Bio-Rad Firmware Software Updates User Manual
MiniOpticon™ System
Instruction Manual
For MiniOpticon real-time PCR detection
™
system with CFX Manager
Catalog #CFB-3120
software
©2012 Bio-Rad Laboratories, Inc. Reproduction in any form, either print or electronic, is prohibited
without written permission of Bio-Rad Laboratories, Inc.
Adobe, Acrobat, and Reader are trademarks of Adobe Systems Incorporated. Excel, Microsoft,
Windows, and Windows Vista are trademarks of Microsoft Corporation. EvaGreen is a trademark of
Biotium, Inc. Bio-Rad Laboratories, Inc., is licensed by Biotium, Inc., to sell reagents containing
EvaGreen dye for use in real-time PCR, for research purposes only. FAM, HEX, VIC, and ROX are
trademarks of Applera Corporation. SYBR® is a trademark of Life Technologies Corporation. Bio-Rad
Laboratories, Inc. is licensed by Life Technologies Corporation to sell reagents containing SYBR® Green
for use in real-time PCR, for research purposes only.
LICENSE NOTICE TO PURCHASER
Purchase of this instrument conveys a limited non-transferable immunity from suit for the purchaser's own internal
research and development and for use in human in vitro diagnostics and all other applied fields 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 estoppel 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.
Bio-Rad’s real-time thermal cyclers are licensed real-time thermal cyclers under Applera’s United States Patent No.
6,814,934 B1 for use in research, human in vitro diagnostics, and all other fields except veterinary diagnostics.
This product is covered by one or more of the following U.S. patents, their foreign counterparts, or their foreign
counterparts owned by Eppendorf AG: U.S. Patent Nos. 6,767, 512 and 7,074,367.
Bio-Rad Resources
Table 1 lists Bio-Rad resources and how to locate what you need.
Table 1. Bio-Rad resources
Resource How to Contact
Local Bio-Rad Laboratories
representatives
Technical notes and literature Go to the Bio-Rad website (www.bio-rad.com). Type a
Technical specialists Bio-Rad’s Technical Support department is staffed with
Find local information and contacts on the Bio-Rad website
by selecting your country on the home page
(www.bio-rad.com). Find the nearest international office
listed on the back of this manual.
search term in the Search box and select Documents tab to
find links to technical notes, manuals, and other literature.
experienced scientists to provide customers with practical
and expert solutions. To find local technical support on the
phone, contact your nearest Bio-Rad office. For technical
support in the United States and Canada, call 1-800-4246723 (toll-free phone), and select the technical support
option.
Writing Conventions Used in this Manual
This manual uses the writing conventions listed in Table 2.
Table 2. Conventions used in this manual
Convention Meaning
TIP: Provides helpful information and instructions, including information
explained in further detail elsewhere in this manual.
NOTE: Provides important information, including information explained in
further detail elsewhere in this manual.
WARNING! Explains very important information about something that might
damage the researcher, damage an instrument, or cause data loss.
X > Y Select X and then select Y from a toolbar, menu or software window.
For information about safety labels used in this manual and on the MiniOpticon system, see, “Safety and
Regulatory Compliance” on page iii.
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MiniOpticon Instruction Manual
Safety and Regulatory Compliance
For safe operation of the MiniOpticon system, we strongly recommend that you follow the safety
specifications listed in this section and throughout this manual.
Safety Warning Labels
Warning labels posted on the instrument and in this manual warn you about sources of injury or harm.
Refer to Table 3 to review the meaning of each safety warning label.
Table 3. Meaning of safety warning labels
CAUTION: Biohazard! This symbol identifies components that may become contaminated
with biohazardous material.
CAUTION: Risk of danger! This symbol identifies components that pose a risk of personal
injury or damage to the instrument if improperly handled. Wherever this symbol appears,
consult the manual for further information before proceeding.
CAUTION: Hot surface! This symbol identifies components that pose a risk of personal
injury due to excessive heat if improperly handled.
Instrument Safety Warnings
The warning labels shown in Table 4 also display on the instrument, and refer directly to the safe use of
the MiniOpticon real-time PCR detection system.
Table 4. Instrument Safety Warning Labels
Icon Meaning
Warning about risk of harm to body or equipment.
Operating the MiniOpticon real-time PCR detection system before reading this manual can
constitute a personal injury hazard. For safe use, do not operate this instrument in any
manner unspecified in this manual. Only qualified laboratory personnel trained in the safe
use of electrical equipment should operate this instrument. Always handle all components
of the system with care, and with clean, dry hands.
CAUTION: Biohazard! This symbol identifies components that may become contaminated
with biohazardous material.
Warning about risk of burning.
