BIO RAD MyCycler User manual

BE IS
MyCycler
Thermal Cycler
Instruction Manual
Catalog Number
170-9703
BIO-RAD
For Technical Service Call Your Local Bio-Rad Office or in the U.S. Call 1-800-4BIORAD (1-800-424-6723)

Safety Information
Notice to Purchaser
Purchase of this instrument, Serial No. , conveys a limited non-transfer
able immunity from suit for the purchaser's own internal research and development and for
use in applied fields other than Human In Vitro Diagnostics under one or more of U.S.
Patents Nos. 5,656,493, 5,333,675, 5,475,610 (claims 1, 44, 158, 160-163 and 167 only),
and 6,703,236 (claims 1-7 only), or corresponding claims in their non-U.S. counterparts,
owned by Applera Corporation. No right is conveyed expressly, by implication or by estop
pel under any other patent claim, such as claims to apparatus, reagents, kits, or methods
such as 5' nuclease methods. Further information on purchasing licenses may be obtained
by contacting the Director of Licensing, Applied Biosystems, 850 Lincoln Centre Drive,
Foster City, California 94404, USA.
The sample block of the MyCycler thermal cycler can reach temperatures of 100°C, and
the heated lid can be programmed to maintain temperatures up to 110°C. The heated lid
should remain closed at all times during operation to prevent accidental skin burns. Always
allow the sample block to return to its idle temperature before opening the lid and removing
samples. When placing or removing samples, open the heated lid all the way up to allow
maximum clearance and to avoid accidental skin burns.
This symbol on the reaction module indicates a hot surface.
Always connect the power supply to a 3-prong, grounded AC outlet rated 10 A/100-120 V
or 5 A/220-240 V using the AC power cord provided with the MyCycler. Do not use an
adapter to a two-terminal outlet. Before plugging the instrument in, be sure that the correct
fuse is installed in the rear panel fuse holder. Use the 4A 5 x 20 mm TYPE T fuse for
220-240 V or the 8A 5 x 20 mm TYPE T fuse for 100-120 V.
Never remove the outer casing of the MyCycler. There are no user-serviceable parts for
this instrument. Call your local Bio-Rad office for instrument services.
To insure adequate cooling of the MyCycler, place it on a clean, flat surface, and be sure
that there is at least 4 inches (10 cm) clearance around each side of the thermal cycler.
Make sure that the bench space is free of any foreign objects or debris that could block the
fan vents.
Do not operate the MyCycler in extreme humidity or where condensation can short the
internal electrical circuits of the thermal cycler.
Notice
This Bio-Rad instrument is designed and certified to meet EN-61010 safety standards.
EN-61010 certified products are safe to use when operated in accordance with the instruction
manual. This instrument should not be modified in any way. Alteration of this instrument
will:
Void the manufacturer's warranty,
Void the EN-61010 safety certification,

Create a potential safety hazard. ^
Bio-Rad is not responsible for any injury or damage caused by use of this instrument for
purposes other than those for which it is intended, or by modifications of the instrument not
performed by Bio-Rad or an authorized agent.
This product conforms to the "Class A" standards for electromagnetic emissions intended
for laboratory equipment applications. It is possible that emissions from this product may
interfere with some sensitive appliances when placed nearby or in the same circuit as
these appliances. The user should be aware of this potential, and take appropriate mea
sures to avoid interference.
This instrument is intended for research applications only. ^
—
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Table of Contents
Page
Section 1 Introduction 1
1.1 Overview 1
1.2 Features 2
1.3 System Setup 2
1.3.1 Unpacking 2
1.3.2 Fuse Installation and Power Cable Connection 3
1.3.3 USB Cable Connection 4
1.3.4 Powering Up and Shutting Down 4
1.3.5 Standby Mode 4
1.4 Recommended Tubes and Plates 5
1.5 MyCycler Keypad 5
1.6 What's in this Manual 8
Section 2 Quick Guide for Running the MyCycler 9
Section 3 The Home Screen 10
3.1 Soft Key Functions for the Home Screen 10
Section 4 Thermal Cycling Protocols 11
4.1 Overview 11
4.2 The Protocol Library Screen 11
4.2.1 My Protocols 11
4.2.2 Bio-Rad Protocols 11
4.2.3 Protocol Options 12
4.2.4 Soft Key Functions for the Protocol Library 12
4.3 Protocol Parameters 13
4.3.1 Basic Programming Options 13
4.3.2 Advanced Programming Options 13
4.3.2.1 Increment/Decrement Temperature 13
4.3.2.2 Increment/Decrement Time 14
4.3.2.3 Temperature Gradient 14
4.4 Graphical Representation 14
4.5 Viewing Protocols 16
4.5.1 Soft Key Functions for the View Screen 16
Section 5 Creating and Editing Protocols 17
5.1 Specifying Time Values 17
5.2 Specifying Temperature Values 17
5.3 Specifying Cycle Repeats 17
5.4 Creating and Editing Protocols: Advanced Options 18
5.4.1 Temperature and Dwell Time Options (F3-Option) 18
5.4.2 Temperature Gradient 19
5.4.3 20
5.4.4 Changing the Number of Cycles or Steps (F4-Add/Del) 21
5.5 Soft Key Functions for the Edit Screen 21
5.6 Completing Protocols 21
5.7 Naming a Protocol 22
Section 6 Running Protocols 23
6.1 How to Run a Protocol 23

