Thermo Scientific Applied Biosystems SeqStudio Genetic... Manuel utilisateur

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

SeqStudio™Genetic Analyzer Instrument and

Software

USER GUIDE

for use with:

SeqStudio™Data Collection Software v1.2

SeqStudio™Plate Manager

SeqStudio™Remote Monitoring App

SAE Administrator Console v2.0

SeqStudio™Genetic Analyzer Cartridge (Cat. No. A33671)

SeqStudio™Genetic Analyzer Cartridge v2 (Cat. No. A41331)

Publication Number MAN0018646

Revision A.0

Manufacturer:

Life Technologies Holdings Pte Ltd |

Block 33 |

Marsiling Industrial Estate Road 3 |

#07-06, Singapore 739256

Products:

SeqStudio™Genetic Analyzer

SeqStudio™Data Collection Software

SeqStudio™Plate Manager (desktop)

SeqStudio™Genetic Analyzer Cartridge

SeqStudio™Genetic Analyzer Cartridge v2

Security, Auditing, and E‑signature (SAE) v2.0 module

Manufacturer: Life Technologies

Corporation | 200 Oyster Point Blvd |

South San Francisco, CA 94080 |

USA

Products:

SeqStudio™Remote Monitoring App

Manufacturer: Life Technologies

Corporation | 35 Wiggins Avenue |

Bedford, MA 01730

Products:

SeqStudio™Genetic Analyzer Cathode Buffer Container

The information in this guide is subject to change without notice.

DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, THERMO FISHER SCIENTIFIC INC. AND/OR ITS AFFILIATE(S) WILL NOT BE LIABLE FOR SPECIAL,

INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT,

INCLUDING YOUR USE OF IT.

Revision history: Pub. No. MAN0018646

Revision Date Description

A.0 4 November 2019 New user guide for SeqStudio™Data Collection Software v1.2. The v1.2

software includes options for HID kits. This user guide replaces

Pub. No. MAN0016138.

Important Licensing Information: These products may be covered by one or more Limited Use Label Licenses. By use of these products, you accept

the terms and conditions of all applicable Limited Use Label Licenses.

TRADEMARKS: All trademarks are the property of Thermo Fisher Scientiﬁc and its subsidiaries unless otherwise speciﬁed.

Contents

■CHAPTER 1 Product information ...................................... 12

Instrument overview ........................................................... 13

Parts of the instrument ......................................................... 14

Instrument status indicator ................................................. 15

SeqStudio™Genetic Analyzer consumables ........................................ 15

Cartridge ................................................................. 16

SeqStudio™Genetic Analyzer Cathode Buffer Container ........................ 20

Radio frequency identiﬁcation ............................................... 20

Important notice regarding use of consumables that exceed supported limits ..... 21

Software features .............................................................. 22

SeqStudio™Plate Manager overview .............................................. 24

Computer and operating system options ...................................... 25

Recommended browsers ................................................... 25

SeqStudio™Remote Monitoring App overview ...................................... 26

Network connection options ..................................................... 27

Network and password security requirements ..................................... 27

Network conﬁguration and security .......................................... 27

Password security ......................................................... 27

Experiment types .............................................................. 28

Data output .................................................................... 29

Secondary analysis software .................................................... 29

Workﬂow: Connect cloud-based platform or desktop ............................... 31

Workﬂow: instrument .......................................................... 32

■CHAPTER 2 Prepare the samples and the instrument .............. 33

Precautions for use ............................................................ 33

Power on the instrument ....................................................... 34

Sign out ....................................................................... 35

Parts of the home screen ....................................................... 36

SeqStudio

™

Genetic Analyzer Instrument and Software User Guide

Prepare the samples ........................................................... 37

Sample preparation guidelines .............................................. 37

Plate layout and loading guidelines .......................................... 38

Prepare the plate .......................................................... 38

Prepare the tubes .......................................................... 39

Prepare the instrument ......................................................... 39

Check the consumables status .............................................. 39

Load the CBC, the sample plate, and the cartridge ............................. 41

■CHAPTER 3 Use the instrument with the Connect cloud-

based platform ........................................................... 43

Understanding instrument and Connect cloud-based platform interaction ............. 43

"Connect" versus "link" .................................................... 43

First user who links is assigned administrator role ............................ 43

Local versus Connect cloud-based platform instrument proﬁles ................. 44

If you link when you

are

signed in to the instrument ............................ 44

If you link when you

are not

signed in to the instrument ......................... 45

Connect cloud-based platform instrument proﬁle roles and functions ............ 47

