Eppendorf Mastercycler nexus User Manual

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www.eppendorf.com/myeppendorf

Mastercycler® nexus

Operating manual Istruzioni per l'uso

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Trademarks

Eppendorf and the eppendorf logo, Mastercycler registered trademarks of Eppendorf AG.

Registered trademarks are not marked in all cases in this manual.

Notice

The software of the Mastercycler nexus contains open source software. License information is available as PDF documents via the Eppendorf node. To export the license documents, connect a memory device, select the Eppendorf node in the navigation tree and press the softkey License.

Operating manual. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Istruzioni per l'uso . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111

, flexid®, SteadySlope® and Eppendorf twin.tec® are

6331 900.069-04/012014

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Table of contents

Mastercycler

nexus

English (EN)

Operating manu al Mastercycler® nexusseeon p.Fig.Tab.p.

English (EN)Operating manual

Table of contents

1 Operating instructions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

1.1 Using this manual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

1.2 Danger symbols and danger levels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

1.2.1 Danger symbols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

1.2.2 Danger levels. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

1.3 Symbols used . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

1.4 Abbreviations used . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

1.5 Glossary. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

2 Product description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

2.1 Main illustration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

2.1.1 Master variants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

2.1.2 Master variants with thermoblock (64+32 wells) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

2.1.3 Master variant with flat thermoblock . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

2.1.4 Eco variants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

2.1.5 Terminal block. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

2.1.6 Control panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

2.1.7 Number pad . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

2.1.8 Status lamp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

2.2 Delivery package. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

2.3 Features. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

2.3.1 Features of the Mastercycler nexus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

2.3.2 Control panel and ports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

2.3.3 Consumable. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

2.3.4 Networking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

2.3.5 Service. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

3 Safety. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

3.1 Intended use . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

3.2 User profile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

3.3 Information on product liability . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

3.4 Warnings for intended use . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

3.5 Warning signs on the device. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

4 Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

4.1 Selecting the location . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

4.2 Installing the instrument. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

4.3 Shut down . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

5 Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

5.1 Initial steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

5.1.1 Using the flexlid heated lid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

5.2 Starting the Mastercycler nexus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

5.2.1 Defining the administrator PIN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

5.2.2 Other steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

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nexus

5.3 Logging in and out as a user. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

5.3.1 Logging in as a user . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

5.3.2 Changing users . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

5.3.3 Logging out as a user . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

5.4 Overview of software operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

5.4.1 Navigation tree overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

5.4.2 Navigating in the navigation tree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

5.4.3 Using external storage media . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

5.4.4 Selecting export file formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

5.5 Managing folders and programs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

5.5.1 Creating folders and programs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

5.5.2 Copying folders and programs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

5.5.3 Deleting folders and programs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

5.6 Using the schedule . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

5.6.1 Editing a schedule entry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45

5.6.2 Displaying the schedule . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

5.7 Using the power save mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

6 Programming . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

6.1 Overview of the program editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

6.1.1 Opening the program editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

6.1.2 Structure of the program editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50

6.2 Making general settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51

6.2.1 Opening the header. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51

6.2.2 Editing header settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52

6.3 Editing programs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

6.3.1 Inserting a program step. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

6.3.2 Editing parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

6.3.3 Create gradient step . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

6.3.4 Deleting program steps. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57

6.3.5 Exporting a program as a PDF or text file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57

6.3.6 Saving a program and exiting the editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57

6.4 Program templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58

7 PCR run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

7.1 Loading the thermoblock . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

7.1.1 Selecting the sample tubes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

7.1.2 Inserting the sample tubes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60

7.2 Starting a program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61

7.2.1 Status view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62

7.2.2 Common status view for devices with a thermoblock with 64+32 wells. . . . . . . . . . . . 63

7.3 Interrupting or stopping a program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64

7.3.1 Interrupting a program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64

7.3.2 Resuming a program. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64

7.3.3 Stopping a program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64

7.4 Displaying the most recently run programs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64

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8 System management . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

8.1 Administrator functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

8.2 Managing user accounts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

8.2.1 Creating a user account . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

8.2.2 Editing a user account . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68

8.2.3 Deleting a user account . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69

8.2.4 Changing the administrator PIN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69

8.3 System settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70

8.4 Cycler functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73

8.4.1 Cycler system functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74

8.4.2 Self-test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75

8.5 Managing and backing up data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76

8.5.1 Backing up data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76

8.5.2 Exporting and importing programs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77

8.6 Transferring programs from an older Mastercycler model. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77

8.7 Network connection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79

8.7.1 Setting up a network connection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80

8.7.2 Setting up e-mail notifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81

8.7.3 Setting up syslog messages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82

9 Quick start. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85

9.1 Login . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85

9.2 Creating folders and programs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86

9.3 Copying folders and programs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86

9.4 Deleting folders and programs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87

9.5 Editing programs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87

9.6 Stopping and starting programs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89

10 Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91

10.1 Cleaning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91

10.1.1 Cleaning the housing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91

10.1.2 Cleaning the heated lid and the thermoblock . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92

10.2 Disinfection/decontamination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92

10.3 Decontamination before shipment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92

11 Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93

11.1 General errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93

12 Transport, storage and disposal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95

12.1 Packing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95

12.2 Disposal. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96

13 Technical data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97

13.1 Power supply. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97

13.2 Weight/dimensions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97

13.3 Ambient conditions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97

13.4 Application parameters. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98

Page 6

Table of contents

Mastercycler

nexus

English (EN)

14 Ordering Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103

14.1 Mastercycler nexus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103

14.1.1 Master variants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103

14.1.2 Eco variants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104

14.2 Accessories . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105

14.3 Consumables. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105

14.4 Recommended auxiliary materials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108

Page 7

Operating instructions

Mastercycler

nexus

English (EN)

1 Operating instructions

1.1 Using this manual

 Read the operating manual before you operate the device for the first time.  Please view this manual as part of the product and keep it somewhere easily accessible.  If this manual is lost, please request another one. The current version of the operating manual can be

found on our website at www.eppendorf.com

The sequences of actions in this operating manual are described for operation using the control panel. You can also operate the Mastercycler nexus using the mouse (see p. 30).

1.2 Danger symbols and danger levels

The safety instructions in this manual appear with the following danger symbols and danger levels:

1.2.1 Danger symbols

Biohazard Explosion

Electric shock Hot surface

Crushing Toxic substances

Hazard point Material damage

1.2.2 Danger levels

DANGER Will lead to severe injuries or death. WARNING May lead to severe injuries or death. CAUTION May lead to light to moderate injuries. NOTICE May lead to material damage.

Page 8

Operating instructions

Mastercycler

English (EN)

1.3 Symbols used

Depiction Meaning

 Actions without a specified order

• List

Text Display text or software text

nexus

Actions in the specified order

Additional information

Page 9

1.4 Abbreviations used

DHCP

Dynamic Host Configuration Protocol (network)

DNS

Domain Name System (network)

Internet Protocol (network)

MAC

Media Access Control (network)

PCL

Printer Command Language (standard for printer control)

Operating instructions

Mastercycler

nexus

English (EN)

PCR

Polymerase chain reaction

PDF

Portable Document Format

Personal Identification Number

PostScript (standard for printer control)

SMTP

Simple Mail Transfer Protocol (network)

TSP

Thermal Sample Protection

USB

Universal Serial Bus

Page 10

Operating instructions

Mastercycler English (EN)

nexus

1.5 Glossary

flexlid

The heated lid of the thermal cycler automatically adapts to the used tubes or plates. This always ensures that a reliable pressure is applied to the thermoblock and that the tubes are sealed securely. Unlike conventional heated lids, they do not need to be manually adjusted.

Thermal Sample Protection

When the heated lid is being heated, the thermoblock is actively maintained at a constant temperature. This minimizes non-specific annealing and evaporation of the samples.

Triple circuit technology

The thermoblock is controlled by three independent control loops. This is necessary to produce temperature gradients and leads to improved temperature homogeneity.

Page 11

2 Product description

2 3

2.1 Main illustration

2.1.1 Master variants

•Mastercycler nexus

• Mastercycler nexus gradient

•Mastercycler nexus SX1

•Mastercycler nexus GSX1

Abb. 2-1: Front and rear view

Product description

Mastercycler

nexus

English (EN)

Fig. 2-1: Front and rear view

1Lid handle

For opening, closing, locking and unlocking the heated lid.

2Heated lid

3Heating plate

4Thermoblock

5Ethernet port

6 Mains connection socket with power switch

0 = switched off, I = switched on.

7 Eco and Term switches

8CAN out port

9CAN in port

10 Control panel

See detailed drawing (see p. 16)

11 Flap

USB port cover.

12 Name plate

Page 12

flexlid

Product description

Mastercycler

nexus

English (EN)

2.1.2 Master variants with thermoblock (64+32 wells)

•Mastercycler nexus X2

•Mastercycler nexus GX2

Abb. 2-2: Front and rear view

Fig. 2-2: Front and rear view

1Lid handle

For opening, closing, locking and unlocking the heated lid.

2 Thermoblock with 64 wells

3Heated lid

4Heating plate

5 Thermoblock with 32 wells

6Ethernet port

7 Mains connection socket with power switch

0 = switched off, I = switched on.

8 Eco and Term switches

9CAN out port

10 CAN in port

11 Control panel

See detailed drawing (see p. 16)

12 Flap

USB port cover.

13 Name plate

Page 13

2.1.3 Master variant with flat thermoblock

Hot surfaces on block and lid

flat

2 3

Abb. 2-3: Front and rear view of the Mastercycler nexus flat

Product description

Mastercycler

nexus

English (EN)

Fig. 2-3: Front and rear view of the Mastercycler nexus flat

1Lid handle

For opening, closing, locking and unlocking the heated lid.

2Heated lid

3Heating plate

4Thermoblock

5Ethernet port

6 Mains connection socket with power switch

7 Eco and Term switches

8CAN out port

9CAN in port

10 Control panel

See detailed drawing (see p. 16)

11 Flap

USB port cover.

12 Name plate

0 = switched off, I = switched on.

Page 14

eco

2 3

Product description

Mastercycler

nexus

English (EN)

2.1.4 Eco variants

•Mastercycler nexus eco

• Mastercycler nexus gradient eco

•Mastercycler nexus SX1e

•Mastercycler nexus GSX1e

• Mastercycler nexus X2e (with a thermoblock with 64+32 wells; not shown in the figure)

• Mastercycler nexus GX2e (with a thermoblock with 64+32 wells; not shown in the figure)

• Mastercycler nexus flat eco (with a flat thermoblock; not shown in the figure)

Abb. 2-4: Front and rear view

Fig. 2-4: Front and rear view

1Lid handle

For opening, closing, locking and unlocking the heated lid.

2Heated lid

3Heating plate

4Thermoblock

5 Mains connection socket with power switch

0 = switched off, I = switched on.

6 Eco and Term switches

7CAN out port

8CAN in port

9 Pen holder

Holds up to three pens.

10 Name plate

Page 15

2.1.5 Terminal block

1 2

Abb. 2-5: Terminal block

Fig. 2-5: Terminal block

Product description

Mastercycler

nexus

English (EN)

1CAN in port

Connection to an eco device.

2CAN out port

Connection to a second eco device.