6.1.1 Run Setup Screen 23
6.1.2 Run Screen 24
6.1.3 Running Gradient Protocols 25
6.1.4 Converting a Gradient Protocol 25
6.2 Options While a Protocol is Running 26
6.2.1 Displaying the Home Screen while a Protocol is Running 26
6.2.2 A Power Failure while a Protocol is Running 26
6.2.3 Pausing a Running Protocol 27
6.2.4 Terminating a Running Protocol 27
6.2.5 End of Run Screen 27
Section 7 Reports 28
7.1 The Run Report 28
7.2 The Validation Report 28
7.3 Soft Key Functions for Reports 28
7.4 Uploading Reports 29
Section 8 Utilities 30
8.1 The Utilities Menu 30
8.1.1 View Reports 30
8.1.2 Instrument Information 30
8.1.3 Set Date and Time 30
8.1.4 Set Display Contrast 30
8.1.5 Service Options 30
8.2 The Set Preferences Menu 30
8.2.1 Default Hot Start Options 30
8.2.2 Default Temperature Measurement Mode 31
8.2.3 Default Sample Volume 31
8.2.4 Idle Temperature Measurement Mode 31
8.2.5 Lid Temperature Control 31
8.2.6 Auto-Standby Options 31
8.2.7 Instrument Name 32
8.2.8 Beeper Options 32
Section 9 The Help Screen 33
9.1 Soft Key Functions for the Help Screen 33
Section 10 Care and Maintenance 33
10.1 Cleaning the Unit 33
10.2 Replacing a Fuse or a Battery 33
10.3 Troubleshooting Procedure 34
10.4 Error Messages 35
Appendix A Specifications 36
Appendix B Product Information 38
^
IV

Section 1
Introduction
o 1.1 Overview
The Polymerase Chain Reaction (PCR) has been one of the most important
developments in Molecular Biology. This technique has greatly accelerated the rate
of genetic discovery, making critical techniques relatively easy and reproducible.
The MyCycler thermal cycling instrument provides optimum performance for
PCR and other thermal cycling techniques. The MyCycler incorporates a Peltier
driven heating and cooling system for superb thermal cycling performance. See
w Appendix A-Specifications at the end of this manual for detailed information
regarding the rates of heating and cooling, and accuracy and uniformity of the
reaction module's temperature. Rigorous testing of the module's accuracy, uniformity,
"-' and consistency in temperature, and of heating and cooling rates was conducted
to insure reliable and reproducible experimental results.
The MyCycler features a heated lid. This eliminates the need for any oil overlay
in the sample tubes as long as lid temperature control is on and the lid remains
closed throughout the run. The self-adjusting, heated lid provides the versatility to
accommodate a variety of tubes or plates.
.w The MyCycler offers two modes of temperature monitoring and control:
w • Algorithm - uses the experimentally derived sample temperature given a
specific sample volume
• Block - uses the actual sample block temperature
Both modes of temperature control yield excellent results in our test protocols.
The MyCycler comes with an exceptionally intuitive user interface, offering a
graphical view of the programmed protocols. Each protocol may include as many
w as 9 cycles with 9 steps each and up to 99 repeats for each cycle. Additionally, the
MyCycler is capable of advanced protocol options such as time and temperature
increments and decrements. Furthermore, every time a protocol is executed, a
^ detailed report of the run is recorded and stored on the instrument for 30 days.
* Practice of the polymerase chain reaction (PCR) process requires a license. The MyCycler is an authorized thermal
cycler, and may be used with PCR licenses available from Applied Biosystems. Its use with authorized reagents also
provides a limited PCR license in accordance with the label rights accompanying such reagents.

