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Quick Guide
Roche Diagnostics has made every reasonable effort to ensure that all the information contained in this manual
is correct at the time of printing. However, Roche Diagnostics reserves the right to make any changes necessary
without notice as part of ongoing product development.
This LightCyler 480 Instrument Quick Guide was created by the Roche Diagnostics Corporation Commercial
Education department. Direct questions or concerns regarding the contents of this document to:
Roche Diagnostics Corporation
Commercial Education Department
9115 Hague Road
P.O. Box 50457
Indianapolis, IN 46250-0457
USA
5125-00-1113
LIGHTCYCLER is a trademark of Roche. The technology for LightCycler is licensed from Idaho Technologies,
Inc.
All other trademarks are the property of their respective owners.
2013, Roche Diagnostics.
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LightCycler 480 Instrument Basics
General Required Materials
Standard Laboratory Equipment
Product Name
Microwell Plate Centrifuge
Nuclease-free, aerosol-resistant pipette tips
Microcentrifuge and 1.5 mL microcentrifuge tubes
Micropipettes (P10 or P20, P200, P1000 or equivalent)
Disposables
Product Name Catalog Number Description
LightCycler 480 Multi-well Plate 96-well - White 04 729 692 001 50 plates and sealing foils
LightCycler 480 Multi-well Plate 384-well - White 04 729 749 001 50 plates and sealing foils
LightCycler 480 Multi-well Plate 96-well - Clear 05 102 413 001 50 plates and sealing foils
LightCycler 480 Multi-well Plate 384-well - Clear 05 102 430 001 50 plates and sealing foils
LightCycler 480 Sealing Foil 04 729 757 001 50 sealing foils
Reagents
Reaction Type Product Name Catalog Number Description
Reverse Transcription Transcriptor 1st Strand 04 379 012 001 For 50 (20 L) reactions
with RNAse H activity cDNA Synthesis Kit
SYBR Green Master LightCycler 480 SYBR 04 707 516 001 5 mL (5 x 20 L)
Green I Master 2x concentrated Master Mix for
250 (20 L) reactions
High Resolution LightCycler 480 High 04 909 631 001 5 mL (5 x 1 mL)
Melting Resolution Melting Master 2x concentrated 25 mL MgCl2
stock solution for 500 (20 L)
reactions
Hybridization Probes LightCycler 480 04 707 524 001 1.5 mL
Genotyping Master 5x concentrated Master Mix for
250 (20 L) reactions
Hydrolysis Probes LightCycler 480 Probes 04 707 494 001 5 mL (5 x 1 mL)
TaqMan Probes or Master 2x concentrated Master Mix for
Universal Probe Library 250 (20 L) reactions
(UPL)
LightCycler 480 Control Kit 04 710 924 001 Kit for quantitative Real-Time
PCR and genotyping reactions
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LightCycler 480 Instrument Basics
Getting Started
1. Log on to the LightCycler computer.
Username: Operator
Password: LC480
3. Enter the username and assigned password to log in to the LightCycler 480 software.
Username: admin
Password: LightCycler480
Normal Login
Username: admin
Password: Roche480
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LightCycler 480 Instrument Basics
Software Navigation Overview
Navigator window: displays the objects stored in the database as folders and files, allowing the user to work with
objects in the database as well as import and export
Exporting as .ixo: creates a copy which can be imported to another computer or database
Tools window: allows user to change passwords, edit system settings, view database status and Error Log,
define filter combination settings
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New Experiment from Template
Create a New Experiment from Template
Templates provide a convenient way to speed up the process of creating an experiment. You can use Roche general
templates for the different types of Real-time PCR reactions, as well as create your own templates based on the
specific conditions of your experiments.
2. The New Experiment from Template window displays the templates that match the connected instrument.
5. Modify run conditions (reaction volume, number of cycles, target temperature, hold, ramp rate, etc.) as
needed.
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New Experiment from Template
6. The Start Run icon becomes active once the multi-well plate is loaded in the instrument.
2. Click the drop-down next to Apply Template and select Save as Template.
3. Name the run template and select a location to save the template.
Note: The default storage location for templates is the users Template folder.