A thermal cycler generates enough heat to cause serious burns. Wear safety goggles or
other eye protection at all times during operation. Always allow the sample block to return
to idle temperature before opening the lid and removing samples. Always allow maximum
clearance to avoid accidental skin burns.
Warning about risk of explosion.
The sample blocks can become hot enough during the course of normal operation to cause
liquids to boil and explode.
iii
Safe Use Specifications and Compliance
Table 5 lists the safe use specifications for the MiniOpticon system. Shielded cables (supplied) must be
used with this unit to ensure compliance with the Class A FCC limits.
Table 5. Safe Use Specifications
Safe Use Requirements Specifications
Indoor use. The system will operate safely when the ambient
temperature is 5 — 40oC and will meet performance
Temperature
Altitude Up to 2,000 meters above sea level
specifications when the ambient temperature is 15—31oC
with a maximum relative humidity of 80% for temperatures
up to 31oC, decreasing linearly to 50% relative humidity at
40oC
Electrical supply
Installation categories (Overvoltage
Categories) II
Pollution degree 2
100—240 VAC, 50—60 Hz, 400W. Main supply voltage
fluctuations not to exceed +/- 10% of nominal voltage
REGULATORY COMPLIANCE
This device complies with Part 15 of the FCC Rules. Operation is subject to the following two conditions:
(1) this device may not cause harmful interference, and (2) this device must accept any interference
received, including interference that may cause undesirable operation.
This device has been tested and found to comply with the EMC standards for emissions and
susceptibility established by the European Union at time of manufacture.
This digital apparatus does not exceed the Class A limits for radio noise emissions from digital apparatus
set out in the Radio Interference Regulations of the Canadian Department of Communications.
LE PRESENT APPAREIL NUMERIQUE N’EMET PAS DE BRUITS RADIOELEC¬TRIQUES DEPASSANT
LES LIMITES APPLICABLES AUX APPAREILS NUMERIQUES DE CLASS A PRESCRITES DANS LE
REGLEMENT SUR LE BROUILLAGE RADIOELECTRIQUE EDICTE PAR LE MINISTERE DES
COMMUNICATIONS DU CANADA.
This equipment generates, uses, and can radiate radio frequency energy and, if not installed and used in
accordance with the instruction manual, may cause harmful interference to radio communications.
Operation of this equipment in a residential area is likely to cause harmful interference in which case the
user will be required to correct the interference at his own expense.
FCC WARNING
NOTE: Changes or modifications to this unit not expressly approved by the party responsible
for compliance could void the user’s authority to operate the equipment.
This equipment has been tested and found to comply with the limits for a Class A digital device, pursuant
to Part 15 of the FCC Rules. These limits are designed to provide reasonable protection against harmful
interference when the equipment is operated in a commercial environment. This equipment generates,
uses, and can radiate radio frequency energy and, if not installed and used in accordance with the
instruction manual, may cause harmful interference to radio communications. Operation of this
equipment in a residential area is likely to cause harmful interference in which case the user will be
required to correct the interference at his own expense.
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MiniOpticon Instruction Manual
Although this design of instrument has been tested and found to comply with Part 15, Subpart B of the
FCC Rules for a Class A digital device, please note that this compliance is voluntary, for the instrument
qualifies as an “Exempted device” under 47 CFR § 15.103(c), in regard to the cited FCC regulations in
effect at the time of manufacture.
Hazards
The MiniOpticon real-time PCR detection system is designed to operate safely when used in the manner
prescribed by the manufacturer. If the MiniOpticon system or any of its associated components are used
in a manner not specified by the manufacturer, the inherent protection provided by the instrument may be
impaired. Bio-Rad Laboratories, Inc. is not liable for any injury or damage caused by the use of this
equipment in any unspecified manner, or by modifications to the instrument not performed by Bio-Rad or
authorized agent. Service of the MiniOpticon system should be performed only by Bio-Rad personnel.
Biohazards
The MiniOpticon system is a laboratory product. However, if biohazardous samples are present, adhere to
the following guidelines and comply with any local guidelines specific to your laboratory and location.
PRECAUTIONS
• Always wear laboratory gloves, coats, and safety glasses with side shields or goggles
• Keep your hands away from your mouth, nose and eyes
• Completely protect any cut or abrasion before working with potentially infectious materials
• Wash your hands thoroughly with soap and water after working with any potentially infectious
material before leaving the laboratory
• Remove wristwatches and jewelry before working at the bench
• Store all infectious or potentially infectious material in unbreakable, leak-proof containers
• Before leaving the laboratory, remove protective clothing
• Do not use a gloved hand to write, answer the telephone, turn on a light switch, or touch
anything that other people may touch without gloves
• Change gloves frequently. Remove gloves immediately when they are visibly contaminated
• Do not expose materials that cannot be properly decontaminated to potentially infectious
material
• Upon completion of the operation involving biohazardous material, decontaminate the work
area with an appropriate disinfectant (for example, a 1:10 dilution of household bleach)
• No biohazardous substances are exhausted during normal operations of this instrument
SURFACE DECONTAMINATION
WARNING! To prevent electrical shock, always turn off and unplug the instrument prior to performing
decontamination procedures.
