Instruction Manual of Medical Equipment

Version: 1.1

MA-6000
Real-Time Quantitative Thermal Cycler

Suzhou Molarray Co., LTD.

 Content
Notes...............................................................................................................................................- 4 -

Safety Introduction......................................................................................................................... - 5 -

Chapter 1 Introduction..................................................................................................................- 10 -

Chapter 2 Overview of MA-6000 Instrument..............................................................................- 12 -

2.1 Description of MA-6000 instrument..............................................................................- 12 -
2.2 Cautions..........................................................................................................................- 16 -
Chapter 3 Unpacking & Installation............................................................................................ - 17 -
3.1 Packing List....................................................................................................................- 17 -
3.2 Installation of the hardware............................................................................................- 17 -
3.3 Installation of MA-6000 Software................................................................................. - 18 -
3.4 System initialization.......................................................................................................- 21 -
Chapter 4 Introduction of MA-6000 Software.............................................................................- 23 -
4.1 Overview of the Software.............................................................................................. - 23 -
4.2 Organization of the Software......................................................................................... - 23 -
4.3 Quick operation of MA-6000 Software......................................................................... - 23 -
Chapter 5 Document.....................................................................................................................- 28 -
5.1 Glossary..........................................................................................................................- 28 -
5.2 Create new experiment...................................................................................................- 30 -
5.3 Result analysis................................................................................................................- 38 -
5.4 Save As Template........................................................................................................... - 46 -
5.5 Export Report................................................................................................................. - 46 -
5.6 Data export..................................................................................................................... - 47 -
5.7 Software Exit..................................................................................................................- 48 -
Chapter 6 Settings........................................................................................................................ - 49 -
6.1 Reporter Management.................................................................................................... - 49 -
6.2 Static Fluorescence.........................................................................................................- 49 -
6.3 History Data................................................................................................................... - 51 -
6.4 The Other Settings..........................................................................................................- 51 -
Chapter 7 Software Strategy........................................................................................................ - 56 -
7.1 Lis system data export....................................................................................................- 56 -
7.2 Color management......................................................................................................... - 57 -
7.3 Medical Report export....................................................................................................- 59 -
7.4 Settings of Relative Quantity......................................................................................... - 60 -
7.5 Software update..............................................................................................................- 63 -
Chapter 8 Maintenance.................................................................................................................- 64 -
8.1 Cleaning the Instrument................................................................................................. - 64 -
8.2 Protecting the Instrument............................................................................................... - 64 -
 8.3 Instrument installation and delivery...............................................................................- 64 -
Chapter 9 Information.................................................................................................................. - 66 -

Chapter 10 Troubleshooting......................................................................................................... - 67 -

Chapter 11 Product Expected Lifetime........................................................................................ - 67 -

Update History..............................................................................................................................- 68 -
 Notes

Hardware:
Molarray Biotech guarantees that the MA-6000 Real-Time Quantitative Thermal Cycler that you

have received has been thoroughly tested and meets its published specifications.

This warrantee is void if the guidelines in this User Instruction Manual regarding the system and

its functions have not been followed.

Included Software:
Any software distributed with this product is provided free of charge as a service to the customer.

The software is intended to be a tool for development and as an example of one possible method

of code implementation..

Software Copyright:
Molarray Biotech maintains the copyright on this material, but grants the customer rights to use

the software described herein without obtaining Molarray Biotech’s permission and without the

requirement to reference Molarray Biotech as the source of material.

Software Changes:
Molarray Biotech reserves the right, without prior or future notice, to make changes to any of its

products described or referred to herein to improve reliability, function, or design.

Liability:
No liability is accepted for loss or incidental or consequential damages arising from the incorrect

use of the MA-6000 system. Molarray Biotech’s liability is limited to the repair or replacement

of the unit. Molarray Biotech is not liable for any consequential damages.

Read this Instruction Manual carefully before using the MA-6000 to ensure that you obtain

optimal results from the machine.

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 Safety Introduction

Before using the MA-6000 Real-Time Quantitative Thermal Cycler, users

must read the safety instructions carefully!

1. Definition of symbols
The following symbols will appear in the instruction manual.
Symbol Title Description
Warning This symbol is used to indicate the following
information: if it does not follow the prescribed
procedure or instruction, it may result in physical injury
or damage to the instrument.

Caution High This symbol is used to identify potential heat

Temperature damage on the surface of the instrument.

Biohazard This symbol is used to express the following

information: you must be careful when touching
material that is potentially contagious.

Crushing This symbol is used to express the potential

damage of crushing when the heated-lid is closed.

The following symbols will appear on the instrument.

Symbol Title Description
Read the Labeled on the instrument's nameplate.
instructions
carefully.

Caution High Labeled on the surface close to the thermo block.

Temperature

Biohazard Labeled on the surface close to the thermo block.

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 Crushing Labeled on the surface close to the thermo block.

2. Operating Requirements
The instrument can only be operated by skilled personnel.
►The instrument is mechanical and electrical equipment, if it is not strictly
used according to the manual, it may cause electric shock or physical damage and
other potential dangers to the user;
►Operation should be in strict accordance with the instrument safety tips;
►The user can replace the fuse according to the manual. Be sure to cut off the
power before replacing. Parameter of the fuse is F8AL 250V. However, the user can
not open the instrument or replace other accessories, and the damage to the
instrument is not included in the scope of warranty;
►Only the professional personnel of this instrument manufacturer can repair
the instrument;
►Do not disassemble when the instrument is running to avoid damage to the
instrument. Be sure to cut off the power before disassembly.
►The track of heated-lid is mechanical moving component. Touch is strictly
prohibited when the instrument is running to avoid hand crushed.
►The instrument must be installed in clean indoor ventilated, avoid corrosive
gas and strong magnetic field interference, avoid sunlight and direct strong light, and
used in the specified temperature and relative humidity conditions;
►According to the product technical specifications, working conditions of the
instrument for indoor air temperature is between 18℃ and 35℃; relative humidity
should be ≤85%.
►Safety goggles and gloves must be taken when dealing with toxic, corrosive
or infectious materials;
► Be careful to guard against the potential hazards of all biological materials
although the nucleic acids are highly purified. The disposal or discard of these

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wastes must comply with local safety regulations.
If the spatter or leak occurs carelessly, it should be disinfected immediately with
appropriate disinfectant to prevent the contamination of laboratory personnel and
equipment.
►The damaged instrument must be returned to the manufacturer for repair; the
surface of the instrument must be disinfected before return.
► It is strictly forbidden to touch thermo block to avoid scald when the
instrument is running and when it is finished.

