Applied Biosystems ViiA 7 Real User manual

ViiA™ 7 Real-Time PCR System
QUICK REFERENCE GUIDE
Note: For safety and biohazard guidelines, refer to the
“Safety” appendix in the Applied Biosystems ViiA™7Real-
Time PCR System User Guide (PN 4442661). For every
chemical, read the SDS and follow the handling
instructions. Wear appropriate protective eyewear, clothing,
and gloves.
In this guide
■Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
■Calibrate the ViiA™7 System . . . . . . . . . . . . . . . . . . . . . . . . . . 2
■Perform an experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
■Maintain the ViiA™7 System. . . . . . . . . . . . . . . . . . . . . . . . . . 15
■Power off the ViiA™7 System. . . . . . . . . . . . . . . . . . . . . . . . . 22
For details on operating and maintaining your ViiA™7 System, refer
to the Applied Biosystems ViiA™7 Real-Time PCR System User Guide
(PN 4442661).
Description
The Applied Biosystems ViiA™7 Real-Time PCR System uses
fluorescent-based polymerase chain reaction (PCR) reagents to
provide:
• Quantitative research detection of target nucleic acid
sequences (targets) using real-time analysis.
• Qualitative research detection of targets using post-PCR
(endpoint) analysis.
• Qualitative analysis of the PCR product achieved by melt curve
analysis that occurs post-PCR.

2
Calibrate the ViiA™7 System
Applied Biosystems ViiA™7 Real-Time PCR System Quick Reference Guide
Calibrate the ViiA™7 System
Calibration types
• Regions of interest (ROI)
•Background
•Uniformity
• Dye (only for dyes used in your experiments)
• Normalization
• Instrument verification
Materials required
384-well sample block
Array-card sample block
96-well sample block
• 384-Well Spectral Calibration Plate with FAM™Dye (PN 4432271)
• 384-Well Spectral Calibration Plate with VIC®Dye (PN 4432278)
• 384-Well Spectral Calibration Plate with ROX™Dye (PN 4432284)
• 384-Well Spectral Calibration Plate with SYBR®Green Dye (PN 4432290)
• 384-Well Spectral Calibration Plate with TAMRA™Dye (PN 4432296)
• 384-Well Spectral Calibration Plate with NED™Dye (PN 4432302)
• 384-Well Region of Interest (ROI) and Background Plates (PN 4432320)
• 384-Well Normalization Plates with FAM™/ROX™and VIC®/ROX™Dyes
(PN 4432308)
• TaqMan RNase P 384-Well Instrument Verification Plate (PN 4455280)
•ViiA
™7 System 384-Well Plate Adapter
(PN 4457087)
• Centrifuge with plate adapter
• Powder-free gloves
• Safety goggles
• Array Card Spectral Calibration Dye Kit (PN 4432314)
•TaqMan
®RNase P Array Card Instrument Verification Reagents Kit
(PN 4432265)
•ViiA
™7 System Array Card Adapter
(PN 4454166)
• Centrifuge with centrifuge array-card carrier
clips and buckets
• Powder-free gloves
• Safety goggles
• 200-µL pipettor, with pipette tips
• Array-card staker/sealer fixture
• 96-Well Spectral Calibration Plate with FAM™Dye (PN 4432327)
• 96-Well Spectral Calibration Plate with VIC®Dye (PN 4432334)
• 96-Well Spectral Calibration Plate with ROX™Dye (PN 4432340)
• 96-Well Spectral Calibration Plate with SYBR®Green Dye (PN 4432346)
• 96-Well Spectral Calibration Plate with TAMRA™Dye (PN 4432352)
• 96-Well Spectral Calibration Plate with NED™Dye (PN 4432358)
• 96-Well Region of Interest (ROI) and Background Plates (PN 4432364)
• 96-Well Normalization Plates with FAM™/ROX™and VIC®/ROX™Dyes
(PN 4432370)
•TaqMan
®RNase P 96-Well Instrument Verification Plate (PN 4432382)
•ViiA
™7 System 96-Well Plate Adapter (PN
4459845)
• Centrifuge with plate adapter
• Powder-free gloves
• Safety goggles