3 Eco switch

Adjusts the position of eco device (left or right

4Term switch

Termination of the CAN data connection if connected to the eco device.

5 Ethernet port (not in the case of an eco device)

Connection of a master variant of the Mastercycler nexus to an Ethernet network.

next to a master variant with control panel).

Only connect devices to the interfaces of the Mastercycler nexus that comply with the IEC 950/EN 60950 (UL 1950) standards.

Page 16

Product description

Mastercycler

nexus

English (EN)

2.1.6 Control panel

Abb. 2-6: Control panel

12 34

1 2

abc3def

ghi5jkl6mno

stop

start

Fig. 2-6: Control panel

1stop key

Stop the running program.

2Standby key

To switch the device to power save mode.

3Display

4Number pad

5 Status lamp

In the case of devices with a thermoblock with 64+32 wells, the status lamp in the control panel is deactivated. The active status lamp for devices with a thermoblock with 64+32 wells is located on the heated lid.

pqrs8tuv9wxyz

del

enter

1011

7enter key

To confirm entries and open selection lists.

8next key

Move the cursor to the next input field.

9Arrow keys

Move the cursor.

10 Softkeys

Function depends on the software dialog and is indicated in the display above the softkey.

11 start key

Start the selected program.

6del key

To delete marked objects and characters to the right of the cursor.

Page 17

Product description

1 2

abc3def

ghi5jkl6mno

pqrs8tuv9wxyz

del

Mastercycler

2.1.7 Number pad

Enter digits and text in input fields. For numeric input fields (e.g. temperature, time), the keys only have numbers. For decimal numbers with numbers after the decimal point, use the period as a decimal point. Alphanumeric input fields have keys with multiple functions.

 To enter text, press the key with the desired letter until the respective letter is displayed.

Example: To enter pcr 3 in a text field, press the following keys one after the other:

1. For p: press 7 once.

2. For c: press 2 three times.

3. For r: press 7 three times.

4. For the space: press 0 (zero) twice.

5. For 3: press 3 four times.

nexus

English (EN)

2.1.8 Status lamp

Status lamp Operating status

Briefly flashes green The device is in standby mode. The display is switched off. Lights up green The device is in idle mode. Flashes green A program run is active. Flashes orange The program run is waiting for a user action in the Pause or Hold step. Flashes red A fault has occurred. Additional information on the fault appears on the display.

2.2 Delivery package

Quantity Description

1 Mastercycler nexus in the ordered version 1Operating manual 1 Certificate of conformity 1Power cord

Page 18

Product description

Mastercycler English (EN)

nexus

2.3 Features

Triple Circuit Technology

The Triple Circuit Technology leads to a homogeneous temperature distribution and enables for Mastercycler nexus gradient, Mastercycler nexus GSX1 and Mastercycler nexus GX2 a selective generation of temperature gradients for PCR optimizations.

SteadySlope

The SteadySlope technology ensures that the heating and cooling rates of the thermoblock in gradient operation are identical to those in normal operation. A reliable transfer of the optimization results to the routine application is ensured.

flexlid

All variants of the Mastercycler nexus have a flexlid heated lid. It enables ergonomic operation with one hand and automatically adjusts the contact pressure for all tubes and PCR plates.

Thermal Sample Protection

The Thermal Sample Protection technology maintains a constant thermoblock temperature of 20°C during the warm-up phase of the heated lid. Thermal Sample Protection reduces the thermal load on your samples and minimizes the probability of non-specific product formation during the PCR.

Self-test function

The master variants of the Mastercycler nexus have an integrated self-test function. The self-test function provides a simple way of testing the correct function of the thermoblock without any further tools. A separately available USB key is required for the self test function (see Accessories on p. 105).

Control

The eco variants of the Mastercycler nexus do not have a control panel. They are controlled via a connected master variant of the Mastercycler nexus.

Standby function

All variants of the Mastercycler nexus can be switched to standby mode automatically or by pressing a key.This reduces energy consumption and ensures that the device is ready for use at any time.

Page 19

2.3.1 Features of the Mastercycler nexus

Product description

Mastercycler

nexus

English (EN)

Thermoblock

version

Thermoblock

material

Freely programmable temperature gradient

(gradient spread)

Mastercycler nexus gradient 96-well format Aluminum X (max. 20°C) Mastercycler nexus gradient eco 96-well format Aluminum X (max. 20°C) Mastercycler nexus 96-well format Aluminum Mastercycler nexus eco 96-well format Aluminum Mastercycler nexus GSX1 96-well format Silver X (max. 20°C) Mastercycler nexus GSX1e 96-well format Silver X (max. 20°C) Mastercycler nexus SX1 96-well format Silver Mastercycler nexus SX1e 96-well format Silver Mastercycler nexus flat flat Aluminum X (max. 20°C) Mastercycler nexus flat eco flat Aluminum X (max. 20°C) Mastercycler nexus GX2 64-well format

Aluminum X (max. 12°C)

and

32-well format

Mastercycler nexus GX2e 64-well format

Aluminum X (max. 12°C)

and

32-well format

Mastercycler nexus X2 64-well format

Aluminum

and

32-well format

Mastercycler nexus X2e 64-well format

Aluminum

and

32-well format

Page 20

Product description

Mastercycler

nexus

English (EN)

2.3.2 Control panel and ports

Control panel Ethernet port USB port

Mastercycler nexus gradient X X 2 Mastercycler nexus gradient eco — — — Mastercycler nexus X X 2 Mastercycler nexus eco — — — Mastercycler nexus GSX1 X X 2 Mastercycler nexus GSX1e — — — Mastercycler nexus SX1 X X 2 Mastercycler nexus SX1e — — — Mastercycler nexus flat X X 2 Mastercycler nexus flat eco — — — Mastercycler nexus GX2 X X 2 Mastercycler nexus GX2e — — — Mastercycler nexus X2 X X 2 Mastercycler nexus X2e — — —

Page 21

2.3.3 Consumable

Product description

Mastercycler

nexus

English (EN)

PCR tubes (0.1 mL or

PCR tubes *)

(0.5 mL)

PCR plates PCR slide

(in situ)

0.2 mL)

Mastercycler nexus gradient 96 71 1x 96-well — Mastercycler nexus gradient eco 96 71 1x 96-well — Mastercycler nexus 96 71 1x 96-well — Mastercycler nexus eco 96 71 1x 96-well — Mastercycler nexus GSX1 96 — 1x 96-well — Mastercycler nexus GSX1e 96 — 1x 96-well — Mastercycler nexus SX1 96 — 1x 96-well — Mastercycler nexus SX1e 96 — 1x 96-well — Mastercycler nexus flat — — — 4 Mastercycler nexus flat eco — — — 4 Mastercycler nexus GX2 64 + 32 45 + 19 2x 32-well

—

1x 32-well

segments of separable

96-well PCR plates

Mastercycler nexus GX2e 64 + 32 45 + 19 2x 32-well

—

1x 32-well

segments of separable

96-well PCR plates

Mastercycler nexus X2 64 + 32 45 + 19 2x 32-well

—

1x 32-well

segments of separable

96-well PCR plates

Mastercycler nexus X2e 64 + 32 45 + 19 2x 32-well

—

1x 32-well

segments of separable

96-well PCR plates

*) In the case of 0.5 mL tubes with a bigger lid, the number of usable sample places can be lower.

Page 22

Product description

Mastercycler

nexus

English (EN)

2.3.4 Networking

You can connect and control up to any two eco devices to a master variant of the Mastercycler nexus.

Master device

Eco device

2.3.5 Service

Eppendorf offers customized service options for preventive maintenance and verification of your thermocycler. For more information, service requests and local offers go to www.eppendorf.com/epservices and see local websites.

Page 23

Safety

Mastercycler

nexus

English (EN)

3Safety

3.1 Intended use

The Mastercycler nexus is intended for use in research and routine laboratories in the biosciences.

The Mastercycler nexus is intended for the incubation of aqueous solutions, suspensions or emulsions in closed tubes for enzymatic reactions, typically polymerase chain reactions (PCR).

The Mastercycler nexus is intended exclusively for indoor use.

All country-specific safety requirements for operating electrical equipment in the laboratory must be observed.

3.2 User profile

The device and accessories may only be operated by trained and skilled personnel.

Before using the device, read the operating manual carefully and familiarize yourself with the device's mode of operation.

3.3 Information on product liability

In the following cases, the designated protection of the device may be compromised. Liability for any resulting property damage or personal injury is then transferred to the operator:

• The device is not used in accordance with the operating manual.

• The device is used outside of its intended use.

• The device is used with accessories or consumables which are not recommended by Eppendorf.

• The device is maintained or repaired by people not authorized by Eppendorf.

• The user makes unauthorized changes to the device.

Page 24

Safety

Mastercycler English (EN)

nexus

3.4 Warnings for intended use

Before using the Mastercycler nexus, read the operating manual and observe the following general safety precautions.

DANGER! Risk of explosion.

 Do not operate the device in areas where work is completed with explosive substances.  Do not use this device to process any explosive or highly reactive substances.  Do not use this device to process any substances which may generate an explosive

atmosphere.

WARNING! Risk of fire.

 Do not use this device to process any highly flammable liquids.

WARNING! Damage to health due to infectious liquids and pathogenic germs.

 When handling infectious liquids and pathogenic germs, observe the national regulations,

the biological security level of your laboratory, the material safety data sheets, and the manufacturer's application notes.

 Wear personal protective equipment.  For full instructions regarding the handling of germs or biological material of risk group II

or higher, please refer to the "Laboratory Biosafety Manual" (Source: World Health Organization, current edition of the Laboratory Biosafety Manual).

WARNING! Lethal voltages inside the device.

 Ensure that the housing is always closed and undamaged so that no parts inside the device

can be contacted by accident.

 Do not remove the housing of the device.  Do not allow any liquids to penetrate the inside of the housing.  Do not allow the device to be opened by anyone except service personnel who have been

specifically authorized by Eppendorf.

WARNING! Biohazard due to temperature control when heated lid is open.

If the heated lid is open, the lids of the reaction vessels may come off during temperature control. This will release sample material.

 Tempering may only be carried out when the heated lid is closed.

WARNING! Biohazard due to unsuitable reaction vessels, plates and lids.

Unsuitable reaction vessels, plates and lids will become damaged in the cycler, This will release sample material.

 Only reaction vessels, plates and lids that meet the requirements described in the

operating manual may be used.

Page 25

Safety

Mastercycler

CAUTION! Risk of burns on thermoblock, heated lid and reaction vessels.

The thermoblock, heated lid and reaction vessels reach temperatures of more than 50 °C very quickly. During gradient operation, the temperature of the heated lid and thermoblock is higher on the right side than on the left side.

nexus

English (EN)

 Wait until the temperature of the thermoblock, heated lid and reaction vessels is below 30

°C.

 Then the heated lid may be opened.

CAUTION! Poor safety due to incorrect accessories and spare parts.

The use of accessories and spare parts other than those recommended by Eppendorf may impair the safety, functioning and precision of the device. Eppendorf cannot be held liable or accept any liability for damage resulting from the use of incorrect or non-recommended accessories and spare parts, or from the improper use of such equipment.

 Only use accessories and original spare parts recommended by Eppendorf.

WARNING! Risk of injury when lifting the device.

If the device is moved using the lid, the lid may break, causing the device to fall.