4. Click . The template is saved and will appear in the New Experiment from Template window in the future.
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Basic Real-Time Chemistry Protocols
Typical SYBR Green Reaction Protocol
Reaction Setup
Reagent Final Concentration Volume (L) / one reaction
Water 1.0
Primer - Forward (5 M Stock) 0.5 M 2.0
Primer - Reverse (5 M Stock) 0.5 M 2.0
LightCycler 480 1x 10.0
SYBR Green I Master
Total 15.0
Add 5 L template DNA for a total volume of 20 L
Run Program
Program Name Cycles Analysis Mode
Pre-incubation 1 None
Run Program
Program Name Cycles Analysis Mode
Pre-incubation 1 None
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Basic Real-Time Chemistry Protocols
Typical Hybridization Probe (HybProbe) Reaction Protocol
Reaction Setup
Reagent Final Concentration Volume (L) / one reaction
Water 6.2
Primer - Forward (5 M Stock) 0.5 M 2.0
Primer - Reverse (5 M Stock) 0.5 M 2.0
Fluorescein Probe (10 M Stock) 0.2 M 0.4
Red Fluor Probe (10 M Stock) 0.2 M 0.4
LightCycler 480
1x 4.0
Genotyping Master
Total 15.0
Add 5 L template DNA for a total volume of 20 L
Run Program
Program Name Cycles Analysis Mode
Pre-incubation 1 None
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Absolute Quantification
Absolute Quantification Analysis
Sample concentrations are calculated based on a standard curve created with standard samples along a
concentration range with specific assigned values. The standard curve can be included within the run (internal
standard curve) or generated in a previous run (external standard curve).
Important: To use an external standard curve imported from a previous run, the software needs a
reference point included in the current run. One concentration standard must be on every run
to align the standard curve into the new run. The software shifts the imported standard curve
based on how the reference standard compares to the previously run concentration.
For more information, please consult Chapter D, Section 4.2.3 (pages 164-166) of the
LightCycler 480 Operators Manual.
Crossing point (Cp) values (Cp is equivalent to Ct) are used to determine unknown sample concentrations from a
standard curve.
Note: Once the experimental run has completed, it remains open and ready to analyze. Previous
experiments are located in the Experiments folder of the Navigator.
2. If sample information was entered during run setup, proceed to step 5. Otherwise, click Sample Editor on the
left side of the active display.
b. In Sample Editor > Step 3: Edit Abs Quant Properties, enter the appropriate sample information for
the selected wells. Identify samples as Unknown or Standard samples, entering the appropriate
concentration for each standard.
c. For reactions in replicate, select all the wells and click Make Replicates.
5. Click Analysis.
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Absolute Quantification
6. Select an analysis to create from the list.
Important: Two algorithms are available to determine the crossing point:
Absolute quantification/2nd derivative max
automated, user input not required
the point at which the maximum change in slope of the amplification curve becomes the
crossing point
Absolute quantification/Fit Points
user must set a threshold line
the point at which the log-linear curve crosses the threshold line becomes the crossing point.
7. In the Create New Analysis dialog box, select an analysis subset and Quantification program (selected by
default) and click OK.
8. If a standard curve was included in the experiment, select std curve (in run) from the drop-down menu.
If an external standard curve needs to be imported, select std curve external.
By default, all samples are included in results
Double-click the check box next to the sample, or press the <space bar> to exclude a specific sample
from the analysis
Important: External Standard Curve - the external standard curve must be from an experiment with
the same detection format, filter combination, and color compensation settings as the current
experiment. The external curve and current experiments can be generated on different blocks
(96 or 384). If using an External Standard Curve, you must include at least one of the
Standard concentrations in the new experiment as a standard reference point for
calculation.
For more information, please consult Chapter D, Section 4.2.3 (pages 164-166) of the
LightCycler 480 Operators Manual.
To view the amplification curves for one or more samples, highlight the sample names in the sample list
or click the corresponding well in the plate diagram.
10. To export individual data figures or tables, right-click within the information section you want to export, then
choose the external format to use. Click the browse (...) button to browse to the location to save the file and
assign a name to your export file. Click Export.
11. Export the entire experiment through the Navigator using the Export button. Map to the appropriate drive/
folder for saving. The complete file experiment can be imported into another computer with the same release
of LightCycler 480 software.
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Relative Quantification
Relative Quantification Analysis
Relative Quantification compares the levels of two different target sequences in a single sample (e.g., target gene of
interest (GOI) and another gene) and expresses the final result as a ratio of these targets. For comparison purposes
the second gene is a reference gene that is found in constant copy numbers under all test conditions. The reference
is used for normalization of sample-to-sample differences.
The ratio of the same two sequences can be compared to a standard sample called a calibrator. The calibrator
is typically a positive sample with a stable ratio of target-to-reference and is used to normalize all samples within
one run, but in addition provides a constant calibration point between several LightCycler 480 System runs.
Important: For more information, please consult Chapter D, Section 4.3 (pages 179-205) of the
LightCycler 480 Operators Manual.
Important: Relative Quantification Analysis uses the following identifiers for calculation, please note
there are mandatory identifiers required:
Note: If you are performing an experiment using different filter combinations, make sure you select
the appropriate filter combination for entering the sample information.
a. In Sample Editor > Step 2: Select Samples, select the wells that contain the same DNA samples.
b. In Sample Editor > Step 3: Edit Rel Quant Properties, enter the appropriate sample name and sample
type information for the selected wells.