The following areas can be cleaned with any hospital-grade bactericide, virucide, or fungicide
disinfectant:
• Outer lid and chassis
• Inner reaction block surface and reaction block wells
• Control panel and display
v
To prepare and apply the disinfectant, refer to the instructions provided by the product manufacturer.
Always rinse the reaction block and reaction block wells several time with water after applying a
disinfectant. Thoroughly dry the reaction block and reaction block wells after rinsing with water.
WARNING! Do not use abrasive or corrosive detergents or strong alkaline solutions. These agents can
scratch surfaces and damage the reaction block, resulting in loss of precise thermal control.
DISPOSAL OF BIOHAZARDOUS MATERIAL
The MiniOpticon system contains no potentially hazardous chemical materials. Dispose of the following
potentially contaminated materials in accordance with laboratory local, regional and national regulations:
• Clinical samples
• Reagents
• Used reaction vessels or other consumables that may be contaminated
Chemical Hazards
The MiniOpticon system contains no potentially hazardous chemical materials.
Explosive or Flammability Hazards
The MiniOpticon system poses no uncommon hazard related to flammability or explosion when used in a
proper manner as specified by Bio-Rad Laboratories.
Electrical Hazards
The MiniOpticon system poses no uncommon electrical hazard to operators if installed and operated
properly without physical modification and connected to a power source of proper specification.
Transport
Before moving or shipping the MiniOpticon system, decontamination procedures must be performed.
Always move or ship the MiniOpticon system with the supplied packaging materials that will protect the
instrument from damage. If appropriate containers cannot be found, contact your local Bio-Rad office.
Storage
The MiniOpticon system can be stored under the following conditions:
• Temperature range: –20 to 60oC
• Relative humidity: maximum 80%
Disposal
The MiniOpticon real-time PCR detection system contains electrical or electrical materials; it should be
disposed of as unsorted waste and must be collected separately according to the European Union
Directive 2002/96/CE on waste and electronic equipment —WEEE Directive. Before disposal, contact
your local Bio-Rad representative for country-specific instructions.
vi
Table of Contents
Bio-Rad Resources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ii
Writing Conventions Used in this Manual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ii
Safety and Regulatory Compliance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . iii
Hazards . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
MiniOpticon Instruction Manual
Chapter 1. System Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
System Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
System Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Setting Up the system . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Running Experiments. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Chapter 2. CFX Manager™ Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Main Software Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Startup Wizard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Detected Instruments Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Status Bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Instrument Properties Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Master Mix Calculator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Scheduler. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Chapter 3. Performing Runs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Run Setup Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
PrimePCR Runs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Protocol Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Plate Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Start Run Tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Run Details Window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Instrument Summary Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Chapter 4. Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Protocol Editor Window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Protocol Editor Controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Temperature Control Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Protocol AutoWriter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
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Table of Contents
Chapter 5. Plates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Plate Editor Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Setup Wizard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Select Fluorophores Window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
Well Loading Controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Experiment Settings Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Well Selector Right-Click Menu Items . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Well Groups Manager Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Plate Spreadsheet View/Importer Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Chapter 6. Data Analysis Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Data Analysis Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Quantification Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Data Analysis Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Well Selectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Charts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Spreadsheets. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Export . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Chapter 7. Data Analysis Windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Quantification Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Quantification Data Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Melt Curve Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
Melt Curve Data Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
End Point Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Allelic Discrimination Tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Custom Data View Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
QC Tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
Run Information Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Data File Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
Well Group Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Chapter 8. Gene Expression Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Gene Expression . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Plate Setup for Gene Expression Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
Guided Plate Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
Bar Chart . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
Experiment Settings Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
Clustergram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Scatter Plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
Volcano Plot. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
Heat Map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
Gene Study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
Gene Study Report Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
Gene Expression Calculations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
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MiniOption Instruction Manual
Chapter 9. Users and Preferences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
Log in or Select User . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
User Preferences Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
Files Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
Protocol Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
Plate Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
Data Analysis Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
Gene Expression Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
QC Tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
Custom Export Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
User Administration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
Chapter 10. Resources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
LIMS Integration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
Calibration Wizard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
Instrument Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
Application Log . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
Troubleshooting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
ix
Table of Contents
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MiniOpticon Instruction Manual
1 System Installation
Read this chapter for information about setting up the MiniOpticon™ real-time PCR detection
system:
• System overview (page 1)
• System requirements (page 3)
• Setting up the system (page 4)
• Installing CFX Manager™ software (page 4)
• Running experiments (page 8)
System Overview
The MiniOpticon system uses an array of 48 light-emitting diodes (LEDs) to sequentially
illuminate each of the 48 wells in the cycler block. The LEDs efficiently excite fluorescent dyes
with absorption spectra in the 470–505 nm range. The MiniOpticon system uses two filtered
photodiodes for fluorescence detection. The first channel is optimized to detect dyes with
emission spectra in the 523–543 nm range, such as SYBR® Green I and FAM. The second
channel is optimized for dyes with emission spectra of 540–700 nm. The MiniOpticon detector
is calibrated at the factory and requires no further calibration before use.