 Lift the device by holding it at the bottom of the housing.  Use both hands to carry the device.  Do not lift the device using the lid.

CAUTION! Risk of injury due to lifting and carrying heavy loads

The device is heavy. Lifting and carrying the device can lead to back injuries.

 Transport and lift the device with an adequate number of helpers only.  Use a transport aid to transport the device.

NOTICE! Damage to electronic components due to condensation.

Condensate can form in the device after it has been moved from a cool environment to a warmer environment.

 After installing the device, wait for at least 12 h. Only then connect the device to the mains

power supply.

Page 26

Safety

Mastercycler English (EN)

nexus

3.5 Warning signs on the device

This section explains the warning signs on the Mastercycler nexus.

1CAUTION

Risk of burns from hot surfaces. Risk of burns from hot thermoblock and hot heating plate when the heated lid is open. In gradient operation mode, the temperature of the thermoblock is higher on the right side than on the left side.

Page 27

4 Installation

4.1 Selecting the location

WARNING! Risk of injury due to unsuitable work surface.

The device may fall over if placed on an unsuitable work surface.

 Observe the criteria in the operating manual on selecting a location.

NOTICE! Damage from overheating.

 Do not install the device near heat sources (e.g. heating, drying cabinet).  Do not expose the device to direct sunlight.  Ensure unobstructed air circulation. Maintain a clearance of at least 30 cm around all

ventilation grilles.

Installation

Mastercycler

English (EN)

nexus

When the device is in operation, ensure that the power switch of the device and the mains isolating device (e.g. FI safety switch) are accessible.

Information regarding the dimensions and weight of device components can be found in a separate section (see Weight/dimensions on p. 97).

Take the following criteria into account when selecting the location for the Mastercycler nexus:

• The surface must have sufficient bearing capacity and ensure the required stability.

• The surface must be free of vibration.

• The device feet must not slip.

• The height of the location should allow for convenient and safe operation of the device.

Page 28

Installation

Mastercycler English (EN)

nexus

4.2 Installing the instrument

This section describes how to put the device into operation and how to connect one or two eco devices to a master variant of the Mastercycler nexus.

4.2.1 Connecting the device to the power supply

WARNING! Risk from incorrect supply voltage

 Only connect the device to voltage sources which correspond to the electrical

requirements on the name plate.

 Only use sockets with a protective earth (PE) conductor and suitable power cable.

NOTICE! Sample loss due to interruption of the mains/power supply.

If you use multiple sockets, the current consumption of several devices may exceed the power current strength. The mains/power fuse interrupts the mains/power supply. The devices do not receive any power. The running programs will be aborted.

 Connect the mains/power cord of each device to an earth/grounded socket.  Do not use multiple sockets.

Information on the power consumption of the Mastercycler nexus is provided separately (see Power supply on p. 97).

 Connect the mains connection socket to the power socket using a power cable.

Page 29

Installation

eco

123

Mastercycler

English (EN)

4.2.2 Attaching devices to each other

You can attach adjacent devices to each other to prevent individual devices from slipping and avoid mechanical stress on the cables.

Abb. 4-1: Example: two Mastercycler nexus attached to each other

nexus

Fig. 4-1: Example: two Mastercycler nexus attached to each other

1 Eco variant Mastercycler nexus

3 Master variant Mastercycler nexus

2Bracket

CAUTION! Danger from devices falling down.

The bracket can break or be released from the recess in the housing if you move or lift devices that are attached to each other. Devices could fall down and cause injury.

 Do not lift devices that are attached to each other with the bracket.  Do not move devices that are attached to each other with the bracket.  Separate the devices before lifting or moving them.

Page 30

Installation

Mastercycler

nexus

English (EN)

1. Position the devices next to each other.

1 2

2. Fold out the bracket of the device on the left . Insert the bracket into the recess in the housing of the device on the right .

3. Align the devices attached to each other in parallel.

4.2.3 Separating devices

1. Switch off the devices at the power switch. Disconnect the cable connections at the rear of the devices.

2. Hold the bracket and push the device on the right back until the bracket comes out of the recess in the housing.

3. Fold the bracket away.

4.2.4 Using the USB ports

The master variants of the Mastercycler nexus have two USB ports for the connection of a mouse, printer, storage medium or the self-test USB key.

• Use a USB hub if you would like to connect more than two USB devices at the same time.

•The USB printer must be compatible with the PostScript Further information can be found in the operating manual for your printer.

• The eco devices do not have any USB ports.

or PCL printer standards.

Page 31

Installation

Eco device 2 Eco device 1Master device

Mastercycler

nexus

English (EN)

1. Open the flap (1) to access the USB ports (2).

2. Insert the USB device into one of the two ports. Newly connected USB devices are automatically detected during operation.

3. Close the flap.

4.2.5 Connecting the eco device

This section explains how to operate one or two eco devices together with a master variant of the Mastercycler nexus. The eco device is controlled via a master variant Mastercycler nexus. This requires a cable connection between the devices. Use Eppendorf CAN-bus cables for this (see Accessories on p. 105).

Connecting a single eco device

Abb. 4-2: Wiring diagram showing rear view of the devices

Eco device 1Master device

Fig. 4-2: Wiring diagram showing rear view of the devices

Connecting two eco devices

Abb. 4-3: Wiring diagram showing rear view of the devices

Fig. 4-3: Wiring diagram showing rear view of the devices

The connections and switches are located on the rear of the devices.

4.2.5.1 Establishing the data connection

1. Switch off all devices at the power switch.

Connecting the first eco device

2. Connect the CAN bus cable to the CAN out port of the Mastercycler nexus (with control panel) and to the CAN in port of the eco device.

Connecting the second eco device

3. Connect the second CAN bus cable to the CAN out port of the first eco device and to the CAN in port of the second eco device.

Page 32

Installation

Mastercycler English (EN)

nexus

4.2.5.2 Setting the Eco and Term switches

You must set the Eco and Term switches on all devices depending on whether you have connected one or two eco devices to a master variant of the Mastercycler nexus.

 Set the Eco and Term switches on the rear of all connected devices as follows:

Connected devices Master device Eco device 1 Eco device 2 One eco device — —

Two eco devices

• The position of the Eco switch of the eco device should reflect its installation position on the left or right next to a master variant of the Mastercycler nexus with control panel.

• If you operate the Mastercycler nexus on its own, the position of the Eco and Term switches is not important.

4.3 Shut down

Proceed as follows if you do not want to use the Mastercycler nexus for longer than a week.

1. Load the block with an empty PCR plate or tube.

2. Close the heated lid and flip the handle forwards .

3. Disconnect the Mastercycler nexus from the power supply.

Never leave the lid of the Mastercycler nexus open to prevent contamination of the block.

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5 Operation

5.1 Initial steps

Checking the correct installation

Before the Mastercycler nexus is commissioned for the first time, ensure that the following requirements are met:

• The device is correctly connected.

• The device is free of damage.

• Free circulation of air around the ventilation slots at the rear of the device and at the fan behind the front feet has been guaranteed.

5.1.1 Using the flexlid heated lid

The Mastercycler nexus is equipped with a flexlid heated lid. The flexlid heated lid automatically adjusts to the height of the used PCR tubes or PCR plates. It can be operated with one hand. Manual adjustment to the tube height, or adjusting the contact pressure to the tube lids, is not required.

The heated lid ensures uniform contact between the tubes and the thermoblock, and secures the tube lids against leaks. The heating process prevents condensation from forming in the upper area of the tube during the tempering of the reaction liquid.

5.1.1.1 Open heated lid

WARNING! Biohazard due to temperature control when heated lid is open.

If the heated lid is open, the lids of the reaction vessels may come off during temperature control. This will release sample material.

 Tempering may only be carried out when the heated lid is closed.

CAUTION! Risk of burns on thermoblock, heated lid and reaction vessels.

 Wait until the temperature of the thermoblock, heated lid and reaction vessels is below 30

°C.

 Then the heated lid may be opened.

Open the heated lid in one go as follows:

 Flip the lid handle up over the heated lid and flip the heated lid up at the lid handle as far as it will go.

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5.1.1.2 Closing the heated lid

Prerequisites Thermoblock loaded with sample tubes or a PCR plate.

CAUTION! Risk of crushing when closing the heated lid.

 Grip the heated lid handle in the middle.  When you close the heated lid, do not place your fingers between the heated lid and the

housing.

Comply with the guidelines for loading the thermoblock with PCR tubes (see Loading the thermoblock on p. 59).

1 2

1. Grip the heated lid at the center of the lid handle and close it (1).

2. Continue to move the lid handle further down until it is in a horizontal position (2).

The force required to move the lid handle into the horizontal position depends on the type of PCR tubes or PCR plate used.

The heated lid is now locked. You can now start a program run or manually temper the heated lid and samples.

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5.2 Starting the Mastercycler nexus

Prerequisites The Mastercycler nexus is properly set up and connected to the power supply.

 Switch on the device using the power switch at the back (see p. 11).

The status lamp lights up and the fan starts. The display illumination is switched on (not for Mastercycler nexus eco).

5.2.1 Defining the administrator PIN

The first time the device is started, you can define an administrator PIN to protect it against unauthorized access. The administrator PIN is saved and will be maintained even when the Mastercycler nexus is switched off.

If an administrator PIN has not been defined, you will be prompted to define one.

NOTICE! Data loss due to unauthorized use of the administrator password.

The administrator password protects the device software from unwanted access.

 Make a note of the administrator password.  Keep the administrator password at a secure location.  Only provide the administrator password to individuals who work with the system

configuration.

 Please contact Eppendorf AG if you have any problems with the administrator password.

• If you do not want to use user management, you do not need to define an administrator PIN. In this case, leave the input fields in the Input Admin PIN window blank and deactivate the PIN function. Further information on user management can be found separately (see System settings on p. 70).

•If the PIN function is activated (see System settings on p. 70), you must define an administrator PIN. If you do not do this, the input prompt will appear each time the device is switched on.

• You can also change the administrator PIN at a later time (see Changing the administrator PIN on p. 69).

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To define the administrator PIN, perform the following steps in the sequence described.

1. Switch on the Mastercycler nexus at the power switch. The Input Admin PIN window appears.

2. Enter the desired administrator PIN using the numeric keys.

3. Re-enter the PIN in the Confirmation: field.

del

4. An error message appears if the two PIN entries do not match. If this happens, delete the incorrectly entered PIN and reenter the PIN twice.

5. Optional: enter the administrator's e-mail address for receiving messages from the Mastercycler nexus in the

E-mail address: field (see p. 81).

6. Optional: select Enable e-mail notification to activate e-mail notifications for the administrator.

7. Press the OK softkey.

After the successful confirmation of the administrator PIN, the navigation tree appears on the display. You are now logged in as the administrator.

5.2.2 Other steps

5.2.2.1 Changing the language

You can change the language of the user interface of the Mastercycler nexus (see System settings on p. 70).

5.2.2.2 Set date and time

The date and time are shown in the upper right corner of the display. As the administrator, you can change this internal clock at any time (see System settings on p. 70).

5.2.2.3 Setting up user accounts

To be able to use the Mastercycler nexus, you must set up at least one user account. Detailed information on user management and how to set up user accounts can be found separately (see Managing user accounts on p. 67).

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5.3 Logging in and out as a user

The functions described here are only available if the PIN function is activated (see System settings on p. 70).