3. Electrical safety
►The electrical safety design protection level of the MA-6000 Real-Time
Quantitative Thermal Cycler is Class I (IEC);
► In order to prevent the shock hazard, the instrument must be connected to a
three-core grounding socket that meets the standard of the safety standard. The
voltage is 220V (50Hz).
►Before the instrument is connected to the power line, it is necessary to ensure
that the voltage, frequency is consistent with the requirements of the instrument.
When the power cord is connected, the power supply must be cut off.
►Before the instrument is connected to the computer, it is necessary to ensure
that the power supply of instrument and computer is cut off to prevent any
unfortunate damage to the instrument;
► Do not touch the power switch and power cord with wet hand;
► Do not remove the power cord when the instrument is not cut off;
► Do not clean the instrument when the instrument is not cut off;
► Do not replace the fuse when the instrument is not cut off;
►Please turn off the power when the instrument is not in use.

4. Electromagnetic Compatibility
Real-Time Quantitative Thermal Cycler should comply with the emission and
noise immunity requirements of GB/T 18268.1-2010 Electrical Equipment for
Measurement, Control and Laboratory Use-EMC Requirements-Part1: General

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 requirements and Part 26: Special requirements in vitro diagnosis (IVD) medical
equipment.
Manufacturer is responsible to provide electromagnetic compatibility
information of Real-Time Quantitative Thermal Cycler.
User should ensure to use the instrument in proper electromagnetic compatibility
environment.
Real-Time Quantitative Thermal Cycler complies with GB/T 18268 noise
immunity requirements:

Port Testing items EMC Criterion Test Values

Electrostatic Air discharge: 2kV、4kV、8kV,
GB/T 17626.2
Discharge Contact discharge: 2kV、4kV
EM Field GB/T 17626.3 3V/m,80MHz~2.0GHz,80% AM
Shell
Rated power
frequency magnetic GB/T 17626.8 3A/m,50Hz
field a
Voltage sags c GB/T 17626.11 Cycle 1 0%; Cycle 5 40%; Cycle 25 70%
Voltage interruption
GB/T 17626.11 5%, Duration：250Cycles
c
AC Power Pulse group GB/T 17626.4 1kV(5/50ns,5kHz)
Surge GB/T 17626.5 Line to ground: 2kV Line to ground: 1kV
Radio frequency
GB/T 17626.6 3V,150KHz~80MHz,80% AM
transmission
Pulse group GB/T 17626.4 0.5kV(5/50ns,5kHz)
I/0 port signal Surge GB/T 17626.5 Null
b Radio frequency
GB/T 17626.6 3V,150KHz~80MHz,80% AM
transmission
A: The testing is only applied to instrument which sensitive to magnetism. Annoyance value is allowed to
more than 1 A/m.
B: The testing only applied to instrument which power cable is longer than 3M.
C: “5/6Cycle” means that 5 cycles for 50Hz testing and 6 cycles for 60Hz testing.

Caution: Real-Time Quantitative Thermal Cycler is designed to follow A

class in GB4824. It will bring radio interference in home environment.
Protective measures are needed.
Propose to evaluate electromagnetic environment before using the
instrument.

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 Prohibit using the instrument near strong radiation source, or the instrument
will be interrupted.

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 Chapter 1 Introduction

This manual provides general information and detailed instructions how to

operate the Real-Time Quantitative Thermal Cycler.
This chapter gives a general description of the manual, a summary of the
hardware and software, and technical support information.

Summary of operation principles, applications and features

The MA-6000 real time quantitative thermal cycler (qPCR) has been designed
specifically to meet the exacting demands of today's molecular laboratories. All
instruments are designed for outstanding optical performance, stable temperature
precision and accuracy. Key features include multi-color detection, real-time data
monitoring, melting curve analysis, user-friendly plate format and space-saving
design.
The highly flexible, fully automated systems can carry out reactions in 96-well
plate, 8-strip tube, or single PCR tube. They feature the familiar Windows-based
operating system, and all instruments set-up and analysis functions are controlled via
an intuitive, easy-to-use software interface that permits rapid experimental set-up
and data analysis. After each cycle, fluorescence value vs. cycle number is
continually updated for all samples. Experiment reports can be exported and
analyzed using Microsoft Word and Excel.
The instruments are designed to carry out any real-time PCR assay, including
fast screening for infectious agents, mutations and SNP analysis, detection of GMO
and quantification of cellular RNA levels. As a closed-tube system, contamination is
minimized. The ability to collect and analyze data in real-time, as well as efficient
data management allows the researcher to generate data rapidly and carry repetitive
experiment.
The MA-6000 system is designed to handle all current fluorescence-based PCR
reaction, such as TaqMan, Molecular Beacon, SYBR Green and MGB which
produce changes in fluorescent emissions upon the formation of specific PCR

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products. A broad spectrum excitation source provides high excitation energies over
a wavelength range from 380 to 780nm. All sample positions are illuminated and the
resulting fluorescent emissions are transmitted through optical fibers to a CCD
camera. Excitation and emission wavelengths are selected from within this range
using interference filters. Five filter sets are provided, which are optimized for the
detection of the most commonly used fluorescence. The filter sets for other new
fluorescence are also available and can be supplied according to customer
requirements.

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 Chapter 2 Overview of MA-6000 Instrument

2.1 Description of MA-6000 instrument

2.1.1 Instrument components

The MA-6000 system consists of control system, power system, electro-optic
system, module component, heated-lid component, shell component and software.

