Thermo Scientific Applied Biosystems SeqStudio Genetic... Manuel utilisateur

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

SeqStudio™Genetic Analyzer

GETTING STARTED GUIDE

Create and run plate setups, monitor runs, and view results

for use with:

SeqStudio™Data Collection Software v1.2

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

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

SeqStudio™Plate Manager

SeqStudio™Remote Monitoring App

Publication Number MAN0018654

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. MAN0018654

Revision Date Description

A.0 1 November 2019 New getting started guide for SeqStudio™Data Collection Software v1.2.

The v1.2 software includes options for HID kits. This getting started guide

replaces Pub. No. MAN0017464.

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 ....................................... 6

Product description ............................................................. 6

Workﬂow ...................................................................... 7

■CHAPTER 2 Prepare the samples and the instrument ................ 9

Prepare the samples ............................................................ 9

Sample preparation guidelines ............................................... 9

Plate layout and loading guidelines .......................................... 11

Prepare the instrument ......................................................... 11

Power on the instrument ................................................... 11

Check the consumables status .............................................. 11

Load the CBC, the sample plate, and the cartridge ............................. 12

Prepare and load the plate or tubes .............................................. 14

Prepare the plate .......................................................... 14

Prepare the tubes .......................................................... 14

Load the plate or the tube assembly .......................................... 15

Unload the plate or the tube assembly ........................................ 15

■CHAPTER 3 Set up a plate using default settings (Plate

Manager) .................................................................. 16

Access the Plate Manager ....................................................... 16

Create or open a plate setup PSM ﬁle ............................................. 17

Enter plate properties .......................................................... 17

Assign wells: Sample and run information ........................................ 18

Save a plate setup in the Plate Manager ........................................... 20

■CHAPTER 4 Set up a plate using default settings (instrument) .... 22

(Optional)

Set up for auto export of sample data ﬁles (AB1 and FSA) .................. 23

Create or import a plate setup ................................................... 24

Export or delete a plate setup (PSM ﬁle) ...................................... 24

Enter plate properties .......................................................... 25

Assign wells: run module, size standard, dye set, and kit ............................ 26

SeqStudio

™

Genetic Analyzer Instrument and Software Getting Started Guide

Assign wells: sample name, sample type, and custom ﬁelds ......................... 26

Save and/or run a plate setup .................................................... 27

■CHAPTER 5 Start and monitor a run .................................. 28

Load the plate or the tube assembly .............................................. 28

Select a plate setup and start a run ............................................... 29

Start a run on the instrument .................................................... 30

Monitor a run from the Connect cloud-based platform .............................. 31

Open the Remote Monitoring App from Instrument Connect App ................ 31

View notiﬁcations from the instrument on your Connect cloud-based

platform account .......................................................... 32

Pause or cancel an injection in the Remote Monitoring App ..................... 32

View results in the Remote Monitoring App on the Connect cloud-based platform .. 33

Monitor a run from a mobile device ............................................... 36

Monitor a run from the instrument ............................................... 39

View the run status ........................................................ 39

View real-time results ...................................................... 39

Pause a plate or cancel or stop injections ..................................... 40

View results when the run is completed ...................................... 41

(Optional)

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

specify replicates and re-injections .......................................... 42

■CHAPTER 6 View and analyze results ................................. 43

View results in the Remote Monitoring App on the Connect cloud-based platform ...... 43

View results on the instrument .................................................. 44

View results when the run is completed ...................................... 44

View results for a previously run plate (run history) ............................ 48

Edit injection parameters and re-inject samples ............................... 50

Export a report (QC report) .................................................. 50

Export results from the instrument (sample data ﬁles and QC reports) ................ 50

Analyze data ................................................................... 51

Secondary analysis software ................................................ 51

■APPENDIX A Link the instrument to your Connect cloud-

based platform account—detailed instructions ....................... 53

Workﬂow: Set up the instrument for access to the Connect cloud-based platform ...... 53

Link the instrument from a mobile device ......................................... 54

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

the instrument ............................................................ 54

Link the instrument using a link code ............................................. 56

Contents

SeqStudio

™

Genetic Analyzer Instrument and Software Getting Started Guide

■APPENDIX B Keyboard shortcuts for Plate Manager ................ 59

Keyboard shortcuts for the sample table .......................................... 59

■Documentation and support ............................................. 61

Related documentation ......................................................... 61

Customer and technical support ................................................. 61

Limited product warranty ....................................................... 62

Contents

SeqStudio

™

Genetic Analyzer Instrument and Software Getting Started Guide

Product information

■Product description .................................................... 6

■Workow ............................................................ 7

Product description

The Applied Biosystems™ SeqStudio™ Genetic Analyzer with SeqStudio™ Data

Collection Software is a uorescent dye-labeled genetic analysis system using

capillary electrophoresis technology. It enables both sequencing and fragment

analysis applications without the need to switch polymer type or capillary array

length.

You can use the data collection software on the instrument to create and run plate

setups, monitor runs, and view results. You can also use the optional SeqStudio™ Plate

Manager and Remote Monitoring App to perform some of these functions.