Note: For more information, please consult Chapter D, Section 4.3.3 (page 183) of the LightCycler
480 Operators Manual.
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Relative Quantification
5. Enter Gene target information.
a. In Sample Editor > Step 2: Select Samples, select the wells that contain the same gene target.
b. In Sample Editor > Step 3: Edit Rel Quant Properties, enter the appropriate target name and select target
type (target or reference) information for the selected wells
Note: Target is the gene of interest and Reference is the housekeeping gene (e.g., actin)
6. In Sample Editor > Step 2: Select Samples, select all the wells and set replicates by clicking Auto Replicate.
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Relative Quantification
8. Select Advanced Relative Quantification.
Important: Two algorithms are available for the Relative Quantification Analysis
Basic Relative Quantification
automated, easy-to-use mode
based upon the CT-method
Advanced Relative Quantification
flexible mode, sophisticated software algorithms
E-Method (Efficiency Method)
For more information, please consult Chapter D, Section 4.2.3 (pages 179-205) of the LightCycler 480
Operators Manual.
Note: For more information about this dialog box, please consult Chapter D, Section 4.3.5 (pages
190-192) of the LightCycler 480 Operators Manual.
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Relative Quantification
11. The software automatically pairs the target to the corresponding reference.
a. To obtain results, click Calculate.
Note: If a calibrator sample was used, the normalized ratio is the fold difference between samples
and calibrator, represented as a red bar in the bar chart.
If a calibrator sample was not used, then the Target/Ref Ratio column will provide results,
comparing only target to reference amounts within a single sample, represented as a blue bar
in the bar chart.
Note: For more information, please consult Chapter D, Section 4.3.7 (pages 198-199) of the
LightCycler 480 Operators Manual.
a. Once sample editing is complete, click Calculate, then click the Back to Rel Quant icon.
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Relative Quantification
b. Click the Rel Quant Results tab, then click Calculate to obtain updated results.
13. To export individual data figures or tables, right-click within the information section you want to export, then
choose the external format to use. Click the browse (...) button to browse to the location to save the file and
assign a name to your export file. Click Export.
14. Export the entire experiment through the Navigator using the Export button. Map to the appropriate drive/
folder for saving. The complete file experiment can be imported into another computer with the same release
of LightCycler 480 software.
488DF20
3000000 Cyan 500
494 nm 521 nm 555 nm 607 nm 640 nm 668 nm
Fluorescein
Hex
2500000
Red 610
Red 640
F luores c enc e Intens ity w.E
2000000 Cy5
1500000
1000000
500000
0
400 450 500 550 600 650 700 750 800
Wav e le ngth nm
Prepare an equimolar mix of all donor HybProbe probes used in the assay.
Check the quality of the dyes and probes used
Note: High amounts of free, unlabeled dye can cause a high background signal that might
impact color compensation.
The free dye can be chosen if using a self-quenched probe (e.g., TaqMan or Molecular Beacon) but a
positive reaction for the individual probe in the mix will also work
DNA template must be added for the TaqMan Probe Color Compensation (adjust water volume)
It is recommended to run the reactions in replicates of five. Below is a typical reaction setup:
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Color Compensation
Example Reaction Setup for Hydrolysis/TaqMan probe-based Assay
Reaction Blank Dye 1 Dye 2
10 L Master Mix 10 L Master Mix 10 L Master Mix
10 L Water 2.6 L Water 2.6 L Water
1 L (10 M stock) 1 L (10 M stock)
primer-forward target 1 primer-forward target 2
1 L (10 M stock) 1 L (10 M stock)
primer-reverse target 1 primer-reverse target 2
0.4 L probe target 1 0.4 L probe target 2
5 L DNA template 5 L DNA template
Procedure
1. Open the LightCycler 480 Basic Software version 1.5.1 and setup a run protocol as follows (adjust the
amplification conditions to mimic the PCR you normally perform). The example below may differ from your
PCR run.
2. Create a Subset including only the samples to create the color compensation.
4. Select samples, identifying the color compensation subset to help navigate and enter sample information
under the Color Comp Properties.
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Color Compensation
5. In the Color Comp Properties, also enter sample information, indicating the appropriate dominant wavelength
for each dye used in a particular well.
3. In the Create New Analysis dialog box, select an analysis subset and a program in the experiment (typically
there is only one color compensation or melting program selected by default). Click OK.
5. Click Save CC Object. By default, the CCC folder in your Special Data folder is selected as the location.
2. Click the down arrow next to the Color Compensation button and choose between the options <In Use> or
<In Database>.
The experiment or the analysis charts are redrawn using the compensated data. Note that the Color Compensation
button label indicates On.
Note: The CC Object may also be applied to the Experiment/Data page, allowing the color compensation to be
selected in all further analyses created on the experiment file.