3
Calibrate the ViiA™7 System
Applied Biosystems ViiA™7 Real-Time PCR System Quick Reference Guide
Fast 96-well sample block
Calibrate the instrument
1Prepare the plate or
array card
To prepare the calibration plate:
a. Remove the plate from the freezer, then allow it to thaw to room temperature (approximately 5
minutes).
IMPORTANT! Do not remove a plate from its packaging until you are ready to run it.
b. Remove the plate from its packaging.
IMPORTANT! Do not discard the packaging. The plate can be used up to three times if it is
stored in its original packaging sleeve.
c. Vortex the plate for 5 seconds, then centrifuge it for 2 minutes.
d. Verify that the liquid is at the bottom of each well of the plate. If not, centrifuge the plate again
at a higher rpm and for a longer time.
IMPORTANT! Do not allow the bottom of the plate to become dirty. Fluids and other
contaminants that adhere to the bottom of the plate can contaminate the sample block(s) and
cause an abnormally high background signal.
To prepare the array card:
a. Remove the calibration mix from the freezer, then allow it to thaw to room temperature in the
dark (approximately 5 minutes).
IMPORTANT! Keep the calibration mix out of the light. The fluorescent dye in the mix is
photosensitive. Prolonged exposure to light can diminish the fluorescence of the dye.
b. Fill the array card with calibration mix. For a normalization calibration, fill two cards with
separate normalization solutions.
• Fast 96-Well Spectral Calibration Plate with FAM™Dye (PN 4432389)
• Fast 96-Well Spectral Calibration Plate with VIC®Dye (PN 4432396)
• Fast 96-Well Spectral Calibration Plate with ROX™Dye (PN 4432402)
• Fast 96-Well Spectral Calibration Plate with SYBR®Green Dye (PN 4432408)
• Fast 96-Well Spectral Calibration Plate with TAMRA™Dye (PN 4432414)
• Fast 96-Well Spectral Calibration Plate with NED™Dye (PN 4432420)
• Fast 96-Well Region of Interest (ROI) and Background Plates (PN 4432426)
• Fast 96-Well Normalization Plates with FAM™/ROX™and VIC®/ROX™Dyes
(PN 4432432)
•TaqMan
®RNase P Fast 96-Well Instrument Verification Plate (PN 4351979)
•ViiA
™7 System Fast 96-Well Plate Adapter (PN
4459846)
• Centrifuge with plate adapter
• Powder-free gloves
• Safety goggles
Correct Incorrect
Liquid is at
bottom of well
• Not centrifuged with enough force, or
• Not centrifuged for enough time

4
Calibrate the ViiA™7 System
Applied Biosystems ViiA™7 Real-Time PCR System Quick Reference Guide
2Start the calibration a. Select the instrument to calibrate:
1. In the ViiA™7 Software, select InstrumentInstrument Console. The console displays
instruments on the network.
2. Select an instrument icon, then click Add to My Instruments.
Note: You must add the instrument to your instrument list before you can manage the
instrument.
b. Start the calibration:
1. Select the instrument, then click Manage Instrument.
2. In the Instrument Manager, select the calibration, click Start Calibration, then perform the
calibration as instructed.
3Load the plate or array
card
Load the calibration plate or array card into the instrument tray.
Confirm that the instrument has the correct plate adapter. Ensure that the plate or array card is
properly aligned in the holder:
• Load plates with the A1 position aligned with the A1 position of the tray.
• Load plates and array cards with the bar code facing the front of the instrument.
IMPORTANT! Plates should be loaded and unloaded by trained operators who have been warned of
the moving parts hazard.
4Start the run a. In the Setup tab, select Please check the box when the calibration plate has been loaded,
then click Next.
b. In the Run tab, click START RUN to start the calibration.
IMPORTANT! Do not attempt to open the access door duing the run. The door is locked while the
ViiA™7 System is in operation.
5Review the results and
complete the calibration
a. After the run, view the results in the Analysis tab to verify that the calibration run passed. If the
run failed, troubleshoot the failed calibration as described in the Applied Biosystems ViiA™7Real-
Time PCR System User Guide.
b. After you inspect results, click Next, then remove the plate or array card when the ViiA™7
System ejects the plate adapter.
WARNING! PHYSICAL INJURY HAZARD. During instrument operation, the plate can be
heated to 100 °C. Before removing the plate, wait until it reaches room temperature.
c. Click Finish to complete the calibration.
d. Discard the array card; discard the plate, unless it can be reused. If you store the plate for reuse,
return it to the packaging sleeve, then return the packaged plate to the freezer.

