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Applied Biosystems 3730xl User Manual

Applied Biosystems 3730xl
170 pages
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For Research Use Only. Not for use in diagnostic procedures.
3730xl DNA Analyzer
USER GUIDE
3730xl Data Collection Software 5
Windows
10 Operating System
Catalog Number A39079
Publication Number 100077621
Revision A

Table of Contents

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Applied Biosystems 3730xl Specifications

General IconGeneral
BrandApplied Biosystems
Model3730xl
CategoryMeasuring Instruments
LanguageEnglish

Summary

Chapter 1 Instrument and software description

Overview

Introduction to the Applied Biosystems 3730xl DNA Analyzer and its capabilities.

Parts of the instrument

Identification and description of the main physical components of the 3730xl DNA Analyzer.

Instrument interior components

Detailed view and identification of the internal components of the 3730xl DNA Analyzer.

Instrument front panel indicators

Explanation of the status lights and indicators on the front panel of the instrument.

Consumables and usage limits

Information on consumables required and their specified usage limits for the instrument.

Computer and software requirements

Details the required computer hardware and software specifications for operation.

Theory of operation

Explanation of the scientific principles and processes behind the instrument's operation.

Overview of the software

Overview of the 3730xl Data Collection Software 5 interface and its main functions.

Use the instrument with Thermo Fisher Connect

Instructions on how to connect and utilize the instrument with the Thermo Fisher Connect feature.

Secondary analysis software

Overview of available secondary analysis software applications for data interpretation.

Data Collection software terminology

Glossary of key terms and definitions used within the Data Collection Software.

Workflow for a typical run

Step-by-step guide illustrating the typical workflow for performing a run on the instrument.

Chapter 2 Prepare the instrument

Power on the computer and the instrument

Steps to power on and log in to the computer and instrument system.

Start the software

Instructions for launching and starting the Data Collection Software.

Prepare buffer and fill the reservoirs

Procedures for preparing and filling the buffer, water, and waste reservoirs.

Place reservoirs into the instrument

Guide on correctly placing the prepared reservoirs into the instrument.

Fill the anode buffer jar

Detailed steps for filling the anode buffer jar with the appropriate buffer.

Check the polymer level

How to check and maintain the correct level of polymer in the instrument.

Check for bubbles in the pump system

Procedure to identify and address air bubbles within the instrument's pump system.

Check the active spectral calibration

Verifying the active spectral calibration is appropriate for the current run.

Prepare and load sample plates

Steps for preparing sample plates and loading them into the instrument.

Default injection positions—48-capillary arrays

Default well positions for sample injection on 48-capillary arrays.

Default injection positions—96-capillary arrays

Default well positions for sample injection on 96-capillary arrays.

Seal and assemble plates

Instructions for sealing and assembling sample plates prior to instrument loading.

Place plate assemblies into the instrument

Guidance on properly placing the assembled plates into the instrument's stacker.

Chapter 3 Use the instrument with Thermo Fisher Connect

Thermo Fisher Connect features

Overview of the functionalities and benefits of the Thermo Fisher Connect feature.

Register and obtain a Thermo Fisher Connect account

Steps to create an account for the Thermo Fisher Connect service.

Connect the instrument to your Thermo Fisher Connect account

Procedure to link the instrument to the user's Thermo Fisher Connect account.

Set up the data storage location and email notifications

Configuring data storage paths and email notification settings for the Connect account.

Monitor a run from InstrumentConnect

How to monitor instrument runs remotely using the InstrumentConnect web interface.

Monitor a run from a mobile device

Instructions for monitoring instrument runs using a mobile device application.

View notifications from the instrument on the Cloud

Accessing and viewing instrument notifications and alerts through the cloud platform.

Thermo Fisher Connect administrators for an instrument

Information on managing administrator roles and functions within Thermo Fisher Connect.

Chapter 4 Create results groups and plate records using default settings

Create a results group (using defaults)

Procedure to create a results group with default naming and storage conventions.

Create a plate record

Steps to create and configure a plate record for instrument runs.

Chapter 5 Run the instrument

Understanding run modes and default injection positions

Explanation of different run modes and default injection configurations.

Run the instrument in auto mode

Detailed steps for running the instrument using the automated mode.

Run the instrument in manual mode

Instructions for operating the instrument in manual run mode.

Change injection order of plate quadrants

Procedure to modify the injection order of plate quadrants.

Move a plate in the Input stack during a run

How to move plates within the input stack while a run is in progress.

Controlling the run

Using the software toolbar to control active instrument runs.

Monitor the status of the run

Methods for monitoring the real-time status of an ongoing instrument run.

Add reinjections to a plate record

Steps to add reinjections to an existing plate record for a run.

Check instrument status

How to check the current operational status and calibration information of the instrument.

View the Event Log

Accessing and reviewing the instrument's event log for error diagnosis.

View data from the run

Procedures for viewing run data using Capillary Viewer and Array Viewer.

Check the autoextraction status and manually re-extract

Verifying autoextraction status and performing manual re-extractions.

Chapter 6 Create and manage plate records and results groups

Overview of plate records

Explanation of what a plate record is and its purpose in instrument operation.