The MiniOpticon system (Figure 1) includes:
• Optical tower. This tower includes an optical system to collect fluorescent data
NOTE: The serial number of the MiniOpticon system is located on a sticker on the
back of the optical tower.
1
System Installation
• MJ Mini™ thermal cycler base. The MiniOpticon system includes a thermal cycler
block that rapidly heats and cools samples.
Figure 1. Front view of the MiniOpticon system.
When open, the MiniOpticon system includes these features:
• Inner lid with heater plate. The heater lid maintains temperature on the top of the
reaction vessel to prevent sample evaporation. Avoid touching or otherwise
contaminating the heater plate. Never poke anything through the holes, the apical
system can be damaged.
• Block. Load samples in this block before the run
WARNING! Prevent contamination of the instrument by spills, and never run a
reaction with an open or leaking sample lid. For information about general cleaning
and maintenance of the instrument, see “Instrument Maintenance” (page 127).
WARNING! Avoid touching the inner lid or block: These surfaces can be hot.
The back panel of the MiniOpticon system includes these features (Figure 2):
• Power switch. Press the power switch to turn the power on
• Power input. Plug in the power cord here
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MiniOpticon Instruction Manual
• USB connections. Use these ports to connect the MiniOpticon system to a computer
Figure 2. Back panel of MiniOpticon System.
WARNING! Avoid contact with the back panel during operation.
System Requirements
To operate the MiniOpticon system, use the following power sources and cables:
• Input power. 100—240 VAC, 50—60 Hz
• Indoor use. Ambient temperature of 15—31oC. Relative humidity maximum of 80%
(non-condensing)
• Air Supply. The MiniOpticon system requires a constant supply of air that is 31°C or
cooler in order to remove heat from the heat sink. Air is taken in from the lower vents
located on the sides and front of the instrument and exhausted from the fan in the back.
If the air supply is inadequate or too hot, the instrument can overheat, causing
performance problems and even automatic shutdowns
WARNING! Do not place the MiniOpticon system on a lab bench covered by bench
paper. The bench paper can prohibit sufficient air circulation.
• USB cable. Control the MiniOpticon system using only the USB cable provided from
Bio-Rad. This cable is sufficiently shielded to help prevent data loss
3
System Installation
Setting Up the system
The MiniOpticon system should be installed on a clean, dry, level surface with sufficient cool
airflow to provide adequate air supply to run properly. The MiniOpticon system requires a
location with power outlets to accommodate the MiniOpticon system and the computer.
NOTE: Only one MiniOpticon system should be connected to a computer at one
time.
Installing the MiniOpticon System
To install the MiniOpticon system:
1. Your MiniOpticon system shipment includes the components listed below. Remove all
packing materials and store them for future use. If any items are missing or damaged,
contact your local Bio-Rad office.
• MiniOpticon system
• USB cable
• CFX ManagerTM software installation CD
• Instruction manual
• CFX Manager software quick guides for protocol, plate, data analysis, and gene
expression analysis
2. Firmly grasp the instrument from beneath to support the weight of the cycler and the
optical tower. Carefully lift the instrument out of the shipping box.
WARNING! Do not lift the instrument by the green handle.
3. Insert the power cord plug into its jack at the back of the instrument.
4. Plug the power cord into a standard 110 V or 220 V electrical outlet. The MiniOpticon
system will accept 220 V automatically. Avoid plugging the MiniOpticon system into a
power outlet that is already being used for other laboratory equipment
NOTE: Turn the system on only after installing CFX Manager software. The power
switch is on the back right-hand side of the MiniOpticon system.
Installing CFX Manager Software
CFX Manager software is run on a personal computer (PC) with either the Windows XP,
Windows Vista, or Windows 7 operating system and is required to run and analyze real-time
PCR data from the MiniOpticon system. Table 6 lists the computer system requirements for
the software.
Table 6. Computer requirements for CFX Manager software.