Handl
Keypad
<"■>
LCD Display
/—N
1.2 Features
• Self-adjusting lid and reaction module design accommodate 0.2 ml tubes,
strips, and 96-well plates.
• Graphical representation of thermal cycling protocols.
• User-friendly software, including menu driven software, ready-made protocol
templates and user-defined preferences.
• Run status and history are recorded in run reports and validation reports.
Optional sleep mode saves power when the instrument is not in use.
• USB port enables users to transfer and print protocols or reports with a host
computer connected to the instrument and a printer.
Compact design saves bench space.
• Temperature monitoring and control can be specified by instrument algorithm
or reaction module block mode.
• NIST-traceable temperature performance.
1.3 System Setup
1.3.1 Unpacking
The MyCycler is shipped in one box containing the following:
• MyCycler thermal cycler
• Power cord
• Instruction Manual
Fuses
• USB cable for PC interface
• MyCycler utility CD-ROM
^

Carefully remove the contents of the shipping box. To remove the thermal
cycler, lift it out by grasping the underside of the unit. Remove the plastic bag and
inspect the instrument for any external damage. Check off all parts against the
supplied packing list.
Your MyCycler was carefully tested at the factory and was shipped in good
working order. If any part is missing or damaged, contact Bio-Rad Laboratories
immediately.
1.3.2 Fuse Installation and Power Cable Connection
Your MyCycler is configured for 100 to 240 V. You should install the correct
fuse using the following procedure:
Warning: Failure to follow this procedure may result in damage to the unit
and invalidation of the warranty.
1. Disconnect the power cord from the unit.
2. Remove the fuse holder from the rear panel of the instrument with a small
flat-head screwdriver or similar tool.
3. Pull the fuse holder out and install the correct fuse. The MyCycler comes with
the following two fuses:
a. For 100-120 V operation: Use 8.0A, 5 x 20 mm, Type T fuses.
b. For 220-240 V operation: Use 4.0A, 5 x 20 mm, Type T fuses.
4. Reinsert the fuse holder into the rear panel of the instrument, and press the
fuse holder gently until it snaps into place.
5. Insert the power cord plug into the power entry module. Plug the power cord
into a properly grounded outlet.
Fuse
Power Entry
USB Port

••>
^
1.3.3 USB Cable Connection
In addition to the power cable connector, the rear panel of the MyCycler contains
a USB port that may be connected to a personal computer, allowing the transfer of
protocol files, Validation Reports, and Run Reports. Using this link, you may print
out any downloaded protocols or reports if the PC is connected to a printer. The USB
link is not necessary for running the instrument. —.
1.3.4 Powering Up and Shutting Down
Before powering up the MyCycler, place it in a location that has sufficient
ventilation and access to the reaction module and keypad. We recommend at least
4" (10 cm) clearance to the left, right, and rear of the instrument. For convenience,
about 14-15" (36-38 cm) clearance from the bench surface is needed to open the
lid.
To turn the MyCycler on, press the "Standby" button on the front panel of the
instrument once. A green LED next to the Standby button glows when the
instrument is on and receiving power. To shut down the MyCycler completely,
simply unplug the power cord from the power outlet. An alternative to system
shutdown is Standby mode.
1.3.5 Standby Mode
To conserve power, the MyCycler has a user-programmable standby option.
The green LED next to the Standby button blinks to indicate that the MyCycler is in
Standby mode. This option will turn off all non-essential operations in an idle
instrument, including the LCD screen, heated lid, and sample block temperature
control. The fan will turn-off when the internal temperatures have equilibrated.
Auto-Standby settings for the instrument may be programmed as described in
Section 8.2.6. When in Standby mode, briefly press the Standby button once to
turn the instrument back on.
Standby mode can also be initiated by holding down the blue Standby button
once for 3 to 4 seconds. The instrument will go into Standby mode unless you are
running a thermal protocol or have made unsaved changes to a protocol. If you are
running a thermal protocol or have made unsaved changes to a protocol, you will
be asked to verify the standby selection. ^-^
Note: Acceptance of standby initiation will terminate or abandon edits for the active
protocol.