For more information on using the Connect cloud-based platform ............... 47

Connect cloud-based platform administrators for an instrument ..................... 48

Connect cloud-based platform administrator functions ......................... 48

Assign instrument administrator role to other users ........................... 48

Manage the users and administrators of your instrument ....................... 49

Disconnect individual users from an instrument ............................... 50

Link the instrument to your Connect cloud-based platform account .................. 51

Change your own Connect cloud-based platform instrument proﬁle PIN .............. 52

Set up email notiﬁcations from the instrument ..................................... 53

■CHAPTER 4 Use the instrument with the Security, Auditing,

and E‑signature (SAE) v2.0 module .................................... 55

Overview of the Security, Auditing, and E‑signature (SAE) v2.0 module components ..... 56

Conﬁguring the SAE module ..................................................... 57

Instrument functionality when SAE is enabled or disabled ........................... 58

Connect the instrument to an SAE server (administrator only) ....................... 58

Enable SAE on the instrument and specify the SAE server (administrator only) ......... 59

Disable SAE (administrator only) ................................................. 59

Specify audit reasons ........................................................... 61

E-signature requirements when you start a run .................................... 61

Sign a plate setup .............................................................. 63

View E-signature records for a plate setup ........................................ 63

Contents

SeqStudio

™

Genetic Analyzer Instrument and Software User Guide

Sign a dye calibration or an install run ............................................ 64

View E-signature records for a dye calibration or an install run ...................... 64

Signing in after automatic screen locking ......................................... 64

Use the instrument when the SAE server is ofﬂine ................................. 65

Auditing of imported plate setups ................................................ 65

SAE error messages and actions ................................................. 66

■CHAPTER 5 Create or modify a plate setup from the

Plate Manager ............................................................ 67

Overview of plate setup settings ................................................. 67

Set up a plate using default settings (Plate Manager) ............................... 69

Access the Plate Manager on the Connect cloud-based platform ................. 69

Access the Plate Manager on the desktop ..................................... 69

Create or open a plate setup PSM ﬁle ........................................ 69

Enter plate properties ...................................................... 70

Assign wells: Sample and run information .................................... 71

Keyboard shortcuts for the sample table ...................................... 72

Save a plate setup in the Plate Manager ...................................... 73

Additional plate settings (Plate Manager) ......................................... 74

Specify replicate injections ................................................. 74

Edit analysis settings ....................................................... 75

Modify the default ﬁle name convention ....................................... 75

Hide or share a plate (Plate setup security)................................... 76

Deﬁne custom ﬁelds ....................................................... 76

■CHAPTER 6 Create or modify a plate setup from the instrument .. 77

PSM and CSV plate setup ﬁles for import into the instrument ........................ 78

Shared (public), hidden (my plates), and guest plate setup ﬁles ...................... 79

Overview of plate setup settings ................................................. 79

(Optional)

Set up for auto export of sample data ﬁles (AB1 and FSA) .................. 80

Set up a plate using default settings (instrument) .................................. 81

Create or import a plate setup ............................................... 81

Enter plate properties ...................................................... 82

Assign wells: run module, size standard, dye set, and kit ....................... 84

Assign wells: sample name, sample type, and custom ﬁelds .................... 86

Set optional plate settings (instrument) ........................................... 87

Specify replicate injections .................................................. 87

Modify analysis settings .................................................... 87

Modify the default ﬁle name convention ....................................... 88

Hide or share a plate (Plate setup security)................................... 89

Deﬁne custom ﬁelds ....................................................... 89

(Optional)

View the injection list, change injection settings or order, or

specify replicates and re-injections .......................................... 91

Contents

SeqStudio

™

Genetic Analyzer Instrument and Software User Guide

■CHAPTER 7 Start and monitor a run .................................. 92

Load the plate or the tube assembly .............................................. 92

Select a plate setup and start a run ............................................... 93

Automatic ﬁle cleanup ...................................................... 94

Lock the touchscreen ........................................................... 95

Monitor a run from the Connect cloud-based platform .............................. 95

Open the Remote Monitoring App from Instrument Connect App ................ 95

Open the Remote Monitoring App from the Plate Manager ...................... 97

View notiﬁcations from the instrument on your Connect cloud-based

platform account .......................................................... 99

View results in the Remote Monitoring App on the Connect cloud-based platform .. 99

Monitor a run from a mobile device .............................................. 103

Monitor a run from the instrument .............................................. 105

(Optional)

View the injection list, change injection settings or order, or

specify replicates and re-injections ......................................... 105