System Minimum Recommended
Operating system Windows XP Professional SP2 and
above, Windows Vista, or Windows
7 Home Premium and above.
Drive CD-ROM drive CD-RW drive
Hard drive 10 GB 20 GB
Processor speed 2.0 GHz 2.0 GHz
RAM 1 GB RAM (2 GB for Windows
Vista)
Screen resolution 1024 x 768 with true-color mode 1280 x 1024 with true-color mode
Windows XP Professional SP3 or
Windows 7.
2 GB RAM
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MiniOpticon Instruction Manual
Table 6. Computer requirements for CFX Manager software. (continued)
System Minimum Recommended
USB USB 2.0 Hi-Speed port USB 2.0 Hi-Speed port
WARNING! Running a MiniOpticon system with CFX Manager software on a PC
computer with a Windows 64-bit operating system is not supported due to
incompatible USB drivers. A PC computer with a 64-bit processor (like Intel) on a
32-bit Windows operating system is supported.
WARNING! CFX Manager software can be installed on the same computer that
already has Opticon MonitorTM version 3.1 installed. There may be conflicts
controlling the instrument if both software packages are opened at the same time
with the MiniOpticon turned on.
WARNING! If the computer with the CFX Manager software is running a virus scan
program, make sure scans are performed when the MiniOpticon system is idle.
To install the CFX Manager software:
1. Log in to the computer with administrative privileges, the software must be installed on
the computer by a user with administrative privileges.
2. Place the CFX Manager software CD in the computer’s CD drive.
3. The software launch page should appear automatically. Double-click Install Software on
the software launch page (Figure 3).
Figure 3. Software installation screen.
TIP: Click the Documentation button to find searchable PDF copies of instrument
manuals and other documentation.
4. Accept the terms in the license agreement to continue.
5. Follow the instructions on the screen to complete the installation. When completed, the
Bio-Rad CFX manager software icon will appear on the desktop of the computer.
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System Installation
6. If the launch page does not appear automatically, double-click on (CD drive):\Bio-Rad
CFX, then open and follow instructions in the Readme.txt file.
NOTE: For Windows Vista operating system, you will be prompted to install device
software for Jungo during the CFX Manager software installation. Click Install to
proceed. If prompted with the warning “Windows can’t verify the publisher of this
driver software,” Click Install this driver software anyway to proceed.
Installing MiniOpticon System Drivers
The MiniOpticon system drivers must be installed on the computer in order to properly
communicate with the device and perform real-time PCR experiments. The drivers are
installed automatically during CFX Manager software installation for computers running
Windows Vista operating system. Drivers must be installed manually for computers running
Windows XP operating system.
NOTE: For Windows XP operating system, three drivers must be installed: Bio-Rad
Thermal Cycler (EEPROM Empty), Bio-Rad Mini Optical Module and Bio-Rad Mini
Cycler. The driver installation package provides instructions on how to install the
drivers correctly.
To install the system drivers for Windows XP:
1. Connect the MiniOpticon system to the computer by plugging a USB cable (square end)
into the USB 2.0 port located on the back of the MiniOpticon system, and then
connecting the cable (flat end) into the USB 2.0 port located on the computer.
2. Turn the MiniOpticon system on by pressing the switch on the back of the system so that
the side marked “I” is depressed.
3. Follow the instructions in the Found New Hardware Wizard that launches after the
instrument is first detected by the computer.
4. On the first screen, select Yes, this time only to instruct the Windows operating system
to connect to Windows Update to search for software (Figure 4). Click Next.
Figure 4. Found New Hardware Wizard.
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MiniOpticon Instruction Manual
5. Select Install the software automatically to install the Bio-Rad Thermal Cycler
(EEPROM Empty) driver. Click Next (Figure 5).
Figure 5. Software (Driver) installation screen.
6. A window will appear indicating the driver being installed has not passed Windows Logo
testing to verify its compatibility with Windows XP. Click Continue Anyway to proceed.
7. Click Finish (Figure 6) at the software installation completion screen when the driver is
installed.
Figure 6. Finished Driver installation screen.
8. Repeat the driver installation for the Bio-Rad Mini Optical Module and the Bio-Rad
MiniCycler drivers.
7
System Installation
Running Experiments
Be sure that the MiniOpticon system is connected to the computer and turned on before
launching the CFX Manager software. The green protocol-indicator light on the front of the
MiniOpticon detector is illuminated only during a protocol run.
WARNING! Remove the shipping plate from the thermal cycler block to operate.
Loading the Block
1. To access the MiniOpticon system’s block, turn the front green handle counter-clockwise
until it snaps into the open position. Rotate the entire tower outward, to the left.