5.3.1 Logging in as a user

To be able to log in with your user name, your administrator must have set up a user account for you.

Proceed as follows:

1. Open the list by pressing the enter key, and select your user name.

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2. Press the next key. The cursor jumps to the PIN: field.

1 2

abc3def

ghi5jkl6mno

pqrs8tuv9wxyz

del

3. Enter your PIN via the numerical keys. If the PIN is wrong, Wrong PIN appears. Press the Login softkey to return to the User Login window, delete the wrong PIN entry with the Delete key, and enter the correct PIN.

4. Press the OK softkey to confirm. The navigation tree is displayed.

You are now logged in with your user name and can work with the Mastercycler nexus.

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5.3.2 Changing users

Only one user can be logged in at a time. Proceed as follows to switch between users:

1. Select either your user node or the Other Users user node.

2. Press the Login softkey.

3. Log in as a user. The previously logged-in user is automatically logged out.

5.3.3 Logging out as a user

You can log out to protect your programs against unauthorized changes.

1. Select your user node.

2. Press the Logout softkey. You are now logged out.

The guest user is automatically logged in. The guest user cannot start programs and only has read access to all programs and folders.

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5.4 Overview of software operation

2 3

6 7

5.4.1 Navigation tree overview

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1 Window title

Current level in the navigation tree or title of a dialog box.

2 Eppendorf node

The main node which contains all other nodes.

3 User node

Contains the programs and folders as well as the list of the 5 most recently started programs of the logged-in user.

4 Other Users node

Contains the nodes of the users that are not currently logged in if PINs are used (see p. 70).

5Cycler node

Each cycler that is connected and switched on is shown as a separate node. The cycler node can be used to display the cycler status and execute functions.

6 System node

This node contains the most important system settings. Some settings can only be edited by the administrator.

7 USB node

This node is only visible if a USB storage medium has been inserted. Use this node to transfer programs and perform data backups.

8Softkeys

The 5 softkeys have context-specific functions, depending on the selected node or active window.

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5.4.2 Navigating in the navigation tree

5.4.2.1 Opening the node

You have three options:

 Mark the node with the arrow keys and press the enter key or the arrow key.

The node opens and the symbol changes to .

 Alternatively, click on the symbol next to the node.

 Alternatively, use the mouse to double-click on the desired node.

5.4.2.2 Closing the node

Carry out the above-mentioned steps in the reverse order:

 Click on the symbol next to the node.  Alternatively, double-click on the node with the mouse.

 Alternatively, mark the node with the arrow keys and press the enter key or the

arrow key. The node is closed and the symbol next to the node changes to .

5.4.3 Using external storage media

You can back up programs, log files and protocols to a storage medium and, for example, archive them on a PC or print them. External storage media are also needed for data backups and software updates (see p. 70).

5.4.3.1 Connecting a USB storage medium

 Connect a USB storage medium to a USB port.

After a few seconds, the USB node appears in the navigation tree. The programs and user nodes saved on the USB storage medium can be accessed via this node.

The Mastercycler creates a folder called \eppendorf on the USB storage medium where all files will be saved.

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5.4.3.2 Removing the USB storage medium

Caution! The symbol is displayed in the upper right corner while the storage medium is being accessed. Wait until it has disappeared before removing the USB storage medium.

 Remove the USB storage medium.

The USB node disappears from the navigation tree.

5.4.4 Selecting export file formats

When exporting programs, protocols and log files to external storage media, you can choose between text-only format (.TXT) and PDF.

 Select memory device

Storage medium for the exported file.

 Select file format

• PDF: Saves the file as a PDF. Use this setting if you only want to print or view the documents on your PC. You need to have a PDF reader software installed (e.g. Adobe

• Text-only (.TXT): Saves the file in text-only format (.TXT). Use this setting if you want to process the document content electronically (e.g. embed it in a report).

Reader®).

 Confirm your selection with OK.

The file is copied to the external storage medium, and the file name is displayed.

5.5 Managing folders and programs

If you are logged in as a normal user (not as an administrator), you can only create, edit and delete programs below your own user node. Further information on user rights can be found in a separate section (see Administrator functions on p. 67).

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5.5.1 Creating folders and programs

5.5.1.1 Creating a folder

Proceed as follows:

1. Mark the user node.

2. Press the NewFolder softkey.

3. Enter a name for the new folder using the numeric keys.

Instead of the numeric keys, you can also use the software keyboard to make entries in text fields. This can be accessed via the Keybd key.

4. To enter a comment for the new folder, use the next key to go to the Comment: field.

5. Enter your comment via the numerical keys and confirm with OK. The folder is created and appears under your user node in the navigation tree.

You can change the name and comment for the folder at any time using the Prop. softkey.

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5.5.1.2 Creating a new program

You can create programs in the navigation tree on the user node level or on the folder level.

1. In the navigation tree, mark the user node or folder where you want to create the new program.

2. Press the New softkey.

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3. Enter the program name in the Name: field. The maximum number of characters is 21.

4. Select a program template in the Use template: field. An overview of the available program templates can be found separately (see p. 58). If you do not want

to use a template, select none.

5. Optional: enter a comment for the new program in the Comment field.

6. Press the OK softkey. The new program opens in the program editor. You can now configure and save the program (see p. 49).

You can change the program properties at a later time. To do so, mark the program in the navigation tree and press the Prop. softkey. The following properties can be changed:

•Program name

• Comment for the program

• Read/write access rights for the program

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5.5.2 Copying folders and programs

To copy folders or programs into your own user node, proceed as follows. When copying a folder, the programs it contains are also automatically copied.

1. In the user node of any user, mark the folder or program you want to copy.

2. Press the Copy softkey. A message appears informing you that the folder or the program was copied to the clipboard.

3. Press OK to confirm the message.

4. Mark your own user node. If you want to copy an individual program, you can also select a folder under your user node to which you want to copy the program.

5. Press the Paste softkey. If a program or folder already exists with the same name, you will be prompted to enter a new name.

The folder or program is pasted below your user node. You can now start or edit this program.

5.5.3 Deleting folders and programs

1. In the navigation tree, mark the folder or the program.

2. Press the del key. A confirmation prompt appears.

3. Press the Yes softkey. The folder or program is deleted.

5.6 Using the schedule

The schedule enables users to reserve devices for a specific time. You can view the schedule at any time or use it as an automatic screensaver. Use the System > Schedule Settings node to set the devices and weekdays for the schedule. Past schedule entries are automatically deleted.

You can use the schedule as an automatic screensaver (see p. 70)

 Mark the Eppendorf node. Press the Schedule softkey.

The Mastercycler Schedule window appears.

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Schedule Display the schedule. New Create a new schedule entry. Edit Change the schedule entry for the logged-in user. Delete Delete the schedule entry for the logged-in user. Exit Close the window.

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5.6.1 Editing a schedule entry

The following window appears if you choose to display, create or change a schedule entry:

1. Compete the fields as follows.

Day, Month, Year Date of the reservation. Begin: Start of the reservation. End: End of the reservation. User: Name of the respective user. Only users that have been set up can be selected. Cycler Reserved device. Comment Optional: comment for the reservation.

2. Press the OK softkey. The schedule entry appears in the list in the Mastercycler Schedule window.

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5.6.2 Displaying the schedule

You can access the schedule from the Mastercycler Schedule and User Login windows.

You can use the schedule as an automatic screensaver (see p. 70)

1. In the Mastercycler Schedule or User Login windows, press the Schedule softkey. The schedule is displayed on a day-to-day basis.

Only days that have been activated by the administrator are displayed in the schedule(see p. 70).

2. Scroll to the left or right with the arrow keys to view the entries for other days.

3. Press the Exit softkey to exit the schedule.

5.7 Using the power save mode

You can use the power save mode to reduce power consumption when the device is in idle mode.

The Mastercycler nexus eco automatically switches to power saving mode if the thermoblock and heated lid have not been tempered.

The administrator can define that the Mastercycler nexus will automatically switch to the power saving mode (see p. 70).

Prerequisites

• No program and no temperature control is active.

• The program editor is not open.

• No error message is displayed.

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Switching on the power save mode

 Press the standby key.

The device switches to power save mode.

• The display is switched off.

• The USB ports are switched off.

• The fan is switched off.

• The status lamp flashes green at long intervals.

Exiting the power save mode

 Press the standby key.

The device leaves the power save mode.

• The display is switched on.

• The USB ports are switched on.

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6 Programming

6.1 Overview of the program editor

The graphic program editor can be used to view and change existing programs.

6.1.1 Opening the program editor

1. Mark the desired program in the navigation tree or create a new program.

2. Press the Edit softkey. The program editor is displayed.

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6.1.2 Structure of the program editor

A program consists of a program header and up to 99 program steps that are executed by the cycler one after the other. Use the program editor to create and adjust programs.

1 Number of the program step

2 Block temperature [°C]

The thermoblock is heated or cooled in the relevant step at this temperature.

3 Holding time [mm:ss]

The set block temperature is maintained for this time.

4 Average temperature for gradient steps

When using gradient steps, increasing temperatures are generated across the columns of the thermoblock from left to right. The average temperature is displayed here.

5 Program step highlighted marking

The selected program step is highlighted in blue. New program steps are inserted before the marked step.

6 Step number within the cycle

The step number within a cycle and the total number of steps in the cycle are displayed on the top right. Example: 2/3: second step of a 3-step cycle (3 StepCyc).

7 Active input field

Numerical keys are used to make entries.

8 Extended program step

Program steps are marked with a star * if they have a temperature or holding time increment or a reduced heating or cooling rate.

9 Marking of gradient steps

Gradient steps are indicated by three horizontal lines.

10 Number of cycles

The number of cycles indicates how often the program steps indicated by the green horizontal arrow are to be carried out.

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6.2 Making general settings

Each Mastercycler nexus program has a program header where you define the block temperature control mode and the behavior of the heated lid. These settings are valid for the entire program.

6.2.1 Opening the header

1. Open the program editor (see Opening the program editor on p. 49).

2. Press the Header softkey. The header settings are displayed.

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6.2.2 Editing header settings

Lidtemp. Heated lid temperature (37°C to 110°C). The set lid temperature is maintained

constant during the program run. If values below 37°C are entered, the heated lid remains switched off.

TSP heated lid Preheat heated lid

•Switch TSP on and off.

If the TSP heated lid function is activated, the heated lid is heated up to the set temperature upon program start while the block temperature is maintained constant at 20°C. The program run starts once the heated lid temperature has been reached.

switch off lid at low blocktemperature

Lid heater with automatic switch-off

• Activated (default setting): the lid heater switches off if program steps have block temperatures of < 15°C.

• Deactivated: the lid heater switches off after the end of the program. If the last command of the program is a hold step, the heated lid remains switched on until you press the Enter key.

Note: This option is useful if you have inserted a hold step as the last program step in order to automatically cool the samples after the PCR.

Temp. mode Block temperature control mode

• fast: Use this setting for Fast PCR, for low reaction volumes (< 20 µL) and for templates with a low G/C content. With this setting you achieve the shortest program run times.

• standard: Block temperature control mode for standard applications. Use this setting for sample volumes between 20 µL and 50 µL or if the fast setting only results in a weak amplification. The program run times are slightly longer than with the fast setting.