5
Perform an experiment
Applied Biosystems ViiA™7 Real-Time PCR System Quick Reference Guide
Perform an experiment
Materials required
• For all sample blocks:
– DI water/ DEPC water
–Microcentrifugetubes
– Pipettors and pipette tips
–Vortexmixer
–Safetygoggles
– Powder-free gloves
– Sample stock
– Standard stock
– Reaction mix components
• For 384-well, 96-well, or Fast 96-well sample blocks:
– Centrifuge with plate adapter
– Plate or (96-well and Fast 96-well blocks only) tube strip, or single tube
– Optical adhesive film
• For array card sample blocks:
– Centrifuge with centrifuge array-card carrier clips and buckets
– Array-card staker/sealer fixture
–Arraycard
Workflow
Design the experiment (page 6)
Prepare the reactions (page 8)
Start and monitor the experiment (page 12)
View analysis reports (page 13)
Export results (page 14)

6
Perform an experiment
Applied Biosystems ViiA™7 Real-Time PCR System Quick Reference Guide
Design the experiment
1Define experiment name
and type (Experiment
Properties screen)
Define the following properties:
• Experiment name
• User name of the experiment owner
• (Optional) Barcode for the plate or array card
• (Optional) Comments
•Blocktype:384-well, Array Card, 96-well (0.2mL), or Fast 96-well (0.1mL)
• Experiment type: Standard Curve, Relative Standard Curve, Comparative CT(∆∆CT), Melt
Curve, Genotyping, or Presence/Absence
2Select the reagents
(Experiment Properties
screen)
Select reagents to use in the experiment:
Note: If you select SYBR®Green as the reagent, then you have the option of including a melt curve
for that experiment.
3Define the instrument
run properties
(Experiment Properties
screen)
• Ramp speed: Standard or Fast
• (Genotyping and Presence/Absence) Collect data during Pre-PCR Read, Amplification, or Post-
PCR Read
• (Experiments using SYBR®Green) Select whether or not to include a melt curve.
• (Melt Curve) Select whether or not to include PCR.
4Define targets, samples,
biological replicates,
and dye (Define screen)
• (All experiments except Genotyping) Define Targets.
• (Genotyping) Define SNPs.
• (All experiments) Define Samples.
• (Optional) (Standard Curve, Relative Standard Curve, and Comparative CT) Define Biological
Replicate Groups.
• (All experiments except Presence/Absence) Select the Passive Reference dye.
• (Relative Standard Curve and Comparative CT) Select the Reference Sample and the Endogenous
Control.
5Assign targets and
samples (Assign screen)
• (All experiments except Genotyping) Assign targets, tasks, and samples to wells. Tasks include
Unknown, Standard, Positive, and Negative controls, depending on experiment type.
• (Genotyping) Assign SNP assays, tasks, and samples to wells.
• (Standard Curve and Relative Standard Curve) Define and set up standards: Click Define and Set
Up Standards, select a target, define the standard curve, then select and arrange wells for the
standards.
• (Optional) (Standard Curve, Relative Standard Curve, and Comparative CT) Assign Biological
Replicate Groups to wells.
Experiment type Reagent options
Standard Curve TaqMan®Reagents, SYBR®Green Reagents, or Other
Relative Standard Curve TaqMan®Reagents, SYBR®Green Reagents, or Other
Comparative CTTaqMan®Reagents, SYBR®Green Reagents, or Other
Melt Curve SYBR®Green Reagents or Other
Genotyping TaqMan®Reagents or Other
Presence/Absence TaqMan®Reagents or Other

