Applied Biosystems A30207 User manual

For Research Use Only. Not for use in diagnostic procedures.
Automated Thermal Cycler (ATC) System
USER GUIDE
Installation, use, and maintenance
Catalog Numbers A30207, A30208, A31486, A31487, A31488, A31489, A31490, A31491, A33976,
A33977, A33978, A33979, A33980, A33981, and A33982
Publication Number MAN0014558
Revision B.0

Life Technologies Holdings Pte Ltd | Block 33 | Marsiling Industrial Estate Road 3 | #07-06, Singapore 739256
For descriptions of symbols on product labels or product documents, go to thermofisher.com/symbols-definition.
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. MAN0014558
Revision Date Description
B.0 17 June 2021 Addition of the Fleet software appendix, and a sentence in the product description
regarding the Fleet software.
A.0 11 April 2017 New document. Describes installation, operation, and maintenance of the Automated
Thermal Cycler (ATC) System.
Important Licensing Information: This product may be covered by one or more Limited Use Label Licenses. By use of this product,
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.
©2021 Thermo Fisher Scientific Inc. All rights reserved.

Contents
■CHAPTER 1 About the Automated Thermal Cycler (ATC) System ............. 6
Package contents ............................................................... 6
Setup options .................................................................. 7
Site requirements ............................................................... 7
Environmental requirements ...................................................... 8
Temperature and humidity requirements ....................................... 8
Pollution ................................................................... 8
Technical specifications .......................................................... 8
System specifications ........................................................... 9
Location of power points and ports .............................................. 10
Use ATC plate adaptors ......................................................... 11
■CHAPTER 2 Operate the Automated Thermal Cycler (ATC) System as
a stand-alone system ............................................................. 15
Connect the hardware .......................................................... 15
Operate ATC as stand alone using computer ...................................... 15
Program and execute a run on the ATC ........................................... 18
Connect to multiple instruments using the desktop software ......................... 22
Firmware upgrades ............................................................. 23
■CHAPTER 3 Operate the Automated Thermal Cycler (ATC) System as
part of a robotic system .......................................................... 26
Set up the Automated Thermal Cycler (ATC) System on a robotic system ............. 26
Guidelines for robotic configurations ......................................... 28
Connect Automated Thermal Cycler to a robotic system ............................ 28
Perform a thermal protocol run .................................................. 28
(Optional) View the progress of the thermal protocol run ........................ 30
(Optional) Abort the thermal protocol run ..................................... 31
(Optional) Control the automated heated cover lid .............................. 31
Automated Thermal Cycler (ATC) System User Guide 3

■CHAPTER 4 Maintain the Automated Thermal Cycler (ATC) System ......... 32
Clean the instrument ........................................................... 32
Preparation ............................................................... 32
Clean the sample wells ..................................................... 32
Decontaminate the sample wells ............................................. 33
Clean the heated cover ..................................................... 34
Decontaminate the heated cover ............................................ 34
Replace the fuses .............................................................. 34
Separate the heated cover from the block ......................................... 35
■APPENDIX A Parts and materials ................................................ 40
Accessories ................................................................... 40
■APPENDIX B Command dictionaries ............................................ 41
Command directory overview .................................................... 41
Mandatory commands .......................................................... 42
Abort ..................................................................... 42
DoContinue ............................................................... 42
GetDeviceIdentification ..................................................... 43
GetStatus ................................................................. 44
Initialize .................................................................. 44
LockDevice ............................................................... 44
Pause .................................................................... 45
Reset .................................................................... 45
UnlockDevice ............................................................. 46
Required Commands for PCR Cyclers ............................................ 46
Delay ..................................................................... 46
GetParameters ............................................................ 47
PrepareForInput ........................................................... 47
PrepareForOutput .......................................................... 48
SetParameters ............................................................ 48
Optional commands for PCR Cyclers ............................................. 49
GetConfiguration .......................................................... 49
SetConfiguration .......................................................... 50
Optional commands for other device classes ...................................... 51
OpenDoor ................................................................ 51
CloseDoor ................................................................ 51
Specific commands ............................................................ 52
ExecuteProtocol ........................................................... 52
GetDeviceDetails .......................................................... 52
GetProtocolDefinition ...................................................... 53
GetProtocolDetails ......................................................... 54
Contents
4Automated Thermal Cycler (ATC) System User Guide