2. Place the 48-well, 0.2 ml microplate, or tube strips with sealed lids in the block. Check
that the tubes are completely sealed to prevent leakage. For optimal results, load sample
volumes of 15–30 µl.
3. To ensure uniform heating and cooling of samples, sample vessels must be in complete
contact with the sample holder. Adequate contact is ensured by:
• Verifying the sample holder is clean before loading samples
• Firmly pressing tubes, or a 48-well microplate into the sample holder
TIP: Spin down reactions in tubes or microplates before loading into the thermal
cycler block. Air bubbles in samples, or liquid on the plate deck, can affect results.
• Bio-Rad strongly recommends that oil not be used to thermally couple sample
vessels to the block
NOTE: Do not open the MiniOpticon detector while the green protocol-indicator
light is illuminated. Opening the door, particularly during a scan of the plate, may
interrupt the software’s control of the protocol.
4. To close the instrument, rotate the tower back into the closed position and then turn the
green handle clockwise (Figure 1). Both the tower and the handle have spring
mechanisms that facilitate closure.
NOTE: For accurate data analysis, check that the orientation of reactions in the
block is exactly the same as the orientation of the well contents in the software
Plate tab (see “Plate Tab” on page 23). If needed, edit the well contents before,
during, or after the run.
WARNING! When running the MiniOpticon system, always balance the tube strips
or cut microplates in the wells. For example, if you run one tube strip on the left
side of the block, run an empty tube strip (with caps) on the right side of the block
to balance the pressure applied by the heated lid.
WARNING! Be sure that nothing is blocking the lid when it closes. Although there
is a safety mechanism to prevent the lid from closing if it senses an obstruction, do
not place anything in the way of the closing lid.
Recommended Plastic Consumables
Run only white-welled 48-well plates or white-welled strip tubes in the MiniOpticon system.
For optimal results, Bio-Rad provides the following consumables for the MiniOpticon system
(catalog numbers are provided in bold):
• MLL-4851. Multiplate low-profile 48-well unskirted PCR plates, white color wells
• TLS-0851. Low-profile 8-tube strips, 0.2 ml, without caps, white color wells
• TCS-0803. Optical flat 8-cap strips, for 0.2 ml tubes and plates, ultraclear
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MiniOpticon Instruction Manual
2 CFX Manager™ Software
Read this chapter for information about getting started with CFX Manager software.
• Main software window (page 9)
• Startup Wizard (page 12)
• Detected Instruments Pane (page 13)
• Status Bar (page 13)
• Instrument Properties window (page 14)
• Master Mix Calculator (page 15)
• Scheduler (page 16)
Main Software Window
Features available in the main software window are provided in Figure 7.
Figure 7. The main software window.
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CFX Manager™ Software
Menu Bar
The menu bar of the main software window provides the items listed in Table 7.
Table 7. Menu bar items in the main software window
Menu Item Command Function
File New Create a new protocol, plate, run, or Gene Study.
View Application Log Display the application log for the software.
User Select User Open the Select User window to change software
Open Open existing files, including protocol (.prcl), plate
(.pltd), data (.pcrd), Gene Study (.mgxd), and
stand-alone run files (.zpcr).
Recent Data Files View a list of the ten most recently viewed data
files, and select one to open in Data Analysis.
Repeat a run Open the Run Setup window with the protocol and
plate from a completed run to quickly repeat the
run.
Exit Exit the software program.
Run Reports Select a run report to review from a list.
Startup Wizard Open the Startup Wizard.
Run Setup Open the Run Setup window.
Instrument Summary Open the Instrument Summary window.
Detected Instruments Show or hide the Detected Instruments pane.
Toolbar Show or hide the main software window toolbar.
Status Bar Show or hide the main software window status
bar.
Show Open the Block Status window, application data
folder, user data folder, LIMS file folder, PrimePCR
folder, run history, or a window displaying the
properties of all connected instruments.
users.
Change Password Change your user password.
User Preferences Open the User Preferences window.
User Administration Manage users in the User Administration window.
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MiniOpticon Instruction Manual
Table 7. Menu bar items in the main software window (continued)
Menu Item Command Function
Tools Scheduler Open the Scheduler to make reservations for
instrument use.
Master Mix Calculator Open the Master Mix Preparation calculator.
Protocol AutoWriter Open the Protocol AutoWriter window to create a
new protocol.
Ta Calculator Open the Ta Calculator window to calculate the
annealing temperature of primers.
Dye Calibration Wizard Open the Dye Calibration window to calibrate an
instrument for a new fluorophore.
Reinstall Instrument
Drivers
Zip Data and Log Files Choose and condense selected files in a zipped
Options Configure software email settings.
Windows Cascade Arrange software windows on top of each other.
