrument

Safety and Compliance Guide

(document #

1000000009868)

Provides information about operational safety considerations, compliance statements,

and instrument labeling.

RFID Reader Compliance

Guide (document #

1000000030332)

Provides information about the RFID reader in the instrument, compliance

certifications, and safety considerations.

Denaturing and Diluting

Libraries for the NextSeq

System (document #

15048776)

Provides instructions for denaturing and diluting prepared libraries for a sequencing

run, and preparing an optional PhiX control. This step applies to most library types.

NextSeq Custom Primers

Guide (document #

15057456)

Provides information about using custom sequencing primers in place of Illumina

sequencing primers.

BaseSpace help

(help.basespace.illumina.com)

Provides information about using BaseSpace®and available analysis options.

Visit the NextSeq 550Dx instrument support page on the Illumina website for access to documentation,

software downloads, online training, and frequently asked questions.

Instrument Components

The NextSeq 550Dx instrument includes a touch screen monitor, a status bar, and 4 compartments.

Document # 1000000041922 v01

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

NextSeq 550Dx Research Mode Instrument Reference Guide

Figure 1 Instrument Components

AImaging compartment—Holds the flow cell for sequencing or the BeadChip adapter for scanning.

BTouch screen monitor—Enables on-instrument configuration and setup using the control software

interface.

CStatus bar—Indicates instrument status as processing (blue), requires attention (orange), or ready to

sequence (green).

DBuffer compartment—Holds the buffer cartridge and the spent reagents container.

EReagent compartment—Holds the reagent cartridge.

FAir filter compartment—Holds the air filter. Access the filter from the back of the instrument.

GPower button—Powers the instrument and the instrument computer on or off.

Imaging Compartment

The imaging compartment houses the stage, which includes three alignment pins for positioning the flow

cell for sequencing or the BeadChip adapter for scanning. After loading the flow cell or BeadChip

adapter, the imaging compartment door closes automatically and moves components into position.

Reagent and Buffer Compartments

Setting up a sequencing run on the NextSeq 550Dx instrument requires access to the reagent

compartment and buffer compartment to load run consumables and empty the spent reagents container.

Document # 1000000041922 v01

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

NextSeq 550Dx Research Mode Instrument Reference Guide

Figure 2 Reagent and Buffer Compartments

AReagent compartment door—Encloses the reagent compartment with a latch under the lower-right

area of the door. The reagent compartment holds the reagent cartridge.

BReagent cartridge—The reagent cartridge is a prefilled single-use consumable.

CBuffer cartridge—The buffer cartridge is a prefilled single-use consumable.

DSpent reagents container—Spent reagents are collected for disposal after each run.

EBuffer compartment door—Encloses the buffer compartment with a latch under the lower-left corner of

the door.

Air Filter Compartment

The air filter compartment holds the air filter and is located in the back of the instrument. Replace the air

filter every 90 days. For information on replacing the filter, see

Replace Air Filter

on page 38.

NextSeq 550Dx Software

The instrument software includes integrated applications that perform sequencing runs or array

scanning.

uNextSeq Control Software (NCS)—The control software guides you through the steps to set up a

sequencing run or an array scan.

uReal-Time Analysis (RTA) software—For sequencing runs, RTA performs image analysis and base

calling during the run. The NextSeq 550Dx instrument uses RTA v2, which includes important

architecture and feature differences from earlier versions. For more information, see

Real-Time

Analysis

on page 53.

Status Icons

A status icon in the top-right corner of the control signals any change in conditions during run setup or

during the run.

Status

Icon

Status

Name

Description

Status OK System is normal.

Processing System is processing.

Document # 1000000041922 v01

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

NextSeq 550Dx Research Mode Instrument Reference Guide

Status

Icon

Status

Name

Description

Warning A warning has occurred.

Warnings do not stop a run or require action before proceeding.

Error An error has occurred.

Errors require action before proceeding with the run.