View the run status ....................................................... 105

View real-time results ..................................................... 106

Pause a plate or cancel or stop injections .................................... 106

View results when the run is completed ..................................... 107

Unload the plate or the tube assembly ........................................... 109

■CHAPTER 8 View and analyze results ............................... 110

View results in the Remote Monitoring App on the Connect cloud-based platform ..... 110

View results on the instrument ................................................. 111

View results when the run is completed ..................................... 111

Fragment/HID analysis results ............................................. 113

Sequence analysis results ................................................. 115

EPT plot ................................................................. 117

View results for a previously run plate (run history) ........................... 118

Data quality alerts ........................................................ 119

Sizecalling and basecalling quality alerts ................................... 119

Edit injection parameters and re-inject samples .............................. 120

Export a report (QC report) ................................................. 120

Export results from the instrument (sample data ﬁles and QC reports) ............... 121

Analyze data .................................................................. 121

■CHAPTER 9 Manage the software (Plate Manager) ................ 122

Add a custom dye calibration to the Plate Manager ............................... 122

Download a plate setup template as a CSV ﬁle .................................... 122

Save a plate setup as a PDF .................................................... 123

Save a plate setup as a CSV ﬁle ................................................. 123

Create a plate setup template .................................................. 123

Contents

SeqStudio

™

Genetic Analyzer Instrument and Software User Guide

Delete plate setups ............................................................ 124

Manage email notiﬁcations in the Connect cloud-based platform .................... 124

Manage run modules .......................................................... 125

Manage size standards ........................................................ 125

Manage analysis settings ...................................................... 126

Fragment/HID analysis settings (size calling) ................................ 126

Sequencing settings (base calling) .......................................... 129

■CHAPTER 10 Manage the software (instrument) ................... 130

Connect the instrument to a network drive ....................................... 130

Determine IP address for a computer on a network ........................... 130

Create folders and enable network folder sharing ............................ 131

Connect to a network drive ................................................. 132

Set up a default Connect cloud-based platform location for opening plate setups . 132

Set up a default Connect cloud-based platform location for saving results

(auto export) ............................................................. 133

Set up a default network location for opening plate setups ..................... 133

Set up a default network location for saving results (auto export) ............... 134

Link the instrument to your Connect cloud-based platform account ................. 136

Lock the touchscreen .......................................................... 137

Manage plate setups .......................................................... 138

Export or delete a plate setup (PSM ﬁle) ..................................... 138

Import a plate setup from a CSV or PSM ﬁle .................................. 139

Manage run settings (instrument) ............................................... 139

Manage run modules ...................................................... 139

Manage size standard deﬁnitions ........................................... 142

Manage analysis settings .................................................. 142

Modify the default ﬁle name convention ..................................... 146

Manage instrument settings .................................................... 147

Display instrument hardware and software information ....................... 147

Change the instrument name .............................................. 148

Enable Demo mode ....................................................... 148

Manage date and time settings ............................................. 148

Manage the network conﬁguration .......................................... 149

Check for software updates (administrator only) .............................. 150

Manage instrument proﬁles on the instrument .................................... 151

Local instrument proﬁle roles and functions ................................. 151

Create a local instrument proﬁle for another user (administrator only) .......... 151

Change the role of a local instrument proﬁle (administrator only) ............... 152

Delete an instrument proﬁle from an instrument (administrator only) ........... 152

Delete the PIN for a local instrument proﬁle (administrator only) ............... 152

Contents

SeqStudio

™

Genetic Analyzer Instrument and Software User Guide

Create your own local instrument proﬁle .................................... 153

Change your own local instrument proﬁle PIN ................................ 153

Manage storage space ......................................................... 153

Automatic ﬁle cleanup ..................................................... 153

Export or delete a plate setup (PSM ﬁle) ..................................... 154

Export results from the instrument (sample data ﬁles and QC reports) .......... 154

Delete a run history ....................................................... 155

Back up user data (plates and results) (administrator only) .................... 155

■CHAPTER 11 Maintain the instrument .............................. 156

Regular maintenance tasks .................................................... 156

Check the cathode buffer ﬁll level .......................................... 156

Clean the instrument exterior and touchscreen ............................... 157

Clean the autosampler .................................................... 157

Manage the cartridge .......................................................... 158

Cartridge storage ......................................................... 158

Set cartridge storage mode (administrator only) .............................. 159

Check or export the Instrument-cartridge history ............................ 160

Check or export the cartridge history ....................................... 160

Fill the capillary array and refresh the polymer delivery system ................ 161