Tile Vertical Arrange software windows from top to bottom.
Tile Horizontal Arrange software windows from right to left.
Close All Close all open software windows.
Help Contents Open the software Help for more information
Index View the index in the software Help.
Search Search the software Help.
qPCR Applications &
Technologies Web Site
PCR Reagents Web Site View a website that lists Bio-Rad PCR and real-
PCR Plastic
Consumables Web Site
Software Web Site View a website that lists Bio-Rad PCR and real-
Check For Updates Check for software or instrument updates.
About Open a window to see the software version.
Reinstall the drivers that control communication
with Bio-Rad real-time PCR systems
file for storage or to email.
about running PCR and real-time PCR.
Open a website to find information about real-time
PCR.
time PCR reagents.
View a website that lists Bio-Rad consumables for
PCR and real-time PCR runs.
time PCR amplification software.
Toolbar Buttons
Click a button in the toolbar of the main software window (Table 8) for quick access to
common software commands.
Table 8. Toolbar buttons in the main software window.
Button Button Name Function
Open a Data File or
Gene Study
Open a browser window to locate a data file (*.pcrd
extension) and open it in the Data Analysis window or
a gene study file (.mgxd extension) open it in the Gene
Study window.
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CFX Manager™ Software
Table 8. Toolbar buttons in the main software window. (continued)
Button Button Name Function
Scheduler Open the Scheduler to reserve a PCR instrument.
Master Mix Calculator Open the Master Mix Calculator window to set up
reaction mixes.
User-defined Run Setup Open the Run Setup window to set up a run (page 21).
PrimePCR Run Setup Open the Run Setup window with the default
PrimePCR™ protocol and plate layout loaded based
on the instrument selected.
Startup Wizard Open the Startup Wizard that links you to common
software functions (page 12).
Startup Wizard
The Startup Wizard automatically appears when CFX Manager software is first opened. If it is
not shown, click the Startup Wizard button on the main software window toolbar.
Options in the Startup Wizard include the following:
• Run setup. Select the appropriate instrument in the pull-down list to ensure the default
plate settings match the instrument to be used
• User-defined. Set up the protocol and plate to begin a new run in the Run Setup
window (page 21)
• PrimePCR. Open the Run Setup window with the default PrimePCR protocol and
plate layout (for the selected instrument) loaded. PrimePCR plate layouts are
available only for 96- and 384-well plates.
• Repeat Run. Set up a run with the protocol and plate layout from a completed run. If
needed, you can edit the run before starting
• Analyze. Open a data file to analyze results from a single run (page 53) or a gene study
file for results from multiple gene expression runs (page 97)
12
Detected Instruments Pane
The connected instrument appears in the Detected Instruments pane (Figure 8). This list
shows each instrument as an icon named with the serial number (default). Right-click on the
instrument in the Detected Instruments pane to open the Instrument Properties window and
rename the instrument.
Figure 8. Instruments listed in the Detected Instruments pane.
Right-click on the instrument icon to select one of these options:
• View Status. Open the Run Details window to check the status of the selected
instrument block
• Flash Block Indicator. Flash the indicator LED on the instrument
• Rename. Change the name of the instrument
• Properties. Open the Instrument Properties window
• Collapse All. Collapse the list of instruments in the Detected Instruments pane
• Expand All. Expand the list of instruments in the Detected Instruments pane
MiniOpticon Instruction Manual
You can also control a block by clicking an instrument block icon in the Detected Instrument
pane and then clicking a button in the Selected Instrument pane (Figure 9).
• Click View Status to open the Run Details window to check the status of the
• Click View Summary to open the Instrument Summary window
Status Bar
Figure 9. Buttons at the bottom of the Detected Instrument pane.
selected instrument block
The left side of the status bar at the bottom of the main software window shows the current
status of the instruments. View the right side of the status bar to see the current user name,
date, and time. Click and drag the right corner of the status bar to resize the main window.
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CFX Manager™ Software
Instrument Properties Window
To open the Instrument Properties window to view information about an instrument, right-click
on the instrument icon in the Detected Instruments pane (Figure 8). The window includes two
tabs (Figure 10):
• Properties. View serial numbers of the MiniOpticon system
• Calibrated Dyes. View the list of calibrated fluorophores
Figure 10. Instrument Properties window.
Properties Tab
The Properties tab displays important serial numbers for the connected instrument. The
firmware versions are also displayed. The default name for an instrument is the MiniOpticon
serial number, which appears in many locations in the software.
Calibrated Dyes Tab
Open the Calibrated Dyes tab (Figure 11) to view the list of calibrated fluorophores and plates
for the selected instrument. Click an Info button to see detailed information about a
calibration.