• safe: Block temperature control mode for complex templates and large reaction volumes.

Use this setting for sample volumes of 50 µL or more or to amplify templates with a high G+C content. The program run times are slightly longer than with the

standard setting.

Simulate Mastercycler gradient

Simulate the temperature control behavior of the Mastercycler or Mastercycler gradient. This enables you to transfer programs from these cycler models to the Mastercycler nexus without making any adjustments (see Transferring programs from an older Mastercycler model on p. 77). If this option is deactivated, programs created for the Mastercycler will need to adapted for the Mastercycler nexus because of different temperature behavior. This may influence the PCR results.

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6.3 Editing programs

You can add, edit or delete steps in new (see p. 43) or copied (see p. 44) programs.

6.3.1 Inserting a program step

1. Open the program editor (see Opening the program editor on p. 49).

2. Mark the program step with the arrow keys in front of which you would like to insert a new program step.

The marked program step is highlighted in blue.

3. Press the Insert softkey. A list appears containing the available program steps.

4. Select the desired program step with the arrow keys. The following program steps are available:

1 StepCyc to 3 StepCyc

n StepCyc Cycle program step with an adjustable number of temperature steps. After this

Temp Individual temperature step with adjustable block temperature and holding time.

Cycle program step with 1 to 3 temperature steps with an adjustable number of repetitions (1 to 99). With cycle program steps you can increase or reduce the block temperatures and holding times by a preset value after each cycle (see Editing parameters on p. 54).

program step has been selected and confirmed with enter, a dialog window for the following entries is displayed.

• Steps per Cycle: Number of temperature steps per cycle (1 to 40)

• Number of Cycles: Number of cycles (1 to 99). If you have inserted a cycle with more than 6 steps, use the and arrow keys to view the steps that are not

displayed.

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Hold Temperature step with adjustable block temperature and indefinite holding time.

The set temperature is maintained until the user presses the enter key. A corresponding prompt is displayed in the status view and signaled by orange flashing of the status lamp.

Sound This program step emits an acoustic signal. Pause As Hold. The block temperature remains set to the value of the previous temperature

step.

5. Press the Insert softkey. The program step is inserted with standard parameters.

You can now insert additional program steps or edit the parameters of the program steps.

6.3.2 Editing parameters

1. Mark the desired program step with the arrow keys. The marked program step is highlighted in blue.

You can change the temperature, holding time and number of cycles directly in this view.

Tem pera ture Adjustable from 4.0°C to 99.0°C (in 0.1°C increments)

Dwell time Adjustable from 000:00 to 999:59 (mmm:ss) in 1-second

steps

Number of cycles Adjustable from 1 to 99

2. Press the enter key to accept the changes.

Extended options

3. Press the Options softkey. The extended parameter settings for the marked program step are displayed.

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Mastercycler

Temp Temperature of the program step Temp Inc./Dec. Temperature change from one cycle to the next

Adjustable from –10.0°C to +10.0°C in 0.1°C increments. You can switch between positive and negative values by pressing the +/- softkey.

Gradient Temperature gradient in the thermoblock, displayed as columns

Detailed information on how to program a gradient step can be found in a separate section (see p. 55).

Time Holding time for the program step Time Inc./Dec. Holding time change from one cycle to the next

Adjustable from –01:00 to +01:00 in 1 s increments. You can switch between positive and negative values by pressing the +/- softkey.

Ramp Temperature control speed of the thermoblock

Aluminum thermoblock: Adjustable from 0.1 °C/s to 1.5 °C/s. Silver thermoblock: Adjustable from 0.1 °C/s to 3.0 °C/s. Alternatively, max. can be set. If you select max., the maximum heating and cooling speeds specified in the Technical Data will be used.

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4. Press the OK softkey to accept the settings. The program view appears.

5. Press the >> softkey. Press the Save softkey. The changes are saved.

6. Press the Exit softkey to exit the editor.

6.3.3 Create gradient step

You can use a gradient step to optimize the specificity and yield in PCR reactions. A temperature gradient increasing from the left to the right side of the block is generated during the holding time. The temperature control rates before and after the gradient step are constant over the entire thermoblock.

Details about the maximum gradient spread can be found in the product description (Tab. on p. 19).

The gradient function is only available to the following devices:

• Mastercycler nexus gradient

• Mastercycler nexus gradient eco

•Mastercycler nexus GSX1

•Mastercycler nexus GSX1e

• Mastercycler nexus flat

• Mastercycler nexus flat eco

• Mastercycler nexus GX2 (Gradient function only for thermoblock with 64 wells)

• Mastercycler nexus GX2e (Gradient function only for thermoblock with 64 wells)

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Proceed as follows to define a gradient step in a PCR program:

1. Mark the temperature control step in which you would like to define the gradient.

2. Press the Options softkey. The options for the selected temperature control step are displayed.

3. Check the Gradient checkbox.

4. Define the gradient temperatures. The gradient temperatures can be defined in two ways:

• By entering limit temperatures

– from: lower limit temperature (left side of block) – to: upper limit temperature (right side of block)

• By entering the center temperature and the temperature span

– Center: center temperature (center of block) – Span: temperature span (gradient range)

5. Optional: press the Edit Grad. softkey to display the resulting temperatures in the block columns.

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Well type Select the tube type:

• 0.2 ml (12 columns): standard PCR tubes and 96-well plates

• 0.5 ml (11 columns): 0.5 mL PCR tubes

• 0.2 ml GSX1 (12 columns): 0.2 mL PCR tubes

• 0.2 ml GX2 (8 columns): 0.2 mL PCR tubes

• 0.5 ml GX2 (7 columns): 0.5 mL PCR tubes

Gradient Gradient temperature

6. Press the OK softkey to accept the settings and close the window. The gradient step is symbolized in the program editor by three horizontal lines.

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6.3.4 Deleting program steps

1. Mark the desired program step with the arrow keys. To delete all program steps, press the ClearAll softkey.

2. Press the del key.

3. Press the Save softkey to save the change.

Press the Exit softkey to exit the editor.

6.3.5 Exporting a program as a PDF or text file

You can export a program to an external storage medium as a file for archiving.

1. Connect a storage medium (see p. 40).

2. Press the >> softkey.

3. Press the Export softkey.

4. Select the file format (text or PDF). Press the OK softkey. The program is saved to the external storage medium as a file.

6.3.6 Saving a program and exiting the editor

1. Press the >> softkey.

2. Press the Save softkey. The program is saved.

3. Press the Exit softkey.

The navigation tree is displayed. You can now start the program (see Starting a program on p. 61).

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6.4 Program templates

The following table provides an overview of the program templates. The program templates can be used to create new programs.

Program template

none Empty template with standard header settings. 2-step PCR Standard PCR program with two temperatures per cycle and 30 cycles, one hold step

3-step PCR Standard PCR program with three temperatures per cycle and 30 cycles, one hold

Cycle sequencing Standard program for cycle sequencing with ramp rates of 1 °C/s. Fast PCR 3-step PCR with short hold times and temperature mode fast Gradient PCR PCR program with a temperature gradient in the annealing step of each cycle.

Hot start PCR manual

Hot start PCR 10 min enzyme activation at 95 °C and 3-step PCR. Incubation IsoTherm incubation. Large volume PCR 3-step PCR in safe temperature mode. Long range PCR 3-step PCR with 10 min elongation and a time interval of +10 s per cycle. Low volume PCR 3-step PCR in fast temperature mode. Mastercycler 533x 3-step PCR with simulation of the temperature control behavior of the

Nested cycles Program in which 3 cycles, with 3 temperatures each, are summarized in a

Reduced Ramping 3-step PCR with ramp rates of 1 °C/s.

Reverse Transcription

RT-PCR Program for 1-step RT-PCR with series incubation for reverse transcription. Touchdown PCR PCR program with falling annealing temperature. During the first 16 cycles, the

Description

at the end.

step at the end.

PCR program with thermoblock preheating at 95 °C. Start the following PCR run using the start key.

Mastercycler gradient 5331.

9-StepCycle, e.g., for TAIL PCR.

Incubation for reverse transcription and enzyme activation.

annealing temperature will be decreased by 1 °C per cycle.

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7PCR run

7.1 Loading the thermoblock

7.1.1 Selecting the sample tubes

WARNING! Biohazard due to unsuitable reaction vessels, plates and lids.

Unsuitable reaction vessels, plates and lids will become damaged in the cycler, This will release sample material.

 Only reaction vessels, plates and lids that meet the requirements described in the

operating manual may be used.

7.1.1.1 Approved sample tubes for devices with a 96-well thermoblock

The thermoblock can be loaded with the following sample tubes:

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• 0.1 mL PCR tubes

• 0.2 mL PCR tubes

• 0.5 mL PCR tubes (only for aluminum thermoblock)

• PCR tube strips (0.1 mL or 0.2 mL)

• 96-well PCR plates

• segments of separable 96-well PCR plates

7.1.1.2 Approved sample tubes for devices with a 64+32-well thermoblock

The thermoblock can be loaded with the following sample tubes:

• 0.1 mL PCR tubes

• 0.2 mL PCR tubes

• 0.5 mL PCR tubes

• PCR tube strips (0.1 mL or 0.2 mL)

• 64 and 32-well PCR plates

• segments of separable 96-well PCR plates

7.1.1.3 Approved sample tubes for devices with a flat thermoblock

Up to 4 slides

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7.1.1.4 Compatible PCR plate types

The following PCR plate types are compatible. A selection of the PCR micro test tubes and lids can be found separately (see Consumables on p. 105).

Semi-skirted PCR plate Skirted PCR plate Non-skirted/unskirted PCR plate

PCR plate with surrounding half-edge.

PCR plate with a surrounding edge.

7.1.1.5 Requirements

The sample tubes must meet the following requirements:

• Temperature resistance at least 120°C

• Exact fit in the thermoblock

7.1.1.6 Maximum volumes

The possible sample volumes can vary depending on the tubes used.

For devices with an aluminum thermoblock

• PCR plates and 0.1 mL or 0.2 mL PCR tubes: max. 70 L

• 0.5 mL PCR tubes: max. 100 L

For devices with a silver thermoblock

• PCR plates and 0.1 mL or 0.2 mL PCR tubes: max. 100 L

7.1.2 Inserting the sample tubes

PCR plate without any surrounding edge.

WARNING! Biohazard as a result of sample material directly in the thermoblock.

 Do not directly fill sample material into the thermoblock.  Only reaction vessels, plates and lids that meet the requirements described in the

operating manual may be used.

WARNING! Biohazard due to temperature control when heated lid is open.

If the heated lid is open, the lids of the reaction vessels may come off during temperature control. This will release sample material.

 Tempering may only be carried out when the heated lid is closed.

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Observe the following notes when loading the thermoblock with tubes

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 Place the tubes or strips into the center of the thermoblock and ensure that they are symmetrically

positioned. This is applicable for individual tubes, ube strips and segments of separable PCR plates.

 Load the 96-well thermoblock with at least 5 tubes. If you have fewer reaction batches, also add empty

tubes so the thermoblock is loaded with at least 5 tubes.

 Load the 64+32-well thermoblock with at least 2 tubes. If you have fewer reaction batches, also add

empty tubes so the thermoblock is loaded with at least 2 tubes.

Very soft PCR tubes may become deformed at high temperatures. To prevent deformations:

• Increase the number of empty sample tubes in the thermoblock.