StopProtocol .............................................................. 55
SubScribe ................................................................ 55
UnSubScribe .............................................................. 55
SiLA return codes .............................................................. 56
■APPENDIX C About the Thermal Cycler Fleet Control Software .............. 57
Connect the thermal cycler to the network ........................................ 57
■APPENDIX D Safety ............................................................... 58
Symbols on this instrument ..................................................... 58
Conformity symbols ........................................................ 60
Safety alerts on this instrument .................................................. 60
Location of safety labels on the instrument .................................... 60
Safety information for instruments not manufactured by Thermo Fisher Scientific ...... 62
Instrument safety .............................................................. 62
General ................................................................... 62
Physical injury ............................................................. 62
Electrical safety ........................................................... 63
Cleaning and decontamination .............................................. 63
Instrument component and accessory disposal ................................ 63
Safety and electromagnetic compatibility (EMC) standards .......................... 63
Safety .................................................................... 64
EMC ..................................................................... 64
Environmental design ...................................................... 65
RoHS .................................................................... 65
Chemical safety ................................................................ 66
Biological hazard safety ......................................................... 67
■APPENDIX E Documentation and support ...................................... 68
Related documentation ......................................................... 68
Customer and technical support ................................................. 68
Limited product warranty ........................................................ 69
Contents
Automated Thermal Cycler (ATC) System User Guide 5

About the Automated Thermal
Cycler (ATC) System
■Package contents ..................................................................... 6
■Setup options ......................................................................... 7
■Site requirements ..................................................................... 7
■Environmental requirements ............................................................ 8
■Technical specifications ................................................................ 8
■System specifications .................................................................. 9
■Location of power points and ports ..................................................... 10
■Use ATC plate adaptors ............................................................... 11
The Automated Thermal Cycler (ATC) System is designed for integrating with laboratory automation
products of other equipment manufacturers (OEM) for use in automation workflows. The Automated
Thermal Cycler (ATC) System can also be used as a stand-alone device in conjunction with a third-party
desktop software. It is also compatible with the Applied Biosystems™Thermal Cycler Fleet Control
Software.
The Automated Thermal Cycler (ATC) System supports 96-Well, 384-Well, and 0.2-mL sample block
configuration and includes three components:
•A thermal block and heated cover that constitute the thermal cycler unit
•A power box
A power cable is used for connecting the thermal cycler to the power box.
For details on Automated Thermal Cycler (ATC) System specifications and layout, see “System
specifications” on page 9.
Package contents
The Automated Thermal Cycler (ATC) System comes in two boxes.
The ATC Block Module box contains:
•ATC 96-Well Block module and/or 384-Well Block module
•CAT5 Ethernet cable
•Power cord
•Certificate of analysis
•Product documentation
1
6Automated Thermal Cycler (ATC) System User Guide

The ATC Control Module box contains:
•ATC Control Module
Setup options
The system can be set up in two ways.
Table 2 Automated Thermal Cycler (ATC) System configurations
Setup option image
Within a Robotic environment
Automated Thermal Cycler
Stand-alone system
Automated Thermal Cycler
Site requirements
The Automated Thermal Cycler (ATC) System is for indoor use. Ensure that the installation site:
•Meets the spatial and weight requirements (see “System specifications” on page 9)
•Meets environmental requirements (see “Environmental requirements” on page 8)
•Is within 1 m (3 ft.) of an AC power source receptacle
•Is away from water
Chapter 1 About the Automated Thermal Cycler (ATC) System
Setup options 1
Automated Thermal Cycler (ATC) System User Guide 7

Environmental requirements
Temperature and humidity requirements
Ensure that the installation site is maintained under the following conditions:
Table 3 Temperature and humidity requirements
Condition Acceptable range
Temperature 15 to 30°C (59 to 86°F)
Humidity 15 to 80% relative humidity, non-condensing
Avoid placing the instrument adjacent to heaters, cooling ducts, or in direct sunlight. Fluctuations
between day and night temperatures can cause system instability. Place away from any equipment that
vibrates, such as a refrigerator or centrifuge.
Pollution
The Automated Thermal Cycler (ATC) System has a Pollution Degree rating of 2. It may be installed in
an environment that has non-conductive pollutants only, such as dust particles or wood chips. Typical
environments with a Pollution Degree II rating are laboratories and sales and commercial areas.
Technical specifications
Table 4 Automated Thermal Cycler (ATC) System technical specifications:
Feature Specification
Block format •96-well, 0.2-mL
•384-well, 0.02-mL
Maximum block ramp rate[1] •3.5°C/sec (96-well)
•2.8°C/sec (384-well)
Maximum sample ramp rate[1] •1.8°C/sec (96-well)
•1.6°C/sec (384-well)
Temperature range for
protocol run
0.0°C to 105.0°C
Temperature uniformity ≤0.50°C (20 sec after reaching 95°C)
Temperature calibration Calibrated to standards traceable to the National Institute of Standards and
Technology (NIST™)
Dimensions Thermal Module Control Module
Chapter 1 About the Automated Thermal Cycler (ATC) System
Environmental requirements
1
8Automated Thermal Cycler (ATC) System User Guide