Fig. 2.1.1 The front view of MA-6000 instrument

2.1.2 Scope of application

MA-6000 system is designed for diagnostic and research use only.

2.1.3 Contraindication
No.

2.1.4 Intended use

This instrument is intended to use with proper reagents together to carry
quantitative/qualitative detection and melt curve analysis for nucleic acid deriv
ed from human body, such as pathogen and human nucleic acid etc.

2.1.5 Main Features

Real time quantitation as well as endpoint PCR;
Range of excitation wavelength from 380 to 780nm;
Multi-channel fluorescence detection in one sample tube;
Melting curve detection;
Six independent temperature modules to provide six different annealing
temperatures;

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 Gradient temperature range over 32℃ in 12 columns;
Dynamic range: linear dynamic range of sample concentration up to 10 orders
of magnitude;
Rapid data acquisition;
Capacity to simultaneously track 96 samples;
Accessibility of raw data files by the user;
Ability to re-analyze data;
User-friendly, intuitive software to speed up setup and data analysis;

2.1.6 Temperature control system

The temperature control system is comprised of a heating block module and a
temperature control unit. The block is heated by six independently controlled TE
modules, and it ensures the heating is quickly, uniformly and precisely controlled.
Specifications of temperature:
Temperature control range: 4℃~100℃;
Max heating rate: from 50℃ to 90℃, ≥ 2.5℃/s;
Max cooling rate: from 90℃ to 50℃, ≥ 2.0℃/s
Temperature control accuracy: ≤ 0.5℃;
Temperature precision: ≤ 0.5℃;
Temperature uniformity of wells: ≤ ±1℃
Heated lid: up to 104℃

Fig.2.1.6 Temperature control system of sample block

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2.1.7 Fluorescence detection system
The fluorescence system of MA-6000 consists of two optical parts: an
excitation system and a detection system. The excitation system, comprised of a
halogen lamp and a set of optical filters, allows simultaneous illumination of the 96
wells through 96 optical fibers. The detection system includes a set of optical fibers,
a wheel with five emission filters, a set of lenses, and a cooled CCD camera. The
fluorescence signal transmits through the optical fibers, emission filters and the
lenses and is then detected by the CCD camera.
Specifications of optical system:
Light source: halogen lamp.
Fluorescence detection range: 380 to 780nm.
Excitation wavelength: up to 5 channels (380~780nm)
Emission wavelength: up to 5 channels (380~780nm).

Fig.2.1.7 Optical System of MA-6000

Specification of fluorescence intensity and sample detection:

Repeatability of fluorescence intensity: CV≤ 3%;
Precision of fluorescence intensity: CV≤ 5%;
Fluorescence crosstalk among different channels: fluorescence intensity of
other channels is lower than the fluorescence threshold of target channel;
Repeatability of sample detection: CV≤ 3%;
Linear correlation coefficient of sample: absolute value of R≥ 0.980;
Linear correlation coefficient of fluorescence: absolute value of R≥ 0.990.

2.1.8 Software

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 The MA-6000 software should be run in Win7 operation system and above. It
can monitor all the process of gene amplification via computer. User can setup PCR
protocol, setup sample parameters, set file location, collect and analyze the data
signal quickly and easily in the software.

2.1.9 Connection of the instrument

One end of MA-6000 power line should connect to instrument, another end
connects to socket, and it should be properly grounded.
One end of the attached USB cable should connect to the instrument, another
end connects to the computer. The computer intended to install MA-6000 software
must follow below configurations.
Table 2.1.9 Minimum configuration to install MA-6000 software

Computer configuration Minimum requirement

Operation system Windows 7

Processor Inter i3

RAM 4G

Hard disk 300G

USB 3.0

USB
Location: Lower left on back of the instrument.

USB cable connects the instrument and computer via their USB 3.0 ports.
Power port
Location: Lower left on back of the instrument.

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 Three core power cord connects to the port in above picture, another end
connects to 220V AC power. Ground wire of power should be properly grounded.
The length of power line should be less than 1.5m. The socket should be installed in
where user can pull and plug power line conveniently.

2.2 Cautions
Some sample maybe contain infection source, must be sure deal with samples
following relative safe operation rules. User can wear safe glasses, latex gloves and
lab coat. Please operate in corresponding environment if needed.
Person in charge must take prevention measures to train for whom will operate
this instrument and avoid touching samples containing infection source directly.
Follow applicable local bylaws and safety regulations during handling or
disposal of the waste. In the accident of spills or leaks, appropriate disinfection
procedures must be followed to prevent and eliminate personnel or instrument
contamination.

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 Chapter 3 Unpacking & Installation

Generally, the MA-6000 instrument should be installed by engineer of Molarray

Biotech or engineer from authorized agency.

3.1 Packing List

(1) MA-6000 instrument
(2) Power cord & USB cable
(3) Installation software driver
(4) Instruction manual
(5) A warranty form and qualification documents

3.2 Installation of the hardware

1. Place the MA-6000 instrument on the bench which can bear weight of 300kg.
 Do not connect the instrument to the power supply immediately.
 The instrument is cooled by fans and therefore should be situated with at least
15cm clearance at the rear and 8cm on either side of the machine.
 Do not place MA-6000 in direct sunlight or excessive moist environment,
which may affect the performance of the instrument.
 Avoid connecting the instrument to a circuit that may be subject to
fluctuations such as those shared by ultra-centrifuges, freezer, or refrigerators.
Operation Conditions:
Ambient Temperature: 18℃ to 35℃
Humidity: ≤ 85% to prevent condensation
Storage Conditions:
Ambient Temperature: -20℃ to 55℃
Humidity: ≤ 85% to prevent condensation
Caution: if humidity is excessive or large temperature difference between day
and night, please preheat the instrument.
2. Connect the MA-6000 instrument to a suitable plug using the power cord
provided. The system has the following voltage and power requirements:

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  Voltage: 220V±22 V, 50Hz±1Hz.
 Power: 1000VA

3.3 Installation of MA-6000 Software

Connect installation software driver to computer, launch
“MA-6000AutoRun.exe” in the driver, installation window is as follow:

Fig 3.3 MA-6000 software installation steps

3.3.1 Installation of software running platform (Step1)

Click “Next” to install step by step. Software running platform will be installed
successfully after clicking “Finsh”.