1.4 Recommended Accessories
For optimal performance of the MyCycler, we recommend Bio-Rad tubes,
plates, and accessories as follows:
Catalog
Number Product Description
TWI-0201 0.2 ml Tubes With Domed Caps, natural, 1,000
TFI-0201 0.2 ml Tubes With Flat Caps, natural, 1,000
TBS-0201 0.2 ml 8-Tube Strips Without Caps, natural, 125
TCS-0801 Domed 8-Cap Strips, for 0.2 ml tubes and plates, natural, 120
TCS-0803 Optical Flat 8-Cap Strips, for 0.2 ml tubes and plates, ultraclear, 120
TBS-1201 0.2 ml 12-Tube Strips Without Caps, natural, 100
TCS-1201 Domed 12-Cap Strips, for 0.2 ml tubes and plates, natural, 200
MLP-9601 Multiplate 96-Well 0.2 ml Unskilled PCR Plates, natural, 25
MSB-1001 Microseal 'B' Adhesive Seals, 100
223-9442 96-Well PCR Plate Sealing Mats, 5
170-8870 iTaq DNA Polymerase, includes 250 U polymerase, 10x PCR buffer
and MgCI2 solution
170-8872 MgCI2 Solution, 1.25 ml of 50 mM MgCI2
170-8874 dNTP Solution, 200 u.l of 10 mM of each dNTP
The recommended sample volume for 0.2 ml tubes or 96 well plates is 15-100 ul.
Note: When using individual 0.2 ml tubes in the MyCycler, place at least 10 tubes
in the reaction block (in wells A1, A4, A9, A12, E1, D12, H1, H4, H9, and H12)to
ensure that the tubes are not deformed over the course of the protocol
F1 F2 F3 F4 F5
MyCyc

1.5 MyCycler Keypad
The MyCycler keypad has 26 keys on the front panel. These keys are described
in the following table (Table 1):
r~\
Table 1. Front Panel Controls
Key(s)
Description
Softkeys F1-F5 The five function keys (referred to as "softkeys") are
labeled F1 through F5. These keys are used to navigate
through the software screens and make selections in the
screen displays. The operations associated with these
keys are displayed in inverse video immediately above the
softkey. These operations change as the display changes.
For example, in the Home screen, the F1 softkey will take
you to the Protocol Library, and the F2 softkey will
enable you to Create a protocol.
Back The Back key will return you to the immediately previous
screen or, depending on the context, to some other, more
appropriate previous screen. From most places in the
firmware you can repeatedly press Back until, eventually,
you return to the Home screen. When the Home screen
is displayed, the Back key has no further function.
When menus or option boxes are presented, Back acts
as a Cancel key.
Alphanumeric Keys Centered below the display are ten alphanumeric keys
(keys 0-9), which are arranged like the keys on a telephone.
Each numeric key (except 1 and 0) is used to represent
three or more letters.
The alphanumeric keys are usually used as number keys
for the entry of time, temperature, and cycle repeats.
When entering a protocol or instrument name into a
screen display, the keys automatically shift to alpha mode
for the entry of letters. The word ALPHA is displayed in
the top right corner of the screen. You can toggle
between alpha and numeric by pressing the Shift key. To
enter uppercase letters, press F2-Caps Lock before
pressing the alphanumeric key.
To specify an alphabetic character, press the key until the
desired character is displayed. For example, the 2 key is
used for a, b, or c entries. To input the letter a, press the
2 key once. To input b, press the 2 key twice and to input
c, press the 2 key three times. If the 2 key is pressed a
fourth time, it will display the letter a.
. (Decimal Point)
' (Infinity)
When entering numeric decimal values, press this key to
enter values after the decimal.
The 0 key is labeled with an infinity symbol above the 0 to
indicate that it has a secondary function of Infinite Dwell
Time. Like the alphabetic characters, this secondary func
tion is accessed by first pressing the Shift key. The
Infinity key is used to indicate dwell times that are to be
terminated by user intervention.