Table 4 Automated Thermal Cycler (ATC) System technical specifications: (continued)
Feature Specification
Dimensions •Height: 133.6 mm (5.3 in)
•Width: 179.6 mm (7.1 in)
•Depth: 317.5 mm (12.5 in)
•Height: 76.4 mm (3.0 in) —
(including rubber feet)
•Width: 257 mm (10.1 in)
•Depth: 342.0 mm (13.5 in) —
(including air vents)
Weight •Weight of Thermal Module: 6.0 kg (13.2 lb)
•Weight of Control Module: 3.4 kg (7.48 lb)
•Weight of 1m Interface Cable: 0.35 kg (0.77 lb)
PCR volume range •10−100 µL (96-well)
•5−10 µL (384-well)
Instrument memory USB
Power 100-240 V, 50-60 Hz Max: 600 W
[1] Reaction volume @ 1 µL
System specifications
Table 5 Physical dimensions and weight, and power consumption
Dimension
Instrument footprint Recommended clearance
Thermal module Control box Thermal module Control box
Height 133.6 mm (5.3 in) 76.4 mm (3.0 in) N/A N/A
Width 179.6 mm (7.1 in) 257.0 mm
(10.1 in)
N/A N/A
Depth 317.5 mm
(12.5 in)
342.0 mm
(13.5 in)
Front: 51 mm
(2 in)
Rear: 102 mm
(4 in)
Front: 10 mm
(0.39 in)
Rear: 10 mm
(0.39 in)
Chapter 1 About the Automated Thermal Cycler (ATC) System
System specifications 1
Automated Thermal Cycler (ATC) System User Guide 9

Location of power points and ports
1
2
35
4
Figure 1 Back panel of the ATC control module
1Power port
2Power button
3Ethernet port
4Automated Thermal Cycler (ATC) System DSUB
5USB port
1
Figure 2 Back panel of the ATC block module
1Automated Thermal Cycler (ATC) System DSUB
Chapter 1 About the Automated Thermal Cycler (ATC) System
Location of power points and ports
1
10 Automated Thermal Cycler (ATC) System User Guide

Use ATC plate adaptors
The plate adaptor helps to ensure that the supported consumables (full skirt and semi-skirt plates)
are ejected properly, and that the temperature is kept uniform. The Automated Thermal Cycler comes
factory configured with a full-skirted adaptor (amber color) already installed.
Note: ATC plate adaptors are only installed/required on the 96-well block. Adaptors are not required for
the 384-well block.
Figure 3 Automated Thermal Cycler 96-well block with full-skirted plate adaptor installed
•To uninstall the full-skirted adaptor, follow the instructions in Figure 4.
Chapter 1 About the Automated Thermal Cycler (ATC) System
Use ATC plate adaptors 1
Automated Thermal Cycler (ATC) System User Guide 11

123
Figure 4 Uninstall the full-skirted plate adaptor
1Slightly push the tabs highlighted in red.
2Grab the bottom of the adaptor, and tilt up.
3Remove the adaptor.
•To install full-skirted plate adaptor follow the instructions in Figure 5.
Chapter 1 About the Automated Thermal Cycler (ATC) System
Use ATC plate adaptors
1
12 Automated Thermal Cycler (ATC) System User Guide

12
3 4
Figure 5 Install full-skirted plate adaptor
1Remove half skirted adaptor, if any. place full skirted adaptor by tilting an angle allowing the front to insert under
the frame.
2Push the two tabs allowing it to be inserted into the frame.
3Ensure the full-skirted plate adaptor sits freely under the frame.
4Full-skirted plate adaptor is installed.
•To install the semi-skirted plate adaptor, follow the instructions in Figure 6.
Chapter 1 About the Automated Thermal Cycler (ATC) System
Use ATC plate adaptors 1
Automated Thermal Cycler (ATC) System User Guide 13

12
34
Figure 6 Installation of semi-skirted plate adaptors and ejector buttons
1Slot the semi-skirted plate adaptor to the gap between the Alu top plate and drip pan.
2Slot in the adaptor and center it.
3Snap fit the ejector buttons.
4There are four ejector buttons.
Chapter 1 About the Automated Thermal Cycler (ATC) System
Use ATC plate adaptors
1
14 Automated Thermal Cycler (ATC) System User Guide