Create and manage plate records

Procedures for creating, editing, deleting, and exporting plate records.

Search for a plate record

How to search for existing plate records based on various criteria.

Import a plate record

Instructions for importing plate records from a text file.

Overview of results groups

Understanding the purpose and configuration of results groups for data organization.

Create and manage results group

Procedures for creating, editing, duplicating, and exporting results groups.

Create a results group (detailed procedure)

Step-by-step guide for creating a results group with custom settings.

Specify custom sample file naming in a results group

Customizing file naming conventions for sample data within results groups.

Chapter 7 Create and manage instrument protocols, run modules, and analysis protocols

Create and manage instrument protocols

Overview of managing instrument protocols, including creation and editing.

Create an instrument protocol

Steps to create a new instrument protocol for run configuration.

Create run module

Procedure for creating and configuring run modules for instrument operation.

Overview of analysis protocols (sequence analysis)

Explanation of analysis protocols, particularly for sequence analysis.

Create and manage analysis protocols

Managing analysis protocols, including creation, editing, and deletion.

Create an analysis protocol

Detailed steps for creating a new analysis protocol.

Chapter 8 Calibrate the instrument

Perform spatial calibration

Procedure for calibrating the instrument's spatial positioning for accurate data.

Perform spectral calibration for sequencing and fragment analysis

Steps for performing spectral calibration for DNA sequencing and fragment analysis.

Chapter 9 Maintenance

Maintenance schedules

Schedule of recommended daily, weekly, and monthly maintenance tasks.

Wizards types and functions

Overview of the available maintenance wizards and their purposes.

Typical conditions for using maintenance wizards

Guidance on when to use specific maintenance wizards based on instrument conditions.

Clean the instrument

General instructions for cleaning the exterior surfaces of the instrument.

Replenish or change polymer type

Procedures for replenishing or changing the polymer used in the instrument.

Clean the polymer delivery pump (PDP) and lower polymer block

Steps for cleaning the polymer delivery pump and associated components.

Flush the water seal trap

Procedure for flushing the water seal trap in the polymer delivery pump.

Install the capillary array

Instructions for installing a new or used capillary array.

Store a capillary array

Proper methods for storing capillary arrays to maintain their integrity.

Clean the detection cell

Detailed instructions for cleaning the instrument's detection cell.

Perform a short-term shutdown

Steps for safely shutting down the instrument for short periods of inactivity.

Maintain adequate space for database and sample data storage

Guidelines for managing disk space for instrument data and the database.

Troubleshooting

Restart the instrument and the computer

Procedure for restarting the instrument and associated computer system to resolve issues.

Display the Event Log

How to access and view the instrument's event log for error diagnosis.

Review a run log file

Guidance on locating and reviewing run log files for troubleshooting.

Hi-Di Formamide preparation and storage

Information on the preparation and storage of Hi-Di Formamide.

Front panel status light troubleshooting

Troubleshooting guide for interpreting and resolving issues indicated by front panel status lights.

Instrument run troubleshooting

Common issues and solutions related to instrument run failures or errors.

Re-extraction troubleshooting

Troubleshooting specific problems encountered during sample re-extraction.

Service console troubleshooting

Diagnosing and resolving issues related to the service console software.

Spatial calibration troubleshooting

Addressing common problems encountered during spatial calibration.

Spectral calibration troubleshooting

Troubleshooting guide for spectral calibration failures and data issues.

General troubleshooting

General tips and common problems encountered during instrument operation.

Instrument specifications

Physical Specifications

Technical specifications including physical dimensions, weight, and power consumption.

Environmental requirements

Conditions for installation site, altitude, and operating environment.

Electrical requirements

Details on power supply, voltage, and current requirements for the instrument.

Power and communication connections

Information on power supply and data communication connections for the instrument.

Run modules

Fragment analysis run times

Approximate run times for various fragment analysis modules.

Sequence analysis run times

Approximate run times for different sequence analysis modules.

Dye sets: G5, G5-RCT, Any4Dye, Any4Dye-HDR, and Any5Dye

Supported dye sets and calibration standards

List of supported dye sets and their corresponding calibration standards.

Dye sets G5 and G5-RCT for fragment analysis

Specific details on G5 and G5-RCT dye sets for fragment analysis.

Catalog numbers

Plates, bases, retainers, and septa

Catalog numbers for plates, bases, retainers, and septa.

Instrument consumables

Catalog numbers for various instrument consumables.

Sequencing and fragment analysis calibration standards

Catalog numbers for calibration standards for sequencing and fragment analysis.

Fragment analysis size standards

Catalog numbers for fragment analysis size standards.

Safety

Symbols on the Instrument

Explanation of hazard symbols, their meanings, and locations on the instrument.

Control and Connection Symbols

Symbols related to instrument controls, power sources, and data connections.

Conformity Symbols

Symbols indicating compliance with safety and regulatory standards.

Instrument Safety Precautions

General safety guidelines and warnings for operating the instrument safely.

Documentation and support

Related documentation

List of related documents and their publication numbers.

Customer and technical support

Information on how to contact customer and technical support services.

Limited product warranty

Details regarding the limited product warranty terms and conditions.

Index

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