w
Directional Arrows
< > A . V
-
Typically this feature is used at the end of a protocol, but it
can be used at other points as well. When an infinite dwell
time is specified, the MyCycler will pause the protocol at
the selected temperature until you terminate or resume
execution.
Clear The Clear key is used to clear the entire entry in an input
field. For example, if you have specified an incorrect
duration for a step, pressing the Clear key erases the
entire entry, not just the last character entered.
Shift The Shift key is located to the left of the alphanumeric
keys. The Shift key is used in conjunction with the
alphanumeric keys to switch between alphabetic and
numeric character (see the discussion above for the
alphanumeric keys), when naming a protocol or instrument.
The four Directional Arrow keys surround the Enter key
and direct the cursor when navigating the screen.
Normally the right and left arrows are used to move from
field to field, not within a field. The exception is the case
when you are assigning a protocol or instrument name
using the alphanumeric keys: in this instance the right
and left arrows move the cursor within the name field and
the only way to move out of the field is with the Enter key.
The up and down arrows are used to move the cursor from
line to line within selection boxes, or from one field to field
when editing or creating protocols. In some of the Utilities
screens, the up and down arrows are used to set the time,
date, and default conditions. When a time or temperature
field has a default value and that field is highlighted, pushing
an arrow key is an implied Enter, accepting the default
entry.
Enter In the middle of the arrow keys is the Enter key. When
you press Enter the current selection or input field is
accepted.
Stop Below the LCD screen and to the left of the F1 softkey is
the Stop key. If the Stop key is pressed while a protocol
is running, the protocol will be paused (as described in
section 6.2.3). Pressing the Stop key again, while the
protocol is paused will terminate the protocol.
Standby
When the instrument is in Standby mode, pressing the
Standby key once turns the instrument back on. When
the instrument is on, holding the Standby key for 3 to 4
sefonds puts the instrument into Standby mode. A
warning will appear if you attempt to initiate Standby
mode while running a protocol, or when unsaved changes
have been made to a protocol.

1.6 What's in this Manual
This manual is organized into the following sections.
• Section 1, Introduction: This chapter provides an overview of the instrument
and how to set it up.
• Section 2, Quick Guide for Running the MyCycler: This chapter is a quick
guide for the user that wants to start running the MyCycler immediately.
• Section 3, The Home Screen: This chapter describes the Home screen and
the functions associated with it.
• Section 4, Thermal Cycling Protocols: This chapter describes how to use
the Protocol Library, as well as the parameters, organization, and layout of
thermal cycling protocols.
• Section 5, Creating and Editing Protocols: This chapter explains how to use
the Edit screen, and the process of creating and editing protocols.
• Section 6, Running Protocols: This chapter provides instructions on how to
run any protocol. This includes a number of options for controlling the execution
and monitoring the progress of the protocol.
• Section 7, Reports: This chapter describes Validation reports and the Run
reports in detail, and explains how to read them.
• Section 8, Utilities: This chapter describes the features of the Utilities screen.
This screen supports a number of features for customizing the environment.
• Section 9, The Help Screen: This chapter describes how to access and use
the MyCycler's onboard help screens.
• Section 10, Care and Maintenance: This chapter provides information on
cleaning the unit, replacing fuses, a troubleshooting guide, and a list of error
messages.
• Appendix A, Specifications: This appendix provides the MyCycler system
specifications.
• Appendix B, Warranty: This appendix includes the MyCycler warranty and
technical support information.
• Appendix C, Product Information.