• Reduce the temperature of the heated lid (see p. 52).

• Use original Eppendorf PCR consumables. Eppendorf PCR consumables are optimally suited for the device.

7.2 Starting a program

If the PIN function is activated, you can only start programs that are saved below your user node (see p. 67).

Prerequisites

• Thermoblock loaded (see p. 59)

• Heated lid closed (see p. 34)

1. Mark the program in the navigation tree with the arrow keys or open it in the editor.

2. Press the start key. If multiple cyclers are available, the Cycler Selection window appears.

3. Mark the desired cycler.

4. Press the OK softkey.

The program is started and the status view appears.

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7.2.1 Status view

The status view is automatically displayed immediately after a program is started. It shows the progress of and information on a running program. The currently active step is displayed as a flashing line.

1 User, program name and cycler

2 Remaining run time

3 Start and end time of the program

4 Block and heated lid temperature

5 Device status

6Cycle number

7 Block target temperature

8 Remaining holding time

9 Information on the current program step

10 Specification of the selected cycler

If you have activated the TSP function in the program header (see p. 51), the heated lid is first brought to the correct temperature before the program run starts. This process is indicated in the status view by the message TSP heated lid.

You can exit the status view and return to the navigation tree at any time by pressing the Exit softkey, e.g. to edit another program or start a program on a different cycler. Use the left/right arrow key to access the status view of other connected cyclers. The program that was already started is not interrupted as a result.

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7.2.1.1 Displaying the status view

Proceed as follows:

1. Mark the cycler in the navigation tree.

2. Press the Status softkey.

The status of the cycler is shown with an icon:

• Idle

• Running

• Paused

• Fault

7.2.2 Common status view for devices with a thermoblock with 64+32 wells

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The common status view shows the progress and most important information on the running programs of both thermoblocks.

You can display the status views of the individual programs via the Block 64 and Block 32 softkeys.

The status views of the individual programs can be accessed via the up/down arrow keys.

Use the right/left arrow keys to call up the common status views of other connected cyclers.

To open the common status view, proceed as follows:

1. Mark the cycler in the navigation tree.

2. Press the Overview softkey.

The common status view can also be opened via the Overview softkey in the status view of the respective program.

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7.3 Interrupting or stopping a program

7.3.1 Interrupting a program

1. Open status view (see Starting a program on p. 61).

2. Press the stop key.

Paused is displayed in the status view.

7.3.2 Resuming a program

1. If the heated lid is open: close the heated lid.

2. Press the Resume softkey.

running appears in the status view, and the program run continues.

7.3.3 Stopping a program

 Press the Abort softkey.

The Idle status is displayed. The program has been aborted and cannot be continued.

A hold step at the end of a PCR program is completed via the enter key. In the common status view, you can end the PCR program out of a hold step via the End 64 or

End 32 softkeys.

7.4 Displaying the most recently run programs

The device can display a list of the 5 most recently run programs.

If the PIN function is switched on and a user is logged in, the Recently Used node is positioned in the user node.

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If the PIN function is switched off or the administrator is logged in, the Recently Used node is located below the Eppendorf node.

If no user is logged in, the Recently Used node is not available.

The following functions are available:

Key: start Start the last run program. Softkey: Prop. Display the properties of the last run program. Softkey: Edit Edit the last run program. Softkey: Copy Copy the last run program. Softkey: Export Export the last run program.

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8 System management

8.1 Administrator functions

The Mastercycler nexus software differentiates between default users and the administrator. All users and the administrator need a PIN to log into the device. Users can only make changes to their own accounts. The administrator has write access to all areas. If you deactivate the PIN function, all users automatically have administrator rights and can make changes to all user accounts (see p. 70).

The access rights differ as follows:

Procedure Default users Administrator

Copying programs From each user node to own user

node

Creating, deleting, editing and starting programs

Managing user accounts and generating PINs

Making system settings None All Performing the self test,

verification and adjustment Performing backups, restores and

software synchronizations

Only programs below their own user node

Only change own user name and PIN

Self test and verification only Self test, verification and

Only backups All

From each user node to each user node

All programs

Create, change, delete user accounts. Change the PIN for each user.

adjustment

8.2 Managing user accounts

• A user name can only be assigned once.

• The administrator uses the set user name _admin.

8.2.1 Creating a user account

Prerequisites If the PIN function is activated: logged in as an administrator

You can set up a user account for each user:

1. In the navigation tree, mark the Eppendorf node (at the top).

2. Press the NewUser softkey. The New User window appears.

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3. Enter the name and PIN of the new user. Re-enter the PIN in the Confirmation: field.

4. Optionally enter the user's e-mail address in the E-mail address: field. To activate e-mail notifications, check the Enable e-mail notification checkbox.

5. Press the OK softkey. The new user account is created. A new user node with this user name is created in the navigation tree.

The user can now log in with his PIN.

8.2.2 Editing a user account

If you have the appropriate user or administrator rights, you can change the following data of existing user accounts:

•PIN

• E-mail address

• Comment

1. Mark the user node in the navigation tree. Press the Prop. softkey. The User Properties window appears.

2. Change the settings for the user account. Press the OK softkey.

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8.2.3 Deleting a user account

You must be logged in as an administrator to be able to delete user accounts.

Deleting a user account will delete the respective user node including all folders and programs it contains. Deleting a user account is a permanent change and cannot be undone.

1. Mark the user node. Press the del key. A query appears whether you really want to delete the user account.

2. Press the OK softkey. The user account is deleted.

8.2.4 Changing the administrator PIN

If you are logged on as an administrator, you can change the administrator PIN at any time.

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NOTICE! Data loss due to unauthorized use of the administrator password.

The administrator password protects the device software from unwanted access.

 Make a note of the administrator password.  Keep the administrator password at a secure location.  Only provide the administrator password to individuals who work with the system

configuration.

 Please contact Eppendorf AG if you have any problems with the administrator password.

1. Switch on the Mastercycler nexus and log in as the administrator.

2. Mark the System node. Press the Prop. softkey. The System Properties window appears.

3. Enter the new administrator PIN using the numeric keys. If you have entered the PIN incorrectly, delete it with the del key and re-enter the PIN.

4. Re-enter the new PIN in the Confirmation: field to confirm.

5. Press the OK softkey. The new administrator PIN is immediately valid.

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8.3 System settings

 To change the system settings, open the System node.

Beeper: Activate or deactivate

signal tones

Country Settings: Change

country settings

Date + Time: Set the date and

time

Log File: Export log file

Network Settings: Change

network settings

PIN: Activate or deactivate PIN

Power Settings: Configure the

automatic power save mode

 Activate or deactivate the Beeper node.

If the function is activated, the signal tones sound when keys are pressed and when error messages are generated. If the function is deactivated, the signal tones only sound when error messages are generated.

The country settings are identified by the international dialing code (e.g. "001" for the U.S.). The language as well as the date and time format (12 or 24 hour format) are defined in the country settings.

1. Mark the Country Settings node. Press the Set softkey.

2. Select the desired settings. Press the OK softkey. The device restarts.

1. Mark the Date + Time node. Press the Set softkey.

2. Set the date and time. Press the OK softkey.

 Mark the Log File node. Press the Export softkey. The log file is

written to the storage medium.

 Optional: to display the log file, mark the Log File node. Press the

Show softkey.

Set up a network connection (see Network connection on p. 79).

 Activate the PIN function (user management) with the Select softkey;

deactivate it with the Unselect softkey.

The device restarts. Use the Power Settings node to define whether and when the device

automatically enters the power save mode.

1. Mark the Power Settings node. Press the Set softkey.

2. To activate the automatic power save mode, check the Enable

automatic standby checkbox.

3. Set the time after which the device should automatically switch to power save mode in the Enter standby mode after (hh:mm) field. Press the OK softkey.

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Schedule Settings: Make

schedule settings

Service Intervals: Setting

intervals for temperature verification and self-test

Use the Schedule Settings node to configure the schedule view and selection options.

 Mark the Schedule Settings node. Press the Set softkey.

•Check the Enable Screensaver checkbox to use the schedule as a screensaver. Set the time after which the screensaver should be activated in the Wait [s] field.

• To select the weekdays that should be displayed in the schedule, check the corresponding boxes for In schedule day view the following

weekdays are displayed.

• To select the device types that should be displayed in the schedule, check the corresponding boxes for In the schedule editor the following

cyclers are enabled.

 Press the OK softkey.

You can determine intervals for a regular temperature verification or self-test via the Service Intervals node.

 Mark the Service Intervals node. Press the Verification or Self-test

softkey.You can set the intervals In the following display.

• Specification of months (1 – max. 24)

• Specification of programs run (1 – max. 2000)

The following details are shown on the display for each cycler:

• The programs run since the last verification or self-test

• The date of the next check

You can also find this information under the Block ((see p. 74)) cycler system functions. You are informed via an info message before the defined intervals expire. The info message contains details about the remaining days or program runs until the interval expires. If email dispatch is activated ((see p. 81)), the administrator receives a corresponding message. When the intervals expire, a temperature verification or self-test must be carried out. Alternatively, you can deactivate the interval setting.

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System Configuration: Set

device-dependent entries for ramp and gradient

User Log File: Display or export

user data

Making changes under System Configuration is only necessary if you operate different variants of master and eco devices together.

 Mark the System Configuration node. Press the Set softkey.  Set entries for the ramp.

• For devices with an aluminum thermoblock, select Mastercycler nexus. Adjustable value range: 0.1 - 1.5 °C/s or max..

• For devices with a silver thermoblock, select Mastercycler nexus SX1. Adjustable value range: 0.1 - 3.0 °C/s or max..

 Set entries for the gradient spread.

• Select the setting 20°C for devices with the 96-well thermoblock, which have a gradient function.If the setting Off is selected, no gradients can be programmed and the corresponding programs cannot be started.

• Select the setting 12°C for devices with the 64+32-well thermoblock, which have a gradient function. If the setting Off is selected, no gradients can be programmed and the corresponding programs cannot be started.

• Use the Show well types checkboxes to define which well types are displayed under Edit Grad. (see p. 55).

Use the User Log File node to export or display all performed actions as a log file. The following data can be displayed or exported:

• Login and logout procedures

• Changes to and interventions in running programs

• Update of the software version

• Creating and deactivating service intervals

 Mark the User Log File node. Press the Show softkey.

The next window enables you to print or export the log file.

 Press the Export softkey to export the log file.  Press the Print softkey to print the log file.

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8.4 Cycler functions

The cycler nodes enable you to view and adjust the status of the thermoblock and the heated lid and access the protocols of the last 20 programs.

The softkeys have the following functions:

Prop. • Change the name of the cycler node.

The name must not contain any special characters.

• Display the installed firmware version

• Display the last logged-in user

• Display the last run program

Incubate Display and change the current temperature of the heated lid and the thermoblock.

• Current temperature: Display the current temperature

• New temperature: Set the target temperature

• Heat/Incubate: Control the temperature of the heated lid/thermoblock

• Keep settings after power on: Automatically keep the current temperature control setting when the cycler is idle. This setting will remain unchanged even after a cycler restart. It can only be changed by an administrator.

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Status • Display the cycler operating status

• Display the temperatures of the thermoblock and the heated lid

• Display the remaining run time for the program

• Stop the program

Protocol Protocols of the last 20 program runs:

 Select the protocol via the arrow keys.