Operate the Automated Thermal
Cycler (ATC) System as a stand-
alone system
■Connect the hardware ................................................................ 15
■Operate ATC as stand alone using computer ............................................. 15
■Program and execute a run on the ATC .................................................. 18
■Connect to multiple instruments using the desktop software ............................... 22
■Firmware upgrades ................................................................... 23
This chapter describes the procedures for setting up and running the Automated Thermal Cycler (ATC)
System as a stand-alone system.
Connect the hardware
1. Connect the connector cable into the insertion points on the ATC block (Figure 1, item 4) and base
module (Figure 2, item 1)
Note: Ensure the DSUB connector is securely fastened.
2. Connect the power cable into the back of the ATC control module (Figure 1, item 1)
3. Connect the ethernet cable into the control module (Figure 1, item 3) and into the
computer/network that you will be using to control the ATC.
4. Power on the ATC.
Operate ATC as stand alone using computer
Make sure all hardware connections are completed.
1. Download the ATC desktop software at thermofisher.com and follow the installation instructions
found in the software release notes.
Note: To fully install the software, the computer will need to be connected to the internet. Once
the software is fully installed, disconnect the computer from the internet for best performance with
the ATC desktop software.
2
Automated Thermal Cycler (ATC) System User Guide 15

2. Once the software is installed, click on the ATC Demo icon to launch the software.
Figure 7 Desktop icon of ATC Demo software
1
4
2
3
Figure 8 ATC Demo software initial screen
1Discover
2A pop up window
3Identified instrument name
4Connect
3. Make sure the ATC is powered on and connected via ethernet cable to your computer.
Note: It will take approximately 1.5 minutes for the ATC to initialize before it can connect to the
software.
4. Once the ATC instrument has initialized, click Discover to identify all devices connected to the
same local network.
A pop up window will appear.
5. Double click on the identified instrument name.
Chapter 2 Operate the Automated Thermal Cycler (ATC) System as a stand-alone system
Operate ATC as stand alone using computer
2
16 Automated Thermal Cycler (ATC) System User Guide

6. Click Connect.
Figure 9 ATC Demo software connected to the ATC instrument
7. Hover mouse over the real time monitoring temperature curves to see black window legend with
graph related information.
8. Click Start to open Protocol Editor
Chapter 2 Operate the Automated Thermal Cycler (ATC) System as a stand-alone system
Operate ATC as stand alone using computer 2
Automated Thermal Cycler (ATC) System User Guide 17

Program and execute a run on the ATC
3
4
1
2
76 8910
5
Figure 10 Run Protocol
1Add (+), Remove (−) stages
2Remove and arrange order
3Run Mode drop down
4Cover Temperature and Sample Volume
5Temperature, Ramp Rate, Hold Time
6Cancel
7Start Run
8Export SiLA
9Save
10 Load
1. In Stages, add or remove protocol stages with the plus and minus signs.
2. Click up and down arrows to arrange the sequence of stages.
Specify the number of cycles required for the particular stage.
3. In the Steps field, specify the temperature set points, ramp rate, and duration.
The ramp rate is indicated as a % where 100% corresponds to a peak block ramp rate of 3.5C/s.
Type in −1 in the Hold Time field to achieve an infinity hold time.
4. Enter cover temperature and sample volume.
5. Click Start Run to start immediately, or Save for future use.
Chapter 2 Operate the Automated Thermal Cycler (ATC) System as a stand-alone system
Program and execute a run on the ATC
2
18 Automated Thermal Cycler (ATC) System User Guide

6. Press Load to display previously protocols.
Note: An empty protocol cannot be saved.
7. Click Export SiLA to export protocol for integration with SiLA based software or scheduler.
Note: Although SiLA exported protocol is an .xml file it should opened using a text editor in
order to see the content, otherwise they might appear empty if opened with a default browser
application. When exporting to SiLA format, no white space is allowed in stage label and protocol
file name. Only alpha numeric characters and “-“, “_” are accepted.
Chapter 2 Operate the Automated Thermal Cycler (ATC) System as a stand-alone system
Program and execute a run on the ATC 2
Automated Thermal Cycler (ATC) System User Guide 19

Note: A message will notify the user if the Protocol Editor is started while the instrument is already
running (Edit Only mode). User can still edit and export a protocol while the software control and
monitor the instrument running, without interfering with the current run.
Figure 11 Instrument not ready for run warning
Figure 12 Run Protocol (Edit Only) mode
Chapter 2 Operate the Automated Thermal Cycler (ATC) System as a stand-alone system
Program and execute a run on the ATC
2
20 Automated Thermal Cycler (ATC) System User Guide