For complete information on using the instrument and software, see SeqStudio™

Genetic Analyzer Instrument and Software User Guide (Pub. No. MAN0018646).

SeqStudio

™

Genetic Analyzer Instrument and Software Getting Started Guide

Workﬂow

Prepare the samples and the instrument

Prepare the samples

(page 9)

▼

Prepare the instrument

(page 11)

▼

Prepare and load the plate or tubes

(page 14)

Create a plate setup

SeqStudio™Plate Manager SeqStudio™Genetic Analyzer

Access the Plate Manager

(page 16)

(page 22)

▼ ▼

Create or open a plate setup PSM ﬁle

(page 17)

Create or import a plate setup

(page 24)

▼ ▼

Enter plate properties

(page 17)

Enter plate properties

(page 25)

▼ ▼

Assign wells: Sample and run information

(page 18)

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

(page 26)

▼ ▼

Save a plate setup in the Plate Manager

(page 20)

Assign wells: sample name, sample type, and custom

ﬁelds

(page 26)

▼

Save and/or run a plate setup

(page 27)

▼

(Optional) Set up for auto export of sample data ﬁles

(AB1 and FSA)

(page 23)

Chapter 1 Product information

Workﬂow

SeqStudio

™

Genetic Analyzer Instrument and Software Getting Started Guide

Start a run

Load the plate or the tube assembly

(page 15)

▼

Select a plate setup and start a run

(page 29)

▼

Start a run on the instrument

(page 30)

Monitor a run

Connect cloud-based platform[1] Mobile device SeqStudio™Genetic Analyzer

• View results in the Remote

Monitoring App on the Connect

cloud-based platform

(page 33)

• View notiﬁcations from the

instrument on your Connect

cloud-based platform account

(page 32)

• Pause or cancel an injection in

the Remote Monitoring App

(page 32)

Monitor a run from a mobile device

(page 36)

• View the run status

(page 39)

• View real-time results

(page 39)

• Pause a plate or cancel or stop

injections

(page 40)

[1] The Connect cloud-based platform is not supported for HID analysis.

View and analyze results

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

(page 33)

▼

View results on the instrument

(page 44)

▼

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

(page 50)

▼

Analyze data

(page 51)

Chapter 1 Product information

Workﬂow

SeqStudio

™

Genetic Analyzer Instrument and Software Getting Started Guide

Prepare the samples and the

instrument

■Prepare the samples ................................................... 9

■Prepare the instrument ................................................ 11

■Prepare and load the plate or tubes ..................................... 14

Prepare the samples

Sample preparation guidelines

Item Guidelines

Plates and tubes • Use MicroAmp™Optical 96-Well Reaction Plate or MicroAmp™Reaction Tubes with

a tray and retainer set.

IMPORTANT! Fast plates are not compatible with the SeqStudio™Genetic

Analyzer. Fast plates will damage the cartridge.

• Use the appropriate septa for plates and tubes.

• See

SeqStudio

™

Genetic Analyzer Instrument and Software User Guide

for more

information.

Fragment and HID analysis

sample preparation

Intensity (RFU)

Size (bp)

• Prepare the samples as recommended by the kit for fragment analysis.

• Use a 10–20 µL sample volume.

• Ensure that Hi‑Di™Formamide is fresh.

– Hi‑Di™Formamide should not undergo more than two freeze-thaw cycles (one

to aliquot and one for use).

– Use the same day after thawing.

• For more information, see

DNA Fragment Analysis by Capillary Electrophoresis

User Guide

(Pub. No. 4474504).

SeqStudio

™

Genetic Analyzer Instrument and Software Getting Started Guide

Item Guidelines

Sequence analysis sample

preparation

• Prepare sequencing reactions according to kit instructions, and purify the

extension products with ethanol precipitation, spin columns, or the BigDye

XTerminator™Puriﬁcation Kit.

– If ethanol precipitation or spin columns are used, dry the samples in a

vacuum centrifuge without heat or at low heat for 10–15 minutes or until dry.

Note: Do not over dry the samples.

– Resuspend in 10–20 µL of Hi‑Di™Formamide.

• Use a 65 µL or 130 µL sample volume for samples that are prepared with the

BigDye XTerminator™Puriﬁcation Kit. See

BigDye XTerminator

™

Puriﬁcation Kit

Protocol

(Pub. No. 4374408).

IMPORTANT! Use the appropriate run modules for samples prepared with

BigDye XTerminator™Puriﬁcation Kit.

• Use a 10–20 µL sample volume for samples that are prepared with Hi‑Di™

Formamide.

• Ensure that Hi‑Di™Formamide is fresh.

– Hi‑Di™Formamide should not undergo more than two freeze-thaw cycles (one

to aliquot and one for use).

– Use the same day after thawing.

• Do not resuspend samples in water, which can decrease sample stability.

• For more information, see

DNA Sequencing by Capillary Electrophoresis

Chemistry Guide Second Edition

(Pub. No. 4305080).

Chapter 2 Prepare the samples and the instrument

Prepare the samples

SeqStudio

™

Genetic Analyzer Instrument and Software Getting Started Guide

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