14
Figure 11. Calibrated Dyes tab in the Instrument Properties window.
Master Mix Calculator
To open the Master Mix Calculator, click the Master Mix Calculator button in the toolbar
(Figure 12) or select Tools > Master Mix Calculator from the main window.
MiniOpticon Instruction Manual
Figure 12. Master Mix Calculator window.
To set up a reaction master mix:
1. Select either SYBR
2. Edit the default target name by highlighting the target name in the dropdown target list,
entering a new target name in the Target box and pressing Enter on the keyboard.
3. Enter the starting and final concentrations for your forward and reverse primers and any
probes.
4. Additional targets can be added by clicking the New button. To delete targets, select the
target using the dropdown target list and click Remove.
®
Green/EvaGreen or Probes detection method.
15
CFX Manager™ Software
WARNING! Removing a target from the target list also removes it from any master
mixes calculations it is used in.
5. Adjust the Supermix concentration, reaction volume per well, excess reaction volume,
the volume of template that will be added to each well, and the number of reactions that
will be run.
6. Check the checkbox next to the target (only one can be chosen per SYBR® Green/
EvaGreen master mix) or targets (for probe multiplex reactions). The calculated volumes
of the components required for the master mix are listed.
7. To print a master mix calculations table click Print.
8. Click the Set as Default button to set the quantities inputed in the Target and Master Mix
Setup sections as new defaults.
9. To save the contents of the Master Mix Calculator window, click OK.
Scheduler
Use the Scheduler to reserve access to an instrument(s). To access the Scheduler click the
Scheduler button in the toolbar (Figure 13) or select Tools > Scheduler from the main window.
16
Figure 13. Scheduler Main Window.
MiniOpticon Instruction Manual
To Set up the Scheduler
1. The first time Scheduler is opened, any User, Instrument, and SMTP email settings will
be imported from CFX Manager software.
2. To add a new instrument, select View > Instrument Details or click the Manage
Instruments button below the Instruments list (Figure 13) in the scheduler main window.
In the Instrument Details window, enter the instrument name in the Name column.
Choose a model from the drop down menu or leave it blank to schedule instrument types
not listed. Entering base and optical head serial numbers is optional.
3. To add a new user, select View > User Details or click the Manage Users button below
the Users list. In the User Details window (Figure 14), enter the new user name in the
Name column. An e-mail address can be entered so that optional electronic notifications
can be sent.
NOTE: The SMTP server needs to be set up in order for electronic notifications to be
enabled.
Figure 14. Scheduler User Details Window.
4. To remove an instrument or user, open the appropriate details window and check the
corresponding box in the Delete column.
WARNING! All events associated with this instrument or user will be removed from
the calendar.
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CFX Manager™ Software
Scheduler Menu Bar
The Scheduler menu bar contents are listed in Table 9.
Table 9. Menu bar items in the Scheduler
Menu Item Command Function
File Print Preview Open the print preview window to adjust print
View Instrument Details Open the instrument details window to view, edit,
Tools Import from CFX
settings.
Print Print the calendar as it appears on the screen.
Exit Exit the scheduler.
add, or delete the name, model, base or optical
head serial numbers.
User Details Open the user details window to view, edit, add, or
delete scheduler users.
Log File View the scheduler activity log.
Imports the instruments, users or SMTP e-mail
Manager
Cleanup Events Delete events from the calendar older than the
Options Open a window to specify default calendar
settings from CFX Manager software.
period of time specified in the options window.
settings, create a desktop icon, choose to run the
scheduler at start up or define cleanup parameters.
Entering Scheduler Events
To schedule an event:
1. Double click in the appropriate cell in the calendar or right click and choose New Event.
2. Select the instrument and user from the drop down list (Figure 15).
3. Adjust the start and end times. Once an event appears in the calendar view it can be
moved to another time period by clicking and dragging the entry to a new position in the
calendar.
4. Assign a color to this event (optional).
5. To include an e-mail or a popup reminder that will appear at a specified time prior to the
start of an event, check the Reminder check box and choose an advance notification
time period for the drop down list.
WARNING! The Scheduler must be running for reminders to be activated.
Minimizing the Scheduler window will enable pop-up and e-mail reminders to
occur at the scheduled time. Selecting Close will quit the Scheduler.
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MiniOpticon Instruction Manual
Figure 15. Scheduler New Event window.
Cleanup events
Select Tools > Cleanup Events to delete events from the calendar older than the period of
time specified in the scheduler options window (Figure 16).
WARNING! All events older than the specified date will be deleted.
Scheduler Options
Select Tools > Options to define Scheduler display, cleanup and launch settings. Click
Restore Defaults to restore the Scheduler default settings.
Figure 16. Scheduler Options window.
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