Section 2
w
Quick Guide for Running the MyCycler
The following procedure is provided for the user wishing to immediately start
using the MyCycler. Detailed information for using the instrument is provided in
subsequent sections.
1. Power up the MyCycler by either plugging in the instrument or, pressing the
Standby key on the front panel of the instrument, if in Standby mode. After a
quick diagnostic routine, the Home screen will be displayed.
2. Press F2-Create from the Home Screen. A selection menu will appear.
3. Select the "Custom" option from the selection menu (it should be selected by
default) and press Enter. You may also choose to edit a Bio-Rad template
protocol listed in this menu if the template protocol is similar to your desired
protocol.
4. Edit the fields of the protocol.
The default, custom protocol is a simple three-step amplification protocol;
30 seconds at 95°C, 30 seconds at 55°C, followed by 0 seconds at 72°C.
To add or delete a step or cycle, press F4-Add/Del and select the appropriate
option. Note that vertical lines demarcate different cycles, and that steps with
in the same cycle are not separated by vertical lines. Cycles are numbered
sequentially in the bottom left corner of their first step's display.
Use the arrow keys to move the selection box between the different fields
for each step of your protocol. Set point temperature fields are shown
immediately above the temperature plot line, whereas dwell time fields are
shown immediately below the temperature plot line. The repeats field,
which specifies the number of times a cycle is to occur, followed by an "x",
is shown in the bottom right corner of the last step of a cycle.
To add an increment or decrement option for either time or temperature
put the selection box on the desired time or temperature field, press
F3-Option, and select the desired option. After selecting the desired
option, a new field will pop up in the display. In this new field, input the
amount of time or degrees Celsius by which you want to increment or
decrement each repeat.
When you are finished editing the protocol, press F5-Done.
5. Save the protocol by choosing "Save Protocol As..." from the selection menu.
Name the protocol using the alphanumeric keys, as described in section 1.5,
and press Enter when finished.
6. The Home screen will appear. Press the F1-Protocol Library to access the
Protocol Library. Using the arrow keys, select the protocol you just created
and press Enter. A selection menu will appear. Select "Run Protocol".
7. The Run Setup screen should appear. Specify whether or not you want a hot
start (and the hot start temperature if you picked "YES"), and which temperature
measurement mode you want (and the sample volume if you picked
"Algorithmic Measurement").
8. Press F5-Begin Run to begin the run.

—
Section 3
The Home Screen
The Home screen is the first screen displayed after the instrument is turned on
and finishes its self-diagnostic routine. The Home screen serves as a starting place
for all functions of the interface and can be accessed from most other screens via
the F4-Home Screen softkey, even while running a protocol. The Home screen
also displays the current date and time, as well as the user-defined instrument
name. The default name is the instrument's serial number. The date, time, and
instrument's name may all be configured in Utilities, (see Section 8.1 Utilities)
r\
BIO-RAD
MyCycler
Monday, January 28, 2002
10:35 AM
My Personal Cycler
Choose an option below.
Protocol
Library
Run
Screen
3.1 Soft Key Functions for the Home Screen
Softkey Option
Description
F1
Protocol Library
F2
Create
Displays the Protocol Library screen, allows
access to all saved protocols
Displays a menu of Bio-Rad protocol templates.
Select either the protocol template most similar
to the desired protocol to begin editing, or
select Custom to create a new protocol from
scratch
F3
F4
F5
Run Screen
Utilities
Help
Displays the Run screen, used to monitor the
current run-status of the MyCycler
Displays the Utilities screen, select this option
to alter instrument settings or for other
miscellaneous functions
Displays the Help screen. You may browse
through an onboard collection of help topics
~
10

w
Section 4
Thermal Cycling Protocols
4.1 Overview
Thermal cycling protocols contain the temperature cycling information to direct
the MyCycler. A protocol is made up of as many as nine cycles, and a cycle is
made up of as many as nine steps. A step is defined by specifying the set point
temperature and dwell time at that temperature. A cycle is defined by specifying
the times and temperatures for all steps and the number of times the cycle is
repeated. The MyCycler comes with a set of predefined Bio-Rad protocols in the
Protocol Library. You may also create new protocols by modifying any existing
protocol in the library, including the Bio-Rad protocols, or you can create a new
protocol from scratch.
4.2 The Protocol Library Screen
The Protocol Library screen contains the list of all thermal protocols saved on
the instrument. All user-defined protocols appear on the left-hand side of the
screen in the column labeled "My Protocols". Bio-Rad template protocols appear
on the right-hand side of the screen in the column labeled "Bio-Rad". Use the
arrow keys to select a protocol and then press Enter for more options. (See
Section 4.2.3 Protocol Options)
t*
Usei-defined Protocols ■
Use arrow keys to select a protocol,
and then press Enter.
i My Protocols
My First Protocol
Bio-Rad |
WIIHSIITilHinU
RT-PCR-2
LONG-PCR-2
CVCLE-SEQ2
NESTED PRIM2
TOUCHDOWN
STflNDfiRD-3
RT-PCR-3
LONG-PCR-3
CYCLE-SEQ3
Bio-Rad Template
Protocols
4.2.1 My Protocols
User-defined protocols are displayed in the Protocol Library under the column
labeled "My Protocols". The MyCycler has sufficient memory to store up to 99
total protocols in the library. You may run, view, edit, delete, or rename any of
these protocols listed in the My Protocols column.
4.2.2 Bio-Rad Protocols
Bio-Rad protocols are displayed in the Protocol Library under the column
labeled "Bio-Rad". These protocols serve as templates for several different PCR
applications. These include standard PCR, reverse transcriptase PCR (RT-PCR),
nested primer PCR, PCR with temperature gradients, long PCR, touchdown PCR,
and cycle sequencing PCR. These Bio-Rad protocols may be run directly, or
modified as needed prior to running or saving. If you wish to modify a Bio-Rad
11