7
Perform an experiment
Applied Biosystems ViiA™7 Real-Time PCR System Quick Reference Guide
6Define the run method
(Run Method screen)
Define run method parameters:
a. Reaction volume:
• 384-well plate: 1 - 30 µL
•Arraycard:1µL
• 96-well plate: 1 - 200 µL
• Fast 96-well plate: 1 - 100 µL
b. Edit the thermal profile as needed:
• Add and delete steps or stages.
• Edit the time, temperature, or ramp rate for a step.
• Click to enable or click to disable data collection.
Note: For real-time data collection during amplification, change the default analysis
settings (Start Cycle and End Cycle) in Preferences.
c. For cycling stages:
• Edit the number of cycles.
• Enable or disable AutoDelta. For an AutoDelta step, enter the Starting Cycle.
d. For a melt curve stage, select the ramp increment:
• Step and Hold: Click the Step and Hold field, select the minutes or seconds, then use the
up or down arrow keys or click the up or down buttons in the field until you reach the desired
time.
• Continuous (default): Click (the ramp rate), select the value in the field, then enter
the desired ramp rate.
7Save the file After you design an experiment, you can also save the experiment as a template, then create
experiments from the template using QuickStart.

8
Perform an experiment
Applied Biosystems ViiA™7 Real-Time PCR System Quick Reference Guide
Prepare the reactions
IMPORTANT! Wear powder-free gloves when you handle the plate or array card.
Prepare the plate
Guidelines for preparing the plate:
• Include excess volume in your calculations to provide for loss during reagent transfers.
• Use TE buffer or water to dilute the standards and samples.
• Prepare the reagents according to the manufacturer’s instructions.
• Keep the dilutions and assay mix protected from light, in the freezer, until you are ready to use it. Excessive exposure to light may
affect the fluorescent probes or dyes.
• To prepare the reactions:
– Mix the master mix thoroughly by swirling the bottle.
– Resuspend the assay mix by vortexing, then centrifuge the tube briefly.
– Thaw any frozen samples, resuspend them by vortexing, then centrifuge the tubes briefly.
• Verify that the liquid is at the bottom of each well of the plate. If not, centrifuge the plate again at a greater rpm and for a longer time.
IMPORTANT! Do not allow the bottom of the plate to become dirty. Fluids and other contaminants that adhere to the bottom of the
plate can contaminate the sample block(s) and cause an abnormally high background signal.
• (Genotyping) Prepare the reactions for each SNP separately
• Place the reaction plate or array card at 4 °C in the dark until you are ready to load it into the instrument.
Correct Incorrect
Liquid is at
bottom of well
• Not centrifuged with enough force, or
• Not centrifuged for enough time

9
Perform an experiment
Applied Biosystems ViiA™7 Real-Time PCR System Quick Reference Guide
Seal the plate
1Load the plate Load the plate with the prepared reactions.
2Apply optical adhesive
film
a. Remove a single optical adhesive film from the box and bend both end-tabs upward. Hold the
film backing side up.
b. In one swift movement, peel back the white protective backing from
the center sealing surface. Do not touch the center sealing surface.
IMPORTANT! Improper peeling of the optical adhesive film may
result in haziness, but it will not affect results. Haziness disappears
when the film comes into contact with the heated cover in the
instrument.
c. Holding the film by the end-tabs, lower the film onto the reaction
plate (adhesive side facing the reaction plate). Be sure that the film
completely covers all wells of the reaction plate.
d. While applying firm pressure, move the applicator slowly across the
film, horizontally and vertically, to ensure good contact between the
film and the entire surface of the reaction plate.
e. While using the applicator to hold the edge of the film in place, grasp
one end of the end-tab and pull up and away sharply. Repeat this step
for the other end-tab.
f. To ensure a tight, evaporation-free seal, repeat step d: While applying firm pressure, run the
edge of the applicator along all four sides of the outside border of the film.
Note: Optical adhesive films do not adhere on contact. The films require the application of
pressure to ensure a tight, evaporation-free seal.
g. Inspect the reaction plate to be sure that all wells are sealed. You
should see an imprint of all wells on the surface of the film. Check
for the perforated tab to be completely torn off to avoid plates sticking
to the instrument after a run.
IMPORTANT! Remove all excess adhesive from the perimeter of the
optical adhesive cover. When the film is applied, the glue from the
optical adhesive cover can adhere to the edges of the plate. If the
excess glue is not removed, the plate may adhere to the gripper of the
Twister®II Robot or to the sample block of the ViiA™7 System.
Note: Go to “Start and monitor the experiment” on page 12.