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3.3.2 MA-6000 workspace installation (Step2)
Click “MA-6000-Workspace”, enter password “molarray”, advise to install to
non-system disk. Please install following below instructions.

3.3.3 Driver installation (Step3)

Click “USB To Serial”, after complete, click “Enter”.

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Click “CCD”.

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 After software installation, connect the instrument and computer using the USB
cable. Turn on the instrument, check the icons of USB and CCD in “My
Computer”-“Device Manager”. The instrument is ready to run if the icons are
displayed correctly.

3.4 System initialization

When the MA-6000 system is first installed, the following procedures must be
carried out to test the instrument:
(1) Switch on the power.
(2) Start up the software of MA-6000.

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 (3) Click main menu-Instrument, and then select Run From Template.
(4) Select “Testing” template to run for a self-test routine. The routine will
check the heating elements, light source, cooling fans, heated lid, filter wheel, lenses
and CCD camera. This approximately takes 30 minutes.
Notes:

 You can carry out qPCR experiment only when the test results are passed.

 The MA-6000 is very easy to operate. For detailed operation procedures, please see

the following instructions in the remainder of this manual.

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 Chapter 4 Introduction of MA-6000 Software

4.1 Overview of the Software

A user-friendly program operating in the Windows  environment, the

MA-6000 software can be used for setting, running, data collection, analysis and
management. Graphic display of the amplification process is shown in real time. The
extensive preferences menu allows the user to easily re-analyze the results.

4.2 Organization of the Software

The software allows the MA-6000 system to perform the following functions
during and/or after qPCR runs.
File (see Chapter 5 for details):
 Create a thermal cycling protocol and plate setup file
 Open the run files
 Save the settings
 Save as template
 Export report
 Exit from software
Settings (see Chapter 6 for details):
 Reporter Management
 Static Fluorescence
 History Data
 Settings
Export procedure of LIS Data (see Chapter 7 for details)
Instrument Maintenance (see Chapter 8 for details)

4.3 Quick operation of MA-6000 Software

This section will give a quick overview of the software and how to complete a
qPCR program, including setup, acquire data, and data management.

4.3.1 Before Starting up MA-6000 Software

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 Make sure that MA-6000 software is properly installed on the computer.

4.3.2 Starting up the software

1. Switch on the computer. Open the MA-6000 software by clicking the
MA-6000 icon. Turn on the instrument.
2. Default user ID is “user”, password is “123456” (Fig 4.3.2 a).

Fig 4.3.2 a

3. There are two run modes to run experiment:

Mode 1(Run from template): Click “Instrument”-“Run From Template”, select
template file to run directly.
Mode 2(Create new experiment): After protocol and sample parameter settings,

click , click to run experiment.

Procedure of setting protocol and sample parameters: click File, select New,
select correct Exp.Mode, enter experiment name or use the default experiment name
(date format), enter Operator. Click the fold of Template to import template which
has been saved or click Finish to set protocol (Fig 4.3.2 b). Edit Location to set the
path to save experiment file. Enter notes in Note textbox. Click Finish to enter Fig
4.3.2 c.

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 Fig 4.3.2 b

Click Add Stage to add a Holding or Cycle, click Add Step to add different
steps in one stage. Set temperature in T column, set time in Hold column, check
Signal Acquisition to collect signal.

Fig 4.3.2 c

For example:
37℃ 2min；1 Cycle；
94℃ 2min；1 Cycle；
94℃ 20s；
55℃ 30s； 40 Cycles; 55℃ Signal Acquisition
Run Melt Curve experiment after amplification completed, Signal Acquisition
of Melt Curve is default. The protocol is as Fig 4.3.2 d.

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 Fig 4.3.2 d

Turn to Plate page to set sample parameters after protocol is completed. Select
well and double click or right click on it, below page will display as Fig 4.3.2 e.
Click on well setting.

Fig 4.3.2 e

Select different SubSet ID to define different groups. Enter sample name and
gene name, select sample type, select reporter from the left table. Select all intended
reporters if need, click Add and Apply to complete the sample parameters setting for
the selected well. Set sample information for other wells as above steps. (Fig 4.3.2 f)

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 Fig 4.3.2 f

After sample parameters setting is completed, click and then click

to run, or click Save As Template from File to save the current file as
template. User can select Run From Template from Instrument to directly run
experiment next time.
4. After experiment run, click File, select Open to open the experiment file just
completes run.

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 Chapter 5 Document

5.1 Glossary

5.1.1 Definition of Protocol

 Stage/step/cycle:
Stage: A protocol can consist of many stages;
Step: A stage can consist of many steps;
Cycle: Define the cycles of certain stage
 Add Stage
Add a Holding or Cycle stage.
 Remove Stage
Remove the selected stage.
Add Step
Add a step in a stage.
 Remove Step
Remove selected step.
 Multiple Temp.
Multiple temperature control mode, set temperature gradient or multiple block.
 Sample Volume
The volume of reaction system, default value in software is 50ul.
 T(℃)
A range from 4℃ to 100℃ can be selected.
 Holding Time
This is the incubation time for every step.
 Ramp Rate(℃/s)
Set up a ramp rate for temperature change from one step to next step.
 Multiple Block
Set temperature in multiple block temperature control mode.
 Signal Acquisition

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 Check it in certain step to collect signal.
 Module
The heating block can be divided into six independent heating modules.

Fig 5.1.1 The distribution of six modules

 Temperature Control Modes

There are two types of temperature control modes for MA-6000 system:
single and multiple temperature modes. The block can be operated using a single
temperature control mode or multiple temperature control mode. If you want to
run the entire block as a single cycling temperature, choose single control mode. If
you want to run the block at different temperatures, click multiple temperature
control mode, and the software will allow you select Gradient or Multiple Block
mode.