• Print softkey: print the protocol

• Export softkey: copy the protocol to a storage medium

• Show softkey: display the protocol

The following applies to devices with a thermoblock with 64+32 wells: The Cycle functions comprise the Properties, Overview, Status 64 and Status 32 softkeys. The Incubate and Protocols softkeys are located under the subnodes Block 64 or Block 32.

8.4.1 Cycler system functions

The System node contains the cycler system level with the following softkeys.

Info • Display the device name

• Display the date of the last verification

• Display the programs run (since the last verification)

• Display the date of the last self-test

• Display the date of the next self-test

• Display the programs run (since the last self-test)

• Display the date of the last adjustment

Details about the next verification or self-test are only given if the settings have been made under Service intervals ((see p. 70)).

Restart Entry for maximum duration of interruption of voltage supply (mm:ss) after which a

running program should be automatically restarted. The program is not restarted after a longer interruption.

Sensors Display current sensor temperatures for the control loops of the thermoblock and the

heated lid.

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Verification Verify temperature accuracy and temperature homogeneity of the thermoblock with

the Eppendorf Temperature Verification System.

Adjustment Adjust temperature accuracy and temperature homogeneity of the thermoblock with

the Eppendorf Temperature Verification System. Can only be done by the administrator.

The Eppendorf Temperature Verification System is required for the Verification and

Adjustment functions (see Accessories on p. 105). For information on how to use this system,

refer to the corresponding operating manual.

8.4.2 Self-test

The self-test function allows you to perform a quick check regarding the following attributes of the thermoblock without requiring an external measurement system:

• Heating and cooling rates

• Proper functioning of the thermoregulation circuits

• Temperature homogeneity in each of the three block zones and across the entire block

After a successful self-test, a certificate can be generated in PDF format.

A separately available self-test USB key is required for performing the self-test (see Accessories on p. 105). Please refer to the documentation of the self-test USB key for a detailed description of the self-test function.

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8.5 Managing and backing up data

8.5.1 Backing up data

The softkeys in the window above show the possibilities the administrator has to transfer data. Default users can only perform backups here.

NOTICE! Loss of data after creation and restoration of a data backup.

 Creating a data backup on a USB storage medium: Before the backup is created, the

\eppendorf folder on the USB storage medium is completely erased.

 Restoring a data backup: Before the data backup is restored, already existing user nodes,

folders and programs on the cycler are erased. Only the data transferred from the storage medium will be available after the restore.

1. Connect a storage medium. The node for the storage medium appears in the navigation tree.

2. Mark the node for the storage medium.

Backup Save user nodes, folders and programs to an external storage medium. Restore Administrator only: Restore the user nodes, folders and programs saved on the storage

medium during a backup.

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8.5.2 Exporting and importing programs

Export

1. In the navigation tree, mark the program.

2. Connect a storage medium.

3. Press the Export softkey. The program is copied to the storage medium.

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You can transfer the exported programs to another device.

Import

1. Connect the storage medium with the exported programs.

2. Open the node for the storage medium and mark the folder or program you would like to import.

3. Press the Copy softkey.

4. Mark the user node or folder at the target location. Press the Paste softkey.

8.6 Transferring programs from an older Mastercycler model

PCR programs from older Mastercycler models can easily be transferred to the Mastercycler nexus without optimization of the temperatures and holding times.

 Enter the program into the Mastercycler nexus editor:

Gradient protocol on the Mastercycler gradient and analog setting on the Mastercycler nexus gradient

 Enter the program into the Mastercycler nexus editor:

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Example

1 T = 94.0° 0:02:00 2 T = 94.0° 0:00:15 3 T = 60.0° 0:00:15 +0.0° +0:00 R = 3.0°/s +0:0°/s G =10.0°

4 T = 72.0° 0:00:30 5 GOTO 2 REP 29 6 T = 72.0° 0:02:00 7 HOLD 4.0° ENTER

For the Mastercycler nexus you need to enter the gradient spreads. A gradient setting of G = 10.0° for the Mastercycler gradient corresponds to a gradient spread of 20.0°C for the Mastercycler nexus gradient. Enter this value in the Span field.

 Make the desired settings in the header (see Editing header settings on p. 52).

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Setting from the Mastercycler 533x program Corresponding setting in the program header

LID 105°C Lidtemp.

WAIT

AUTO

CNTRL

Block temperature control behavior Check the Simulate Mastercycler gradient checkbox.



Press the OK softkey. The editor is displayed.

TSP heated lid

switch off lid at low blocktemperature

Block = Temp. mode fast Tube = Temp. mode standard or safe

Select the Temp. mode setting based on the reaction volume or the sample properties (see p. 52). The temperature control mode for 0.5 mL standard tubes (not thin-walled) is no longer supported on the Mastercycler nexus.

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 Press the >> softkey. Press the Save softkey.

You can start the program without renewed optimization of the parameters.

8.7 Network connection

You can connect the Mastercycler nexus to an Ethernet network to send e-mails and log files. To set up the network connection, you will need the following information from your network administrator:

• IP address, subnet mask and gateway address for the Mastercycler nexus (specified by the network administrator). Alternatively, you can assign the IP address automatically via DHCP.

• IP address of the primary DNS server You can optionally enter the IP address of a backup DNS server. Alternatively, you can assign the IP address automatically via DHCP.

• For sending e-mails:

– E-mail address of the sender with the user name and password to log into the SMTP server (if

required)

– Name or address and port number of the SMTP server

• For sending Syslog messages:

– Name or address and port number of the syslog server

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8.7.1 Setting up a network connection

Prerequisites

• Ethernet cable (RJ45, Cat.5), not included in the delivery package

• Logged in as an administrator (see p. 37)

Proceed as follows:

1. Select the System > Network Settings node.

2. Press the Connection softkey. The Network Connection Settings window appears.

3. To assign the IP address automatically via DHCP, check the Obtain IP settings automatically via DHCP checkbox. Alternatively, enter the IP address, subnet mask and standard gateway as specified by your network administrator.

4. To assign the IP address of the DNS server via DHCP, check the Obtain DNS settings automatically via

DHCP checkbox. Alternatively, enter the IP addresses of the DNS servers as specified by your network

administrator.

5. Insert the Ethernet cable into the Ethernet port on the rear of the device and connect it to an Ethernet port of the Ethernet network.

6. Press the Set softkey to accept the settings.

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Press the Test softkey to test the connection to the default gateway.

If your network administrator needs the MAC address of the Mastercycler nexus, press the

MAC Info softkey.

8.7.2 Setting up e-mail notifications

Prerequisites

• Network connection has been set up (see p. 80)

• Logged in as an administrator (see p. 37)

Proceed as follows:

1. Select the System > Network Settings node.

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2. Press the E-mail softkey. The E-mail Settings window appears.

3. Enter the settings as specified by the network administrator.

If the SMTP server requires identification, check the enable SMTP login checkbox. Enter user name and password.

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4. Select the data you would like to send and their file type.

• Cycler run protocol: Protocol of the program run

• Error log file: Log file with errors that occurred during the program run

• Self test certificate: Self test certificate of a successful self test

Press the Test softkey to send a test e-mail.

5. Press the OK softkey to accept the settings.

8.7.3 Setting up syslog messages

Prerequisites

• Network connection has been set up (see p. 80)

• Logged in as an administrator (see p. 37)

Proceed as follows:

1. Select the System > Network Settings node.

2. Press the Syslog softkey. The Syslog Settings window appears.

3. To activate log files on the syslog server, check the Enable logging to Syslog server checkbox. Enter the server address and the port.

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4. Select the information that you would like to create a protocol for.

• Cycler run protocol entries: Protocol of the program run

• Error log file entries: Errors that occurred during the program run

• User log file entries: Log of user actions (e.g. logging in, logging out, editing program)

Press the Test to send a syslog test message.

5. Press the OK softkey to accept the settings.

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9 Quick start

9.1 Login

Quick start

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enter

1 2

abc3def

ghi5jkl6mno

pqrs8tuv9wxyz

del

1. Open the list.

2. Select the user.

3. Confirm your selection.

4. Switch to the PIN: field.

5. Enter and confirm the PIN.

enter

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9.2 Creating folders and programs

1. Select the user or folder.

2. Press the New Folder or New softkey.

9.3 Copying folders and programs

1 2

abc3def

ghi5jkl6mno

pqrs8tuv9wxyz

del

enter

3. Enter the name and comment and confirm.

1. Select the folder or program.

2. Press the Copy softkey.

3. Confirm the prompt.

4. Mark the target folder or user.

5. Press the Paste softkey.

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9.4 Deleting folders and programs

Mastercycler

1. Mark the folder or program.

Quick start

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9.5 Editing programs

del

enter

2. Press the del key.

3. Press the enter key.

1. Select the program.

2. Open the program editor.

3. Press the Header softkey.

enter

6. Set the temperature control.

7. Confirm your entries.

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1 2

abc3def

ghi5jkl6mno

pqrs8tuv9wxyz

del

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8. Select the program step.

9. Press the Insert softkey.

10. Enter the temperatures, holding times and number of cycles.

11. Select the program step.

12. Press the Options softkey.

1 2

abc3def

ghi5jkl6mno

pqrs8tuv9wxyz

del

enter

13. Set the gradient, increment and ramp.

14. Confirm your entries.

15. Press the >> softkey.

16. Press the Save softkey.

17. Press the Exit softkey.

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9.6 Stopping and starting programs

start

Quick start

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English (EN)

1. Mark the program.

2. Insert the sample tubes.

3. Close the heated lid.

4. Start the program.

5. If several cyclers are connected: highlight the cycler.

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enter

6. Confirm input.

7. The following options are available in the status view:

• Stop the program: press the Stop softkey.

• Abort the program: press the Abort softkey.

• Resume the program: press the

Resume softkey.

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10 Maintenance

10.1 Cleaning

CAUTION! Risk of burns on thermoblock, heated lid and reaction vessels.

 Wait until the temperature of the thermoblock, heated lid and reaction vessels is below 30

°C.

 Then the heated lid may be opened.

NOTICE! Damage from the use of aggressive chemicals.

 Do not use any aggressive chemicals on the device or its accessories, such as strong and

weak bases, strong acids, acetone, formaldehyde, halogenated hydrocarbons or phenol.

 If the device has been contaminated by aggressive chemicals, clean it immediately using a

mild cleaning agent.

Maintenance

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DANGER! Electric shock as a result of penetration of liquid.

 Switch off the device and disconnect the power plug before starting cleaning or

disinfection work.

 Do not allow any liquids to penetrate the inside of the housing.  Do not spray clean/spray disinfect the housing.  Only plug the device back in if it is completely dry, both inside and outside.

DANGER! Electric shock.

 Switch off the device and disconnect the power plug before starting maintenance or

cleaning work.

10.1.1 Cleaning the housing

 Clean the surfaces of the Mastercycler nexus with a damp, lint-free cloth.  If necessary, use a neutral lab cleaner.

Instructions on disinfecting and decontaminating the device can be found separately (see Disinfection/ decontamination on p. 92).

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Maintenance

Mastercycler English (EN)

nexus

10.1.2 Cleaning the heated lid and the thermoblock

1. Open the heated lid.

2. Remove contamination on the thermoblock and the base of the heated lid. Use a damp, lint-free cloth. If necessary, use a neutral lab cleaner.