10
Perform an experiment
Applied Biosystems ViiA™7 Real-Time PCR System Quick Reference Guide
Prepare the array card
IMPORTANT! Wear powder-free gloves when you handle the plate or array card.
Note: Visit www2.appliedbiosystems.com/lib/multimedia/taqman_tlda/tlda_1.cfm to view an online video of loading, centrifuging, and
sealing an array card.
1Remove the array card Remove the Applied Biosystems Array Card from the box and place it on a clean, dry surface.
2Load chemicals and
solutions into the array
card port
For each chemical and solution transferred:
a. Place the array card on a lab bench, with the foil side down.
b. Load 100 µL of fluid into a pipette.
c. Hold the pipette at an angle (~45 degrees) and place the tip into the fill port.
Note: The fill port is the larger of the two holes on the left arm of each fill reservoir.
IMPORTANT! Do not allow the tip to contact and possibly damage the coated foil beneath the
fill port.
3Pipette fluid into the fill
reservoir
Dispense the fluid so that it sweeps in and around the fill reservoir
toward the vent port. Pipette fluid into the fill reservoir, but do not go
past the first stop of pipettor plunger when pipetting the reagents into
the array card, or you may blow the solution out of the port.
IMPORTANT! Do not allow the tip to contact and possibly damage the
coated foil beneath the fill port.
4Centrifuge the array
card
a. Place the filled array card into a centrifuge array-card carrier clip
and place empty array cards in the remaining slots. Make sure
that the labels on the buckets and clips face the same way.
IMPORTANT! Balance the loads in opposite buckets in the
centrifuge.
Fill
port
Vent
port
F
i
lled array
Empty
array

11
Perform an experiment
Applied Biosystems ViiA™7 Real-Time PCR System Quick Reference Guide
4Centrifuge the array
card (continued)
b. Place the filled carrier clips into the centrifuge buckets. Make sure that
the array-card fill reservoirs and bucket and clip labels face outward
when loaded into the centrifuge.
You must run the centrifuge with all four buckets in place and each of
the two carriers filled with array cards. Place empty array cards into
unfilled slots.
IMPORTANT! Balance the loads in opposite buckets in the centrifuge.
c. Close the centrifuge cover, then centrifuge the array card for 1 minute at 1200 rpm. When the
run is finished, stop the centrifuge, then centrifuge the array card again for 1 minute at 1200 rpm.
IMPORTANT! Do not try to save time by doing one spin for 2 minutes. Centrifuging twice is
important for a good fill into the array card.
d. Open the centrifuge and check that the fluid levels in the reservoirs of the array card have
decreased by the same amount. Also, check for bubbles in all wells.
If necessary, centrifuge the array card for an additional minute to fill unfilled wells. Do not exceed
three 1-minute runs or centrifuge the array card for longer than 1 minute at a time.
5Seal the array card a. With the carriage (roller assembly) of the staker/sealer
fixture in the Start position, place a filled array card into the
fixture with the foil side up so that the fill reservoirs are the
farthest away from the carriage.
b. Press down on all four corners of the array card to ensure
that it is fully seated within the fixture.
c. Use the two alignment pins in the fixture to position the
array card correctly.
Correct Incorrect
GR2172a
Alignment pins

12
Perform an experiment
Applied Biosystems ViiA™7 Real-Time PCR System Quick Reference Guide
5Seal the array card
(continued)
d. Seal the array card by running the carriage slowly over it, in
one direction only.
e. Remove the sealed array card from the fixture and trim the
fill reservoirs from the array card assembly using scissors. Trim the
foil array card so that the edge is even with the plastic carrier.
Completely remove the fill reservoirs from the array card so that the
edge is free of residual plastic. The plastic from the fill reservoirs
that extends beyond the edge of the card can prevent the card from
seating properly on the sample block and affect amplification.
IMPORTANT! Keep the filled array card out of the light. The fluorescent dye in the array card is
photosensitive. Prolonged exposure to light can diminish the fluorescence of the dye.
Start and monitor the experiment
1Load the plate or array
card
a. Touch on the instrument touchscreen to eject the plate adapter.
b. Place the plate or array card on the plate adapter. Ensure that the plate or array card is properly
aligned in the holder:
• Load plates and array cards with the A1 position aligned with the A1 position of the tray.
• Load plates and array cards with the barcode facing the front of the instrument.
IMPORTANT! Plates should loaded and unloaded by trained operators that have been warned
of the moving parts hazard.
c. Touch to load the plate.
Correct Incorrect