5.1.2 Definition of Plate

 Reporters
It lists all the added reporters.
 Subset ID
The software allows you to define seven different sample groups in one PCR
run, (SI to SVII).
 Sample Name
Enter a Sample Name, such as H-100.
 Gene name
Type a Gene Name, such as HBV.

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  Sample Type
A sample can be designated as one of the following five sample types. They
are Unknown Sample, Negative Control, Positive Control, Weak Positive Control,
and Standard Sample. For Standard Samples, you need to enter the quantity of the
template.
 Quantity
Enter the concentration value of each standard sample dilution gradient.
 Add
Add sample information to select wells.
 Apply
Apply the new sample information to the selected wells.
 Cancel
Cancel the sample information setting.

5.2 Create new experiment

MA-6000 system can run multiple types of PCR experiment.

5.2.1 Setup protocol

A. Single Temperature Control Mode
Click New, enter to Fig 5.2.1 a.

Fig 5.2.1 a

Exp.Mode: user to select experiment type;

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 Name: a file name will be automatically created for the new experiment, or user
can edit it.
Date: date of experiment run. The default value is the date of computer system.
Operator: it is login ID by default; user can edit it to technician name.
Template: click the folder icon of template to import only protocol of the
template, the sample setting information will also be imported if the checkbox (Load
the plate settings) is checked.
Location: the file path to save the experiment file.
Finish: click the Finish to set up a new Thermal Cycling Protocol. (Fig 5.2.1 b)

Fig 5.2.1 b

Click Add Stage to add a Holding or Cycle, click Add Step to add different
steps in one stage. Set temperature in T column, set time in Hold column, check
Signal Acquisition to collect signal.
For example:
37℃ 2min; 1 Cycle;
94℃ 2min; 1 Cycle;
94℃ 20s;
55℃ 30s; 40 Cycles; 55℃ Signal Acquisition
Run Melt Curve experiment after amplification completed, Signal Acquisition
of Melt Curve is default. The protocol is as Fig 5.2.1 c.

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 Fig 5.2.1 c

A. Multiple Temperatures Control Mode

Based on the six individual modules of MA-6000 system, user can set different
temperatures in the annealing step. Multiple Temperatures Control mode includes of
Gradient and Multiple Block modes.
Gradient Mode
The software allows a temperature gradient to be set by entering the lowest and
highest temperatures desired (Fig. 5.6) in the multiple temperature control mode.
Select the step in which user want to set gradient temperature (it will be
highlighted in blue if the step is selected), (Fig 5.2.1 d), click Multiple Temp, select
Set, and click Gradient (Fig 5.2.1 e). For example, set Start temperature is 55℃, set
end temperature is 60℃, click Apply. Temperature gradient will be displayed in 12
columns. User can get the temperature gradient from the table.

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 Fig 5.2.1 d

Fig 5.2.1 e
Multiple Block
Select the annealing step; click the button of Multiple Temp. Select Set and
click Multiple Block.
Enter a number of the temperature for each module, such as 55℃ for Module 1,
56℃ for Module 2,
58℃ for Module 3, 60℃ for Module 4, 59℃ for Module 5 and 57℃ for
Module 6.
Note:

Temperature interference can occur in the wells between modules when the multiple

temperature control mode is used.

It is strongly recommended that the differences in temperature between the two

adjacent modules be as small as possible.

It is suggested that the difference in temperature should be smaller than 5℃, and do

not use the margin wells.

Set 6 different temperatures in the block (Fig 5.2.1 f):

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 Fig 5.2.1 f

Set 3 different temperatures in the block (Fig 5.2.1 g):

Fig 5.2.1 g

Set 2 different temperatures in the block (Fig 5.2.1 h):

Fig 5.2.1 h

Cancel the Multiple Temp. function: Click Multiple Temp, select Cancel. The default

temperature of this step will be the temperature of the first module.

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5.2.2 Plate Setup
The Plate Setup window allows you to edit sample information for each well,
such as the sample ID, primer names, sample types, and reporters.
After protocol setting, click Plate (Fig 5.2.2 a), edit sample parameters for
selected wells. Click on a well and drag the mouse to select the desired well or wells
from Well Selection Panel. The color of the selected area will change from white to
gray. Right click of the mouse then click well setting to enter the screen of ‘Well
Settings’ (Fig. 5.2.2 b) and to edit Subset ID, Sample name, Gene name, Sample type
and Reporters.
1) Subset ID: The software allows you to define seven different samples in one
PCR run, (SI to SVII);
2) Sample Name: Enter a Sample Name, such as H-100;
3) Gene Name: Typing a Gene Name, such as HBV;
4) Sample Type: A sample can be designated as one of the following seven
sample types. There are five types, such as Unknown Sample, Negative Control,
Weak Positive Control, Positive Control, and Standard Sample. For Standard
Samples, you can easily enter the quantity of the template;
5) Reporter Selection: After the wells have been defined, the channel can be
selected. Click on the desired reporter name, such as FAM, and then click the button
of Add button to confirm;
6) Click Apply button to finish the well setting;
7) The results of Well Setting will be displayed.

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 Fig 5.2.2 a

Fig 5.2.2 b

Sample parameters information copy and paste:

Select wells, right click, selelct Copy(Fig 5.2.2 c), right click on intended wells
to paste these information.

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 Fig 5.2.2 c

Remove the sample parameters:

Select wells and right click on them, select Well Setting, uncheck the checkbox
of in the first column, and click Apply button to delete the settings (Fig 5.2.2 d).

Fig 5.2.2 d

After sample setting is completed, click to save the file, click to

run experiment; or click File, select Save As Template to save this file as template.
The MA-6000 system contains five excitation filters and five emission filters
which allow detecting more fluorescence signal simultaneously. The excitation light
source of each channel emits light signal. The fluorescence with wide wavelength
can be used as reporter. Popular fluorescence is as below.