protocol and save the resulting protocol, you must use the "Save As" option and
specify a new name. Bio-Rad protocols cannot be overwritten or deleted.
4.2.3 Protocol Options
After selecting the desired protocol and pressing Enter, you are presented with
the following choices:
• Run Protocol: The Run Setup screen is displayed. (See section 6.1.1.)
• View Protocol: The protocol is displayed in the View screen. (See section 4.5.)
• Edit Protocol: The protocol is displayed in the Edit screen. (See section 5.)
• Delete Protocol: (Option only available for a user-defined protocol.) You will
be asked to confirm that you want to delete the selected protocol from memory.
Select YES to delete the protocol or select NO to keep the protocol.
• Rename Protocol: (Option only available for a user-defined protocol.) You will
be asked to input a new name for the selected protocol. Protocol names are
limited to 25 characters. Duplicate protocol names are not allowed.
4.2.4 Soft Key Functions for the Protocol Library
Softkey Option
Description
F1
Citations/PageUp
The Citations option is available when the
cursor is in the Bio-Rad template column. This
displays a short list of citations that describes
the currently selected Bio-Rad protocol.
The PageUp option is available when the
cursor is in the My Protocols column. This
scrolls the My Protocols column up one page
from the current page.
F2
Info/PageDown The Info option is available when the cursor is
in
the Bio-Rad column. This displays a short
description of the currently selected Bio-Rad
protocol.
The PageDown option is available when the
cursor is in the My Protocols column. This
scrolls the My Protocols column down one
page from the current page.
F3
F4
F5
Run Screen
Home Screen
Done
Displays the Run screen
Displays the Home screen
Displays more options for the selected protocol.
12

4.3 Protocol Parameters
4.3.1 Basic Programming Options
• Set point temperature: Temperatures between 4.0°C and 100.0°C may be
entered.
• Dwell time: Finite dwell times may be as long as 99 minutes and 59 seconds
O (99:59), or may be set as short as 0 seconds (00:00).
~ When the dwell time is set to 00:00, the MyCycler will heat or cool until it
attains the set point temperature and then immediately begin heating or cooling
to the next set point temperature.
w
Infinite dwell times may be programmed for any steps belonging to a cycle with
— only one repeat. When an infinite dwell time is reached, the instrument maintains
the specified temperature until you intervene. If the infinite dwell time is pro
grammed for any step other than the last step of the protocol, the instrument goes
^ into Pause mode when it reaches that step, and holds the set point temperature
until you press the Resume Run or End Run soft key. You may specify an infinite
dwell time by pressing the Shift key, followed by the 0 key.
• Repeat number: Any cycle without an infinite dwell time may have 1 to 99
^- repeats.
4.3.2 Advanced Programming Options
4.3.2.1 Increment/Decrement Temperature
Most protocols call for the exact same temperature for each repeat of a cycle,
-^ but in some instances you may wish to program an automatic increase or
decrease in the step temperature after each repeat. To input an automatic
increment or decrement function for a step, the cycle containing the step must
have more than one cycle repeat. The automatic increment and decrement
function updates the set point temperature by a specified amount, after every
repeat, starting after repeat one.
For example, you could create a cycle with 3 repeats, a step at 95°C, and a
second step at 55°C. You could then specify a 0.5°C automatic temperature
increment for the second step. Thus, on the first repeat of the cycle, the instrument
would go to 95°C and then to 55°C. Then on the second repeat of the cycle, the
instrument would go to 95°C and then to 55.5°C. Finally, on the third repeat of the
cycle, the instrument would go to 95°C and then to 56.0°C.
Temperature increments or decrements may be as low as 0.1 °C, and they may
be as large as desired, so long as they do not result in values outside the legal
ranges described in section 4.3.1. If you input an increment or decrement function
that would result in an illegal temperature value, the thermal protocol will run, but
the temperature will cease to increment or decrement once the upper or lower limit
has been reached. Furthermore, for every repeat that would result in an illegal tem
perature value, an error is counted on the End of Run screen and displayed in the
Validation and Run reports.
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c