13
Perform an experiment
Applied Biosystems ViiA™7 Real-Time PCR System Quick Reference Guide
2Start and monitor the
experiment
a. Start the experiment. From the ViiA™7 Software:
1. Click Run in the Experiment menu.
2. Click START RUN and select the instrument from the drop-down menu.
IMPORTANT! Do not attempt to open the access door during the run. The door is locked while
the ViiA™7 System is in operation.
b. (Optional) Monitor the experiment.
3Unload the plate or
array card
WARNING! PHYSICAL INJURY HAZARD. During instrument operation, the plate can be
heated to 100 °C. Before removing the plate, wait until it reaches room temperature.
Touch , remove the plate or array card from the plate adapter, then touch to retract the plate
adapter.
If the ViiA™7 System does not eject the plate, remove the plate as follows:
a. Power off and unplug the ViiA™7 System.
b. Wait for 15 minutes, then power on the ViiA™7 System and eject the plate.
c. If the plate does not eject, power off the ViiA™7 System, then open the instrument door.
d. While wearing powder-free gloves, reach into the ViiA™7 System and remove the plate from the
heated cover, then close the instrument door.
e. Perform a background calibration to confirm that the sample block has not been contaminated.
View analysis reports
Plot Applicable experiment type Purpose
Amplification All experiment types (if the experiment includes
amplification)
• To set baseline and threshold
• To compare the data on a per well basis
Multicomponent All experiment types (if the experiment includes
amplification)
To review data for anomalies
Raw Data All experiment types To review data for anomalies
QC Summary All experiment types To view flags triggered by experiment data
Well Table All experiment types To identify well problems
Gene Expression Comparative CTand Genotyping To view the genotypes identified in the experiment
QC Plot Comparative CT, Relative Standard Curve To view the Endogenous Control Profile for an
experiment
Presence/Absence Presence/Absence To confirm the presence or absence of a target gene
Standard Curve Standard Curve, Relative Standard Curve To confirm that the r2 value is acceptable
Derivative Melt Curve Melt Curve and any other type, when the experiment
includes a melt curve
To review melt curve data

14
Perform an experiment
Applied Biosystems ViiA™7 Real-Time PCR System Quick Reference Guide
Export results
1Select the data to export a. From the experiment file, click Export.
b. Select the type and format of the file to which data will be exported:
• ViiA™ 7
•7900
•RDML
c. Select to export all data in one file or in separate files for each data type.
d. Select the contents of the file. Include any of the following information in your export file:
• Sample setup data
•Rawdata
•Amplificationdata
• Multicomponent data
•Results
e. Depending on the file type, enter or select export file properties (name, type, and location).
2Start the export a. (Optional) Save export settings. Select the Save Export Set As check box and name the settings
file. You can select the settings file later when you perform a similar experiment.
b. Click Start Export.

15
Maintain the ViiA™7 System
Applied Biosystems ViiA™7 Real-Time PCR System Quick Reference Guide
Maintain the ViiA™7 System
Maintenance schedule
Accessories required for instrument maintenance
384-well sample block
• Applied Biosystems ViiA™7 System 384-Well/Array Card Heated Cover (PN 4453555)
• Applied Biosystems ViiA™7 System 384-Well Plate Adapter (PN 4457087)
• Applied Biosystems ViiA™7 System 384-Well Sample Block (PN 4453553)
Array card sample block
• Applied Biosystems ViiA™ 7 System 384-Well/Array Card Heated Cover (PN 4453555)
• Applied Biosystems ViiA™ 7 System Array Card Adapter (PN 4454166)
• Applied Biosystems ViiA™ 7 System Array Card Sample Block (PN 4453554)
96-well sample block
• Applied Biosystems ViiA™7 System 96-Well Heated Cover (PN 4453560)
• Applied Biosystems ViiA™7 System 96-Well Plate Adapter (PN 4459845)
• Applied Biosystems ViiA™7 System 96- Well Sample Block (PN 4453556)
Frequency Task
Weekly Check the computer disk space. If necessary, archive or back up your experiment files.
Power off the computer that controls the instrument, wait 30 seconds, then power on the
computer.
Clean the surface of the instrument with a lint-free cloth.
IMPORTANT! Do not use organic solvents to clean the ViiA™7 System.
Perform a ViiA™7 System self test.
Monthly Check the lamp status. If necessary, replace the tungsten halogen lamp.
Perform a background calibration.†
† You can perform a background calibration to check for contamination. If any parts of the optics are replaced or moved, you must run an ROI calibration,
a background calibration, a uniformity calibration, a dye calibration, a normalization calibration, and an RNase P instrument verification run.
Run disk cleanup and disk defragmentation.
Semi-annually (6 Months) Check the lamp status. If necessary, replace the tungsten halogen lamp.
Perform a regions of interest (ROI) calibration.
Perform a background calibration.
Perform an uniformity calibration.
Perform a dye calibration.
Perform a normalization calibration.
Perform an RNase P instrument verification run.
As needed Decontaminate the instrument.
Replace the tungsten halogen lamp.
Replace the fuses.