Table 5.2.2 a Centre Wavelength of Excitation and Emission Light

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 Channel (filter)# Excitation (nm) Emission (nm)
1 470±10 520±5
2 525±5 570±5
3 570±5 620±5
4 620±5 670±5
5 670±5 710±5
Extension User customized User customized

Table 5.2.2 b Popular reporter in qPCR experiment

Channel# Fluorescence
1 FAM/SYBR Green I/Eva Green
2 VIC/JOE/HEX/TET
3 ROX/Texas Red
4 Cy5
5 Cy5.5/Quasar705

5.2.3 Setup Melt Curve protocol

When creates Melt Curve, click Add Stage, select Dissociation to the Melt
Curve protocol page. (Fig 5.2.3)
1. Start Temperature: enter a start temperature; default value is 60℃, 60s.
2. End Temperature: enter an end temperature, default value is 94℃.
3. Ramp Rate: default value is 0.02℃/s; it can be set up to 0.1℃/s.

Fig 5.2.3

5.3 Result analysis

Click Open button, select experiment file, go to Amplification Plot (Fig 5.3 a).

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 Protocol: click it to check the protocol of this experiment.
Plate: click Plate to check the sample parameters, user can edit the sample
parameters after the run; ensure to save the change after editing.
Amplification Plot: this page displays curves of Rn (Rn) vs cycle number, Ct
value, Copy number, standard curve.
Dissociation: check the Melt Curve experiment result.
HRM Analysis: check the HRM experiment result.
ΔΔCt: this analysis method is widely used in gene expression analysis. It
requires same amplification efficiency of reference gene and target gene. 2-ΔΔCt
method is based on assumption that amplification efficiency is 100%.
Quality Control: it can monitor same type experiment in long term, compare
their Ct values and amplification efficiency.
Results: it lists the data of each well.

Fig 5.3 a

Select well and its reporter to check the data in the certain Reporter, or select all
to check the data of all channels.
Data includes: Delta Rn, Rn and Std Curve.
Delta Rn: the normalization of Rn value and plot.
Rn: intensity of fluorescence (Fig 5.3 b), the max Rn value can be detected is
60000, advise to optimize the max Rn value in experiment is 45000. Rn value can be
increase or decrease by adjusting exposure time.

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 Fig 5.3 b

Std Curve: Calculate the amplification plot of dilution gradient to Standard

Curve (Fig 5.3 c, Fig 5.3 d). In MA-6000 system, user can set 7 different groups of
standard sample to quantitate respectively. Different group of standard sample sets to
different Subset ID.

Fig 5.3 c

Fig 5.3 d

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 Line Color: Line Color includes Auto color and Sys color. User can select any
color type to define a color for the amplification plot of one Reporter, or
amplification plot of each well has its own color.
Threshold: Threshold Setting includes Auto Threshold and Manual Threshold.
Baseline: it is the fluorescence value which does not increase in early several
cycles of qPCR experiment. Default values of Baseline Start and End are 3 and 12. If
Ct value is less than 12, user needs to adjust the Baseline End to a cycle less than the
Ct.
Select data: right click on the blank near the amplification plot (Fig 5.3 e).
View Data Table: user can check the well position, group, reporter, sample
name, sample type, Ct value, Mean Ct, StdDev Ct. etc. Right click again to select
Return to return to amplification plot.
Graph Style: Line and Log (Fig 5.3 f).
Curve Setting: set the thickness of plot (Fig 5.3 g).
Auto Scale: auto fit the amplification plot to the window (Fig 5.3 h).
Copy: copy the date to excel.
Save as picture: save the selected amplification plot as picture.

Fig 5.3 e

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 Fig 5.3 f

Fig 5.3 g

Fig 5.3 h

Click Protocol to check the reaction program settings information (Fig 5.3 i).
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 Fig 5.3 i

Click Plate to check the sample parameters (Fig 5.3 j), user can edit the sample
information after experiment run, click Save after editing.

Fig 5.3 j

Dissociation: check the Melt Curve. It has two data types: Rn and Di/Dt (Fig
5.3 k, Fig 5.3 l). User can see the Tm value in Results table, or get the Tm value by
right clicking on the blank near the melt curve and selecting View Data Table.

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 Fig 5.3 k

Fig 5.3 l

Delta Delta Ct: before ΔΔCt analysis, user must set parameters for intended
wells, each well only has one Subset ID, Sample name and Gene name.
Control: define the sample which will be used for control.
Reference: usually a housekeeping gene used as a reference to which compare
the expression of target genes.
Target gene: The gene whose expression is compared to the reference gene
Click Gene Expression, Select RQ from Data Mode dropdown list, Click
Define Reference, select a Subset ID, set a group as Control Group, set a
housekeeping gene as Reference Gene, click Add or Remove, the setting is

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completed. Close the setting page; the gene expression plot will be displayed (Fig
5.3 m).

Fig 5.3 m

Quality Control
The MA-6000 software offers a tool for quality management. To measure any
variability between runs, you can fix a well to carry out the quality control
experiment with the same conditions (same reagent and template) in every qPCR
run.
Channel or reporter Selection;
Well Selection;
Sample Type Selection;
Set the starting and end time for analysis;
Select a display mode: The curve can be displayed as Copy number vs. Days or
Ct value vs. Days;
Click Query to display the result.
Results
Data types: There are two Data types of result, Research and Medical (Fig 5.3
n).
Mean Ct: Mean Ct is the average Ct value of wells which have the same
sample parameters setting.

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 Stdev Ct: Stdev Ct is the standard deviation of Ct values which have the same
sample parameters setting.
Quantity: Quantity is the concentration of standard sample and unknown
sample.
Tm: Tm is the temperature at which 50% of the DNA is double-stranded and
50% of the DNA is dissociated into single-stranded DNA. The Tm is displayed in the
melt curve.

Fig 5.3 n

5.4 Save As Template

Save current settings, user can directly run experiment with this function.

5.5 Export Report

Select intended wells and report format, such as Excel or Word format. (Fig 5.5
a, Fig 5.5 b)

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 Fig 5.5 a

Fig 5.5 b
The exported report is as Fig 5.5 c, click the different worksheet to check
Protocol&Plate, Data&Graph etc.