Service

Needed

A notification requiring attention has occurred. Refer to the message for additional

information.

When a change in condition occurs, the icon blinks to alert you. Select the icon to view a description of

the condition. Select Acknowledge to accept the message and Close to close the dialog box.

NOTE

Acknowledging a message resets the icon, and the message is grayed out. The message is still

visible to the user if they select the icon, but disappears once NCS is restarted.

Power Button

The power button on the front of the NextSeq 550Dx turns on power to the instrument and instrument

computer. The power button performs the following actions depending on the state of instrument power.

By default, the NextSeq 550Dx boots into diagnostic mode.

For information on shutting down the instrument, see

Shut Down the Instrument

on page 41.

Power State Action

Instrument power is off Briefly press the button to turn on the power.

Instrument power is on Briefly press the button to turn off the power. A dialog box appears on the screen to

confirm a normal instrument shutdown.

Instrument power is on Press and hold the power button for 10 seconds to cause a hard shutdown of the

instrument and instrument computer.

Use this method to turn off the instrument only if the instrument is unresponsive.

NOTE

Turning off the instrument during a sequencing run ends the run immediately. Ending a run is final. Run

consumables cannot be reused and sequencing data from the run is not saved.

Reusable BeadChip Adapter Overview

The reusable BeadChip adapter holds the BeadChip during scanning. The BeadChip is secured in the

recessed shelf of the adapter with the retention clip. Then, the BeadChip adapter is loaded onto the

stage in the imaging compartment.

Document # 1000000041922 v01

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

NextSeq 550Dx Research Mode Instrument Reference Guide

Autres manuels pour NextSeq 550Dx

Table des matières

Autres manuels illumina Équipement de laboratoire

illumina

illumina Infinium HD Super Assay Manuel utilisateur

illumina

illumina MiSeqDx Instrument Manuel d'installation et d'exploitation

illumina

illumina NextSeq 550Dx Manuel utilisateur

illumina

illumina MiniSeq Manuel de la liste des pièces

illumina

illumina cBot 2 Manuel de la liste des pièces

illumina

illumina MiSeq System Manuel de la liste des pièces

illumina

illumina NeoPrep Library Prep System Manuel d'installation et d'exploitation

illumina

illumina MiSeq System Manuel utilisateur

illumina

illumina NextSeq 500 Manuel de la liste des pièces

illumina

illumina NovaSeq 6000 Manuel utilisateur

illumina

illumina Infinium LiHa Manuel utilisateur

illumina

illumina MiSeqDx Manuel utilisateur

illumina

illumina HiSeq X Manuel utilisateur

Manuels Équipement de laboratoire populaires d'autres marques

Qiagen

Qiagen DML 3000 Manuel utilisateur

Queensgate

Queensgate NANOSCAN OP400 Manuel de programmation

Conviron

Conviron GEN1000-GE Manuel utilisateur

Parr Instrument

Parr Instrument 4560 Mode d’emploi

IKA

IKA IC control Manuel utilisateur

Integra

Integra DOSE IT Manuel utilisateur

Agilent Technologies

Agilent Technologies 5800 ICP-OES Manuel utilisateur

Endress+Hauser

Endress+Hauser Cleanfit CPA875 Manuel utilisateur

NI PXI-5422 Manuel

Collomix

Collomix Aqix Manuel utilisateur

SPEX SamplePrep

SPEX SamplePrep 6875 Freezer/Mill Series Manuel utilisateur

Ocean Insight

Ocean Insight FLAME-NIR+ Manuel utilisateur

Parker

Parker ALIGN-MG-NA Manuel utilisateur

BD 644787 Manuel utilisateur

DENTAURUM

DENTAURUM Compact Megaplus Manuel utilisateur

Biuged Laboratory Instruments

Biuged Laboratory Instruments BGD 626 Manuel utilisateur

VWR

VWR SAS Super IAQ Manuel utilisateur

Yamato

Yamato BM510 Manuel utilisateur