16
Maintain the ViiA™7 System
Applied Biosystems ViiA™7 Real-Time PCR System Quick Reference Guide
Fast 96-well sample block
• Applied Biosystems ViiA™7 System Fast 96-Well Heated Cover (PN 4459838)
• Applied Biosystems ViiA™7 System Fast 96-Well Plate Adapter (PN 4459846)
• Applied Biosystems ViiA™7 System Fast 96- Well Sample Block (PN 4453559)
Decontaminate the sample block
Clean the sample block to eliminate fluorescent contaminants from the ViiA™7 System sample block. Contamination is generally evident
in failed background calibrations where one or more wells consistently exhibit abnormally high signals.
CAUTION! PHYSICAL INJURY HAZARD. Do not remove the ViiA™7 System cover. There are no instrument components that you
can safely service yourself. If you suspect a problem, contact an Applied Biosystems Service Representative.
CAUTION! PHYSICAL INJURY HAZARD. During instrument operation, the sample block can be heated to 100 °C. Before
performing the following procedure, be sure to wait until the sample block reaches room temperature.
CAUTION! Before using a cleaning or decontamination method other than those recommended by the Applied Biosystems, verify
with Applied Biosystems that the proposed method will not damage the equipment.
Materials required
•Bleach,10%solution
•Chemwipe
• Cotton or nylon swabs
• Lint-free cloths
• Ethanol, 95% solution
• Safety glasses
•Pipette(100-μL) with pipette tips
• Powder-free gloves
• Screwdriver
• Deionized water
How to handle the sample block
To prevent damaging or contaminating the sample block, handle the assembly as shown. Also, when the
assembly has been removed from the ViiA™7 System, place the sample block on a clean, dry surface or
in its shipping container.

17
Maintain the ViiA™7 System
Applied Biosystems ViiA™7 Real-Time PCR System Quick Reference Guide
Clean the sample block
WARNING! PHYSICAL INJURY HAZARD. During instrument operation, the sample block and heated cover can be heated to
100 °C. Before removing the sample block, be sure to wait until it reaches room temperature.
IMPORTANT! Wear powder-free gloves when you perform this procedure.
1Remove the sample
block
a. Power off, then unplug the instrument and allow it to cool for
15 minutes.
b. Open the access door.
c. Firmly grasp the handle of the sample block, press the handle down,
pull the sample block from the instrument, then place it on a clean,
dry surface.
2Clean the contaminated
wells
a. Pipette a small volume of deionized water into each contaminated well.
b. Pipette the water up and down several times to rinse the well, then pipette the water to a waste
beaker.
c. Using a cotton swab, scrub inside of each contaminated well.
d. Using a lint-free cloth, absorb the excess deionized water.
3Install the sample block a. Load the sample block into the ViiA™7 System.
IMPORTANT! After installing the sample block, confirm that the white
indicator on the left side of the sample block is positioned behind the red line
on the instrument rail. If the indicator is on the red line, push the sample
block into the ViiA™7 System until it is seated correctly.
b. Close the access door.
IMPORTANT! Confirm that the instrument door is completely closed. The ViiA™7 Software
displays an error message if the access door is not completely closed and latched, or if the
sample block and heated cover are not seated correctly.
c. Plug in, then power on the ViiA™7 System.