3. Check to see if there is lettering residue from the tube lids on the heated lid. Remove the residue using ethanol or isopropanol.

Keep the thermoblock bores free of dust and lint. Even small deposits affect the heat transfer between the thermoblock and vessels.

10.2 Disinfection/decontamination

NOTICE! Damage from UV and other high-energy radiation.

 Do not use UV, beta, gamma, or any other high-energy radiation for disinfecting.  Avoid storage in areas with strong UV radiation

Required equipment

• Alcohol (ethanol, isopropanol) or disinfectants containing alcohol

Proceed as follows:

1. Choose the disinfection method which corresponds to the legal regulations and guidelines in place for your range of application.

10.3 Decontamination before shipment

If you are shipping the device to the authorized Technical Service for repairs or to your authorized dealer for disposal please note the following:

WARNING! Risk to health from contaminated device

1. Follow the instructions in the decontamination certificate. It is available as a PDF file on our webpage (www.eppendorf.com/decontamination

2. Decontaminate all the parts you would like to dispatch.

3. Include the fully completed decontamination certificate in the package.

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Troubleshooting

Mastercycler

nexus

English (EN)

11 Troubleshooting

11.1 General errors

Technical faults may be triggered by faults such as a power failure or power fluctuations. Therefore, it is usually sufficient to briefly switch off the device and switch it back on after approx. 10 seconds. Check the cable connections if necessary. If the error occurs again, please write down the error code and contact Eppendorf Service.

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Trou bleshooting

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English (EN)

Page 95

12 Transport, storage and disposal

12.1 Packing

CAUTION! Risk of injury due to lifting and carrying heavy loads

The device is heavy. Lifting and carrying the device can lead to back injuries.

 Transport and lift the device with an adequate number of helpers only.  Use a transport aid to transport the device.

NOTICE! Damage as a result of incorrect packing.

Eppendorf AG is not liable for damage caused by improper packing.

 The device may only be stored and transported in its original packaging.

WARNING! Damage to health due to contaminated device and accessories.

 Decontaminate the device and the accessories before storage and shipping.

Transport, storage and disposal

Mastercycler

nexus

English (EN)

Use the supplied packing material when packing the device for transport or storage. If you do not have this anymore or if it is damaged, contact your Eppendorf office.

Prepare the device as follows prior to packing:

1. Pay attention to the decontamination notes (see Decontamination before shipment on p. 92).

2. Let the device sit for 30 minutes and make sure there is no condensate in the thermoblock.

3. Load the thermoblock with an empty PCR plate.

4. Close the heated lid.

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Transport, storage and disposal

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nexus

12.2 Disposal

In case the product is to be disposed of, the relevant legal regulations are to be observed.

Information on the disposal of electrical and electronic devices in the European Community:

Within the European Community, the disposal of electrical devices is regulated by national regulations based on EU Directive 2002/96/EC pertaining to waste electrical and electronic equipment (WEEE).

According to these regulations, any devices supplied after August 13, 2005, in the business-to-business sphere, to which this product is assigned, may no longer be disposed of in municipal or domestic waste. To document this, they have been marked with the following identification:

Because disposal regulations may differ from one country to another within the EU, please contact your supplier if necessary.

Page 97

13 Technical data

13.1 Power supply

Voltage 100 V – 130 V, ±10 %

200 V – 240 V, ±10 % Frequency 50 Hz – 60 Hz Power consumption

(devices with aluminum thermoblock) Power consumption

(devices with silver thermoblock) Overvoltage category II (IEC 61010-1) Degree of pollution 2 Protection class 1

max. 700 W

max. 540 W

Technical data

Mastercycler

English (EN)

nexus

13.2 Weight/dimensions

Dimensions Width: 25.0 cm (9.8 inch)

Depth: 41.0 cm (16.1 inch)

Height: 32.0 cm (12.6 inch)

Height with heated lid open: 44.5 cm (17.5 inch) Dimensions

(devices with a thermoblock with 64+32 wells)

Weight (Master variant)

Weight (eco variant)

Width: 25.0 cm (9.8 inch)

Depth: 41.0 cm (16.1 inch)

Height: 33.0 cm (13.0 inch)

Height with heated lid open: 44.5 cm (17.5 inch)

11.0 kg (24.3 lb)

10.5 kg (23.2 lb)

13.3 Ambient conditions

General operation 15 °C to 35 °C

up to 70 % rel. humidity up to 2 000 m NN (approx. 80 kPa)

Storage conditions –20 °C to 70 °C

up to 85 % rel. humidity

Page 98

Technical data

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nexus

13.4 Application parameters

Mastercycler nexus gradient, Mastercycler nexus gradient eco

Sample capacity Universal block, aluminum

96 × 0.1 mL or 0.2 mL PCR tubes 71 × 0.5 mL PCR tubes one 96-well PCR plate (unskirted, semi-skirted, skirted;

standard and low-profile) Block temperature control range 4 °C to 99 °C Ramp rate

(measured at the block) Block temperature homogeneity

(with the gradient function switched off) at 35°C

at 90°C Control accuracy

(with the gradient function switched off) Gradient range max. 20°C Gradient temperature control range 30 °C to 99 °C Heated lid temperature control range 37 °C to 110 °C

max. 3°C/s

≤ ±0.3°C

≤ ±0.4 °C

±0.2°C

Mastercycler nexus, Mastercycler nexus eco

Sample capacity Universal block, aluminum

96 × 0.1 mL or 0.2 mL PCR tubes

71 × 0.5 mL PCR tubes

one 96-well PCR plate (unskirted, semi-skirted, skirted;

standard and low-profile) Block temperature control range 4 °C to 99 °C Ramp rate

(measured at the block) Block temperature homogeneity at 35°C

at 90°C Control accuracy ±0.2°C Gradient range – Gradient temperature control range – Heated lid temperature control range 37 °C to 110 °C

max. 3°C/s

≤ ±0.3°C

≤ ±0.4 °C

Page 99

Mastercycler nexus GSX1, Mastercycler nexus GSX1e

Sample capacity Silver block

96 × 0.1 mL or 0.2 mL PCR tubes

one 96-well PCR plate (unskirted, semi-skirted, skirted;

standard and low-profile) Block temperature control range 4 °C to 99 °C Ramp rate

max. 5°C/s (measured at the block)

Block temperature homogeneity (with the gradient function switched off)

at 35°C at 90°C

Control accuracy

≤ ±0.3°C

≤ ±0.4 °C

±0.2°C (with the gradient function switched off)

Gradient range max. 20°C Gradient temperature control range 30 °C to 99 °C Heated lid temperature control range 37 °C to 110 °C

Technical data

Mastercycler

English (EN)

nexus

Mastercycler nexus SX1, Mastercycler nexus SX1e

Sample capacity Silver block

96 × 0.1 mL or 0.2 mL PCR tubes

one 96-well PCR plate (unskirted, semi-skirted, skirted;

standard and low-profile) Block temperature control range 4 °C to 99 °C Ramp rate

max. 5°C/s (measured at the block)

Block temperature homogeneity at 35°C

at 90°C

≤ ±0.3°C

≤ ±0.4 °C Control accuracy ±0.2°C Gradient range – Gradient temperature control range – Heated lid temperature control range 37 °C to 110 °C

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100

Technical data

Mastercycler

nexus

English (EN)

Mastercycler nexus flat, Mastercycler nexus flat eco

Sample capacity Flat block, aluminum

4 slides Block temperature control range 4 °C to 99 °C Ramp rate

max. 3°C/s (measured at the block)

Block temperature homogeneity (with the gradient function switched off)

at 35°C at 90°C

Control accuracy

≤ ±0.3°C

≤ ±0.4 °C

±0.2°C (with the gradient function switched off)

Gradient range max. 20°C Gradient temperature control range 30 °C to 99 °C Heated lid temperature control range 37 °C to 110 °C

Mastercycler nexus GX2, Mastercycler nexus GX2e

Sample capacity Universal block, aluminum

96 × 0.1 mL or 0.2 mL PCR tubes

64 × 0.5 mL PCR tubes

one 64-well PCR plate, one 32-well PCR plate (unskirted,

semi-skirted, skirted; standard and low-profile) Block temperature control range 4 °C to 99 °C Ramp rate

max. 3°C/s (measured at the block)

Block temperature homogeneity (with the gradient function switched off)

at 35°C at 90°C

Control accuracy

≤ ±0.3°C

≤ ±0.4 °C

±0.2°C (with the gradient function switched off)

Thermoblock (64 wells)

Gradient range max. 12°C Gradient temperature control range 30 °C to 99 °C Heated lid temperature control range 37 °C to 110 °C Thermoblock (32 wells) no gradient function Gradient range – Gradient temperature control range – Heated lid temperature control range 37 °C to 110 °C

Eppendorf Mastercycler nexus User Manual

Specifications and Main Features

Frequently Asked Questions

User Manual

1 Operating instructions

1.1 Using this manual

1.2 Danger symbols and danger levels

1.2.1 Danger symbols

1.2.2 Danger levels

1.3 Symbols used

1.4 Abbreviations used

1.5 Glossary

2 Product description

2.1 Main illustration

2.1.1 Master variants

2.1.2 Master variants with thermoblock (64+32 wells)

2.1.3 Master variant with flat thermoblock

2.1.4 Eco variants

2.1.5 Terminal block

2.1.6 Control panel

2.1.7 Number pad

2.1.8 Status lamp

2.2 Delivery package

2.3 Features

2.3.1 Features of the Mastercycler nexus

2.3.2 Control panel and ports

2.3.3 Consumable

2.3.4 Networking

2.3.5 Service

3Safety

3.1 Intended use

3.2 User profile

3.3 Information on product liability

3.4 Warnings for intended use

3.5 Warning signs on the device

4 Installation

4.1 Selecting the location

4.2 Installing the instrument

4.2.1 Connecting the device to the power supply

4.2.2 Attaching devices to each other

4.2.3 Separating devices

4.2.4 Using the USB ports

4.2.5 Connecting the eco device

4.3 Shut down

5 Operation

5.1 Initial steps

5.1.1 Using the flexlid heated lid

5.2 Starting the Mastercycler nexus

5.2.1 Defining the administrator PIN

5.2.2 Other steps

5.3 Logging in and out as a user

5.3.1 Logging in as a user

5.3.2 Changing users

5.3.3 Logging out as a user

5.4 Overview of software operation

5.4.1 Navigation tree overview

5.4.2 Navigating in the navigation tree

5.4.3 Using external storage media

5.4.4 Selecting export file formats

5.5 Managing folders and programs

5.5.1 Creating folders and programs

5.5.2 Copying folders and programs

5.5.3 Deleting folders and programs

5.6 Using the schedule

5.6.1 Editing a schedule entry

5.6.2 Displaying the schedule

5.7 Using the power save mode

6 Programming

6.1 Overview of the program editor

6.1.1 Opening the program editor

6.1.2 Structure of the program editor

6.2 Making general settings

6.2.1 Opening the header

6.2.2 Editing header settings

6.3 Editing programs

6.3.1 Inserting a program step

6.3.2 Editing parameters

6.3.3 Create gradient step

6.3.4 Deleting program steps

6.3.5 Exporting a program as a PDF or text file