4.3.2.2 Increment/Decrement Time
Most protocols call for the exact same dwell time for each repeat of a cycle, but
in some instances you may wish to program an automatic increase or decrease in
the step dwell time after each repeat. To input an automatic increment or decrement
function for a step, the cycle containing the step must have more than one cycle
repeat. The automatic increment and decrement function updates the dwell time by
a specified amount, after every repeat, starting after repeat one.
For example, you could create a cycle with 3 repeats, with a first step at 95°C
for 10 seconds and a second step at 55°C for 45 seconds. You could then specify
a 5-second automatic dwell time decrement for the second step. Thus, on the first
repeat of the cycle, the instrument would hold at 55°C for 45 seconds. Then on the
second repeat of the cycle, the instrument would hold at 55°C for 40 seconds.
Finally, on the third repeat of the cycle, the instrument would hold at 55°C for 35
seconds.
Dwell time increments or decrements may be as low as 1.0 seconds, and they
may be as long as desired, so long as they do not result in values outside the legal
ranges described in section 4.3.1. If you input an increment or decrement function
that would result in an illegal dwell time value, the thermal protocol will run, but the
dwell time will cease to increment or decrement once the upper or lower limit has
been reached. Furthermore, for every repeat that would result in an illegal dwell
time value, an error is counted on the End of Run screen and displayed in the
Validation and Run reports.
4.3.2.3 Temperature Gradient
The MyCycler Thermal Cycler offers a temperature gradient option for
optimization of assay conditions. Gradients may be programmed at any step of any
cycle of the protocol. The gradient option allows input of a temperature gradient of
1-25 degrees in total temperature span at temperatures as low as 30°C and as
high as 99°C.
Thermal Gradients in the MyCycler are formed from the front to the rear of the
sample block resulting in eight specific temperatures for assay optimization. This
innovative design allows for evaluation of the maximum assay components at each
specific temperature. Each row includes twelve wells for evaluation of assay
components such as MgCI2 or primer concentrations.
The temperature gradients formed by the MyCycler take a non-linear yet highly
reproducible shape that allows for excellent prediction of actual sample temperatures
at each row. Extensive validation of the gradient temperatures indicate that the non
linear gradient is both predictable and reproducible.
4.4 Graphical Representation
Thermal protocols are displayed graphically as a temperature plot. The graphical
representation shows a left-to-right plot of the thermal cycling program and reflects
approximate values of the set point temperatures along its y-axis. The plot displays
the set point temperature, dwell times, and advanced options, such as time or
temperature increments and decrements, for each step.
At each step, the set point temperature in Celsius (e.g., 95.0°C) is shown immediately
above the temperature plot, and the dwell time (in mm:ss format) is shown immediately
below the temperature plot. Temperature increments and decrements are denoted within
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the graphical display of a particular step, immediately above the set point temperature,
and followed by a thermometer icon and an up-arrow for increments or a down-arrow for
decrements. Time increments and decrements are denoted within the graphical display of
a particular step, below the dwell time, and followed by a clock icon and an up-arrow for
increments or a down-arrow for decrements.
Cycles are demarcated within the plot by vertical bars, and are labeled by cycle
number in the bottom left corner of their first steps. The number of repeats for
cycles are displayed in the bottom right corner of their last steps, e.g., 30 repeats
would be displayed as "(30x)", and 1 repeat would be displayed as "(1x)". For
cycles with an infinite hold, the "repeats" portion of the plot displays "(1x)".
The graphical representation of the protocol accommodates a maximum of five
steps on the screen at any one time, even if this results in a partial display of a
cycle. Cycle numbers and repeats are shown only in the first step of the cycle,
whether or not this step gets cut off from the display. If the protocol continues off
the left edge of the screen, a left arrow appears under the bottom left corner of the
graphical display. Likewise, if the protocol continues off the right edge of the
^_ screen, a right arrow appears under the bottom right corner of the graphical
display. In either case, if the protocol continues off the screen, you may use the left
and right arrow keys to scroll through the protocol when viewing or editing a protocol.
w
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