Fig 5.5 c

5.6 Data export

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 Data export is for Lis system data, select intended wells, export following
below Fig 5.6, export location is lis interface folder in the MA-6000 installation
path.

Fig 5.6

5.7 Software Exit

After experiment running or result checking, click Exit from File menu to exit
software, or exit by clicking the x in the top right of the software interface. When
exit software, a window will prompt to ask user if want to save the settings just make.
Please select Yes if you want to save.

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 Chapter 6 Settings

This chapter lists some settings used before experiment running and when
analyses experiment, such as Static Fluorescence and History Data. The settings
before experiment running includes Reporter Management, Common Reporters,
CCD Setting, etc., analysis setting includes threshold setting and baseline setting,
etc.

6.1 Reporter Management

Click Tools and Reporter Management (Fig 6.1) to enter a new screen.
Common reporters are listed in the left. If you want to add a reporter, you can enter a
name in the Reporter Name textbox, select excitation wavelength and then click Add
button. User also can remove a reporter. User can select to combine excitation and
emission wavelength, emission wavelength is not allowed to be less than excitation
wavelength.

Fig 6.1

6.2 Static Fluorescence

The Static Fluorescence offers a tool to measure fluorescence of the sample
before or after a PCR run.

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 Put the PCR plate into the instrument, turn on the instrument and launch the
software. Click Tools- Static Fluorescence, the page of Fig 6.2 a will display, click
Run, the page will display as Fig 6.2 b after running.
The table data is consistent with the PCR plate.
Exposure time: user can customize it, the default value is 1s.

Fig 6.2 a

Select a channel to run;

Click Run to start the static fluorescence running;
Chose Fluorescence to run the static fluorescence;
Chose Background to run the background;
After run completed, system will prompt to ask user if want to save the data;
Click Exit to exit the static fluorescence window.

Fig 6.2 b

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6.3 History Data
All the experiment data have run will be saved in database. User can search the
experiment in History Data.
Click Tools, select History Data, and enter a keyword such as sample name,
date and click Query to search. The listed experiment can be ordered by clicking the
column name. Click Export to export the report. The exported reports will be saved
in the reports folder in the software installation path (Fig 6.3).

Fig 6.3

6.4 The Other Settings

Click Tools, select Settings, there are General setting, Common Reporters, CCD
setting, Analysis setting and Negative Judgment, etc.

6.4.1 General Setting

There are two languages, English and Chinese (Fig 6.4.1), are designed for this version of

the software.

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 Fig 6.4.1

6.4.2 Common Reporters

User can add reporters from all reporters to common reporter, or remove
reporter from common reporters. User only can select reporter from common
reporters (Fig 6.4.2).

Fig 6.4.2

6.4.3 CCD Setting

Here you can edit CCD exposure time for each channel (Fig 6.4.3). The
Exposure Time function allows the user to adjust the exposure time by the exciting
light source to an optimized dynamic range. The ideal Exposure Time value depends

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on the sample background and the dynamic range of fluorescence intensity. The
Exposure Time can be adjusted channel by channel as the different reporters have
different quantum efficiency. The default value of Exposure Time is set for all
channels. The value of Exposure Time can be adjusted to optimize the background of
baseline and the fluorescence intensity of the Plateau. The dynamic range of
fluorescence intensity for the MA-6000 instrument is recommended to be between 0
and 50,000. Thus, the maximum fluorescence intensity of fluorescence (at the PCR
plateau phase) must be below 50,000 (arbitrary units). It is recommended that
Exposure Time value be set between 0.5 and 3).

Fig 6.4.3

6.4.4 Threshold Setting

The threshold line can be set for different channels (dyes) with different values.
The threshold must be set to greater than the fluorescence of baseline phase (Fig
6.4.4).
The Baseline Start and Baseline End can be set to the range which covers the
baseline phase of qPCR amplification. Their default values are 3 and 12 (Fig 6.4.4).

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 Fig 6.4.4

6.4.5 Negative Judgment

If user has set Negative Judgment, the negative or positive result will be
displayed in the exported report.
Click Negative Judgment (Fig 6.4.5 a), select Qualitative (Ct) or Quantitative
(Copy), if selects Ct, enter Ct threshold in Qualitative (Ct), if select Copy, enter
Copy threshold in Quantitative.

Fig 6.4.5 a

User also can set different judgment threshold for different gene name. Click
Add to go to Fig 6.4.5 b. Enter Gene Name, select Test Mode and corresponding
judgment threshold, click Create button. After an experiment run, if the gene name
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set in the experiment is same with a gene name in the Negative judgment which user
has created, the judgment will be automatically matched and used for the negative or
positive judgment. User also can remove the selected judgment.

Fig 6.4.5 b

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 Chapter 7 Software Strategy

7.1 Lis system data export

1. Open experiment file, select wells (Fig 7.1 a).

Fig 7.1 a

2. Following Fig 7.1 b, select Report Mode (Lis), select File Type (Excel), and
click Export.

Fig 7.1 b

3. Open the exported file in the exported location (Fig 7.1 c).

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 Fig 7.1 c

7.2 Color management

This function allows our user to edit color for the wells before or after running a
qPCR test. The color user set will be the amplification plot color after experiment
run or editing.
1. Move the mouse on the setup well or wells, click the right button of the
mouse to select Color Coding (Fig 7.2 a).
2. Select a color for well or wells and click“other” for more colors (Fig 7.2 b);
3. The edited color for the wells is displayed on the Fig 7.2 c.

Fig 7.2 a

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 Fig 7.2 b

Fig 7.2 c

User also can edit the color for well and amplification plot for experiment after
run. Open an experiment file, go to Plate window, edit the color of selected well,
click Save after editing (Fig 7.2 d).

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 Fig 7.2 d

The amplification plot color is consistent with the well color (Fig 7.2 e).