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4Verify success Perform a background calibration.
If the contamination remains, remove the sample block (step 1) and clean the contaminated wells
(step 2), then clean the contaminated wells again using 95% ethanol solution:
a. Pipette a small volume of 95% ethanol solution into each contaminated well.
b. In each contaminated well, pipette the solution up and down several times to rinse the well.
c. Pipette the ethanol solution to a waste beaker.
IMPORTANT! Always use deionized water to rinse wells after cleaning with bleach or ethanol
solution.
d. Clean the wells again (step 2), to rinse the wells of the sample block.
e. Perform a background calibration, to verify that you have eliminated the contamination.
If the contamination remains, remove the sample block and clean the contaminated wells (step 2),
then clean the contaminated wells again using 10% bleach solution:
a. Pipette a small volume of 10% bleach solution into each contaminated well.
b. In each contaminated well, pipette the solution up and down several times to rinse the well.
c. Pipette the bleach solution to a waste beaker.
IMPORTANT! Always use deionized water to rinse wells after cleaning with bleach or ethanol
solution.
d. Clean the wells again (step 2) to rinse the wells of the sample block.
e. Perform a background calibration, to verify that you have eliminated the contamination.
If the contamination remains, contact Applied Biosystems Technical Support.

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Change instrument parts
Replace the sample block to change the consumable format of the instrument; if you replace the sample block, replace the heated cover
and plate adapter to match the new consumable format.
WARNING! PHYSICAL INJURY HAZARD. The ViiA™7 System and lamp are hot! The lamp can become very hot while in use. Allow
the lamp to cool for 15 minutes and put on protective, powder-free gloves before handling it.
CAUTION! PHYSICAL INJURY HAZARD. Wear disposable, powder-free gloves when handling the lamp to prevent burns and to
prolong the life of the replacement lamp.
Materials required
• Safety glasses
• Powder-free gloves
• Flathead screwdriver (for fuse replacement)
•Replacementparts:
– Sample block
– Heated cover
– Plate adapter
A note on calibration order
When you are instructed to perform calibrations in the following sections, perform them in this order:
1. ROI calibration
2. Background calibration
3. Uniformity calibration
4. Dye calibration
5. Normalization calibration
Change the sample block
IMPORTANT! If you are installing a sample block of a different format, you must also change the heated cover and plate adapter to match
the new consumable format.
1Remove the sample
block
a. Power off, then unplug the instrument and allow it to cool for
15 minutes.
b. Open the access door.
c. Firmly grasp the handle of the sample block, press the handle
down, pull the sample block from the instrument, then place it on
a clean, dry surface.
2Install the new sample
block
a. Load the new sample block into the ViiA™7 System.
IMPORTANT! After installing the sample block, confirm that the white
indicator on the left side of the sample block is positioned behind the red line
on the instrument rail. If the indicator is on the red line, push the sample
block into the ViiA™7 System until it is seated correctly.

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2Install the new sample
block (continued)
b. If you are installing a sample block of a different consumable format, replace the heated cover
and plate adapter if necessary.
c. Close the access door.
IMPORTANT! Confirm that the instrument door is completely closed. The ViiA™7 Software
displays an error message if the access door is not completely closed and latched, or if the
sample block and heated cover are not seated correctly.
d. Plug in and power on the instrument.
3Verify success a. In the ViiA™7 Software, select InstrumentInstrument Console.
b. In the Instrument Console, select your instrument from the list of ViiA™7 Systems, then review
the Block Type field in the Instrument Properties pane.
The installation is successful if the instrument powers on and if the Block Type field displays the
correct type of sample block.
4Perform calibrations Perform calibrations in the order shown in “A note on calibration order” on page 19.
Change the plate adapter
IMPORTANT! If you are installing a plate adapter of a different format, you must also change the heated cover and sample block to match
the new consumable format.
1Open the instrument
drawer
In the instrument touchscreen Main Menu, touch .
2Detach the plate adapter When the tray arm opens, detach the plate adapter by pulling the
side plunger out with one hand and lifting the plate adapter with the
other hand.
3Install the new adapter a. Attach the new adapter to the tray arm. Place the adapter in the
tray-arm slot by pivoting the adapter from the left at an angle,
swinging the right end downward, and pressing the adapter with
your thumb until it clicks into position.
b. In the Main Menu, touch .