Remove the cartridge ..................................................... 161

Insert the cartridge ....................................................... 161

Store the cartridge ........................................................ 163

SeqStudio™Integrated Capillary Protector ................................... 164

Long-term on-instrument cartridge storage ................................. 165

Install cathode buffer .......................................................... 166

SeqStudio™Genetic Analyzer Cathode Buffer Container storage ................ 166

Remove the SeqStudio™Genetic Analyzer Cathode Buffer Container ............ 166

Assemble the SeqStudio™Genetic Analyzer Cathode Buffer Container (CBC) ..... 166

Insert the Cathode Buffer Container ........................................ 167

■APPENDIX A Troubleshooting ........................................ 169

Troubleshooting resources ..................................................... 169

Troubleshooting workﬂow ...................................................... 170

Export log ﬁles for plates, install runs, injections, and instrument ................... 170

View the raw data and the EPT plot .............................................. 171

Data quality alerts ............................................................ 171

Sizecalling and basecalling quality alerts ........................................ 171

Check size standard quality .................................................... 172

Instrument troubleshooting .................................................... 173

Cartridge troubleshooting ...................................................... 174

Sample and data troubleshooting ............................................... 175

EPT data .................................................................... 180

Contents

SeqStudio

™

Genetic Analyzer Instrument and Software User Guide

Software troubleshooting ...................................................... 181

Service tools ................................................................. 183

■APPENDIX B Link the instrument to your Connect cloud-

based platform account—detailed instructions ...................... 184

Workﬂow: Set up the instrument for Connect cloud-based platform access ........... 184

Network requirements ........................................................ 184

Link the instrument from a mobile device ........................................ 185

Create a Connect cloud-based platform PIN and generate the QR code on

the instrument ........................................................... 185

Link the instrument using a link code ............................................ 186

Set up email notiﬁcations from the instrument .................................... 190

■APPENDIX C Dye calibration and install standard checks ......... 192

Calibrate dyes ................................................................ 192

Overview of system dye set and custom dye set calibration .................... 192

System versus custom dyes ................................................ 192

Factory, auto, and manual calibration ....................................... 193

Determine if manual calibration is required .................................. 193

Perform a system dye calibration .......................................... 195

Perform a custom dye calibration ........................................... 197

View the dye calibration history ............................................ 201

Import or export a custom dye set .......................................... 202

Perform an install run ......................................................... 203

Overview of install checks ................................................. 203

Perform an install run ..................................................... 204

View install run results .................................................... 205

Export the install run report ............................................... 208

View the install run history ................................................. 210

■APPENDIX D Create and run an HID plate .......................... 212

HID analysis requirements ..................................................... 212

Pull-up reduction feature ...................................................... 213

Resolution algorithm .......................................................... 214

Workﬂow: HID analysis ........................................................ 215

HID install run ................................................................ 215

HID run module, dye sets, size standard deﬁnitions, and kits ....................... 216

Manage kits (HID applications only) ............................................. 217

Contents

SeqStudio

™

Genetic Analyzer Instrument and Software User Guide

■APPENDIX E Run modules ........................................... 218

Run modules, read lengths, size ranges, and run times ............................ 218

■APPENDIX F Parts and materials .................................... 220

Required materials not supplied ................................................ 220

■APPENDIX G Instrument speciﬁcations and layout ................ 222

Instrument dimensions ........................................................ 222

Instrument clearances ......................................................... 222

Environmental requirements ................................................... 223

Electrical requirements ........................................................ 224

Electrical protective devices .................................................... 224

Network requirements ........................................................ 225

Safety requirements ........................................................... 225

Safety practices .......................................................... 225

Required safety equipment ................................................ 226

■APPENDIX H Safety ................................................... 227

Symbols on this instrument .................................................... 227

Conformity symbols ....................................................... 228

Safety alerts on this instrument ................................................. 229

Safety information for instruments not manufactured by Thermo Fisher Scientiﬁc .... 230

Instrument safety ............................................................. 230

General ................................................................. 230

Physical injury ........................................................... 230

Electrical safety .......................................................... 230

Cleaning and decontamination ............................................. 231

Instrument component and accessory disposal ............................... 231

Laser ................................................................... 231

Safety and electromagnetic compatibility (EMC) standards ......................... 232

Safety compliance ........................................................ 232

EMC .................................................................... 232

Environmental design ..................................................... 233

Radio compliance ......................................................... 233

Chemical safety ............................................................... 234

Biological hazard safety ........................................................ 235

Contents

SeqStudio

™

Genetic Analyzer Instrument and Software User Guide

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