Fig 7.2 e

7.3 Medical Report export

Open the Information Editor in the folder (inspection info editor) under the
software installation path. User can copy this template and edit the patient
information and save it.
Open the test experiment file; click File-Import to import the saved template in
above step (Fig 7.3).

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 Fig 7.3
Select wells user want to export, go to File-Export, select Medical report mode
to export. Go the exported location to check the exported medical report and print it.

7.4 Settings of Relative Quantity

It is supposed that the amplification efficiencies of target gene and
housekeeping gene are the same.
ΔΔCt=(CT of target gene-CT of housekeeping gene) treatment-( CT of target
gene-CT of housekeeping gene) control.
2- Δ Δ Ct is the target gene expression rate of treatment group comparing to
control group.
User can set sample parameters following below steps to calculate relative
quantity (RQ) in software automatically.
A. Set treatment and control groups. Both treatment and control groups consist of
housekeeping gene and target gene. Every parameter must be covered, or RQ
will not be calculated.
B. User can set the sample name and gene name following personal habit or
experiment requirement.
C. User can set different SubSet ID for different genes to compare them.

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Fig 7.4 a

Fig 7.4 b

Fig 7.4 c

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 Fig 7.4 d
After experiment run, go to Gene Expression page. Select RQ in Data Mode
dropdown list (Fig 7.4 e), click Define Reference button to go to Control Group and
Reference Gene Setup page (Fig 7.4 f), click Add after setting.

Fig 7.4 e
If RQ＜1, it indicates that target gene expression of treatment group is less than
it in control group. If RQ＞1, It should be the opposite.

Fig 7.4 f

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 Fig 7.4 g

7.5 Software update

Software updating consists of exe file and accessory files. If some accessory file
is lack, system will prompt error when run experiment. User needs to copy new
accessory file to Data folder.

Steps:
Remove MA-6000.exe from installation location;
Remove the MA-6000 icon from desktop;
Copy new MA-6000.exe file to the installation location folder;
Right click on the new MA-6000.exe file and create shortcut to desktop;
If needs, copy new files to the Data folder and replace the existing file;
Launch software from the MA-6000 icon on desktop;
Create a new experiment and run it. Software updates successfully if system
does not prompt any error.

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 Chapter 8 Maintenance
8.1 Cleaning the Instrument
Cleaning the surface of the instrument
►The surface of the instrument should be regularly cleaned using a soft cloth
with small amounts of clean water, dry the surface after cleaning. Any spillage of
reagents on the instrument surface should be cleaned with 70% isopropyl alcohol.
Reaction well cleaning
►Dust or impurities in the reaction wells can affect PCR amplification and
fluorescence detection. Routine cleaning must be conducted every 3 months. A blow
bulb can be used to carefully blow away dust.
►When the machine is not in use, keep the cover closed to avoid dust entering
the reaction wells.
►Any leakage in the reaction well should be cleaned with 70% isopropyl
alcohol using a soft cloth.
Do not pour liquid into the reaction module(s) or inside the instrument. Do not
use corrosive solvents or organic solvents to wipe the machine.

8.2 Protecting the Instrument

►Do not rapidly turn on and off, wait at least 30 seconds between switching on
and off.
►Do not turn off the system immediately after experiment. Allow the system to
idle for 10 minutes while the internal fans are still running, wait until the modules
have cooled to room temperature to power off.
►Use the manufacturer supplied power cords and data connection cords.
Do not carry out boiling water bath or low temperature insulation on the
instrument (e.g. 4℃).
Unauthorized opening of the instrument by non-manufacturer maintenance
personnel is strictly prohibited.

8.3 Instrument installation and delivery

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 ►This instrument will be transported with carton and wooden box for long
distance.
►Inspect packaging integrity before unpacking, please contact us if any
abnormity.
►Unpacking the package and get the instrument. Inspect the machine and other
accessories according to the packing list. Please contact us if any abnormity.

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 Chapter 9 Information

【Instrument Name】：Real-Time Quantitative Thermal Cycler

【Instrument Model】：MA-6000
【Manufacturer】：Suzhou Molarray Co., LTD.
【 Address 】： 1-2F Unit C7, 218 Xinghu Rd, Biological Nano Garden, Suzhou
Industrial Park (China)
【Manufacturing License(s)】：SSYJXSCX20170105
【Registration Certificate(s)】：GXZZ20173401410
【Tel】 ：+86-512-69561935

MA-6000 package label

Instrument Name: Real-Time Quantitative Thermal Cycler

Instrument Model: MA-6000
Manufacturer: Suzhou Molarray Co., LTD.
Address: 1-2F Unit C7, 218 Xinghu Rd, Biological Nano Garden, Suzhou Industrial
Park (China)

Transportation and storage conditions

Ambient Temperature: -20℃～50℃
Relative Humidity: ≤85%
Gross Weight：28 Kg
Net Weight: 23 Kg
External Size：695*540*470mm (L*W*H)
Internal Size：600*390*336mm (L*W*H)

MA-6000 Nameplate

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 Chapter 10 Troubleshooting

No. Descriptions solutions

1 Does not power on
2 System does not initialize after
connecting to the computer
3 Machine is running normal, no data
result after experiment
1. Check power cord connections;
2. Check the status of power outlet;
3. Check the power switch;
4. Check the safety fuse.
1. Check if the machine power is on;
2. Check the condition and connection
of the USB data cable;
1. Check if the heating cycle parameters
are correctly set;
2. Check if the Plate Parameters are
entered correctly, and fluorescent reporter has
been set;
3. Open the temp file, check for result in
the backup folder.
4. Errors in the computer system need to
re-install or upgrade to an updated version of
operating system.

Chapter 11 Product Expected Lifetime

Product expected lifetime is 5 years. It is determined by key components in the

instrument. User should maintain properly it following the user manual. The data of
key components in the instrument is based on SR-332 Issue 1 May 2001.

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 Update History
Effective
Version Update description Editor
Date
V1.0 Draft. Sun Chin 2016/3/1
Add product expected lifetime and update
V1.1 history, modify the contents in nameplate, add Sun Chin 2017/6/1
intended use.

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