QuantStudio™ 3 Real-Time PCR System, 96-well, 0.1 mL - FAQs

The exact run method and temperatures will be dependent on the particular kit, but it will be important to program a 2-step PCR stage so that sufficient data points can be collected. For example, for a 40 min incubation at 65 degrees C, can be set up as the following:
- PCR, 40 cycles
- Step 1, 65C, 5 sec
- Step 2, 65C, 55 sec (data collection ON)
Times and number of cycles can be adjusted as needed to collect more data points.

Find additional tips, troubleshooting help, and resources within our QuantStudio 3 and QuantStudio 5 Real Time PCR Systems Support Center.

Continuous melt curve: increases the temperature by the ramp increment (degrees C/sec) so that the temperature will change at a constant rate set in the protocol.
Step and Hold melt curve: increases the temperature by the ramp increment (degrees C) and then holds at that temperature for the time specified by the user.

The amount of data collected will depend on the filter(s) selected. The more filters you use, the longer the acquisition will take and the fewer data points will be collected.

Find additional tips, troubleshooting help, and resources within our Real-Time PCR and Digital PCR Instruments Support Center.

You can perform this action if you have access to an Admin account on the QuantStudio instrument and if it is compatible for the downgrade (newer instruments are not compatible with v1.3.3). If your instrument serial number is below the following, then it can be downgraded:
QuantStudio 5 96-well, 0.1 mL block - SN 272514140
QuantStudio 5 96-well, 0.2 mL block - SN 2725210507
QuantStudio 5 384 well block - SN 272533285
Please also check if the instrument is being used with any validated protocols that may require a particular firmware version to be compliant. If you need the firmware itself, you can download it here.
The instructions to downgrade the firmware are on p.4 of the Release Notes: QuantStudioTM 3 & 5 Touchscreen Instrument Operating Software Version 1.3.3. It's the same process as an upgrade.

Yes, you can click okay to the message and continue with the run and calibrate the instrument at a later time. The exception is that the QuantStudio Dx, QuantStudio 5 Dx, and QuantStudio 7 Pro Dx instruments cannot be run in IVD mode with expired calibrations.

Find additional tips, troubleshooting help, and resources within our Real-Time PCR and Digital PCR Instruments Support Center

If the admin PIN has not been changed, 1234 should work. If it does not work, you can also try 0000.
However, if the admin PIN has been changed and none of the above PINs work, follow the instructions in the QuantStudio 3 and 5 Real-Time PCR Systems manual, page 100.

Find additional tips, troubleshooting help, and resources within our Real-Time PCR and Digital PCR Instruments Support Center.

It is possible to import a standard curve into the Design & Analysis Software (v2.x) if you are analyzing results from one of the following Applied Biosystems real-time PCR instruments:
• 7900HT Fast Real-Time PCR System
• 7500/7500 Fast Real-Time PCR System
• StepOne/StepOne Plus Real-Time PCR System
• ViiA 7 Real Time PCR System
• QuantStudio 1 Real-Time PCR System
• QuantStudio 3 & 5 Real-Time PCR System
• QuantStudio 6 & 7 Flex Real-Time PCR System
• QuantStudio 6 & 7 Pro Real-Time PCR Systems
• QuantStudio 12K Flex Real-Time PCR system

Follow the instructions below to import a standard curve for analysis in the Design & Analysis Software (v2.x):
1. Open the data file in the Design & Analysis Software (v2.x).
2. Click on Actions.
3. Click on "Standard Curve Analysis Setting".
4. Select "External Standard Curves" and click on "Import".
5. Browse to the proper .csv file and click "Open".
6. Click "Apply".

If you are analyzing results from the QuantStudio 1 Real-Time PCR System, QuantStudio 3 Real-Time PCR System, or QuantStudio 5 Real-Time PCR System, it is possible to import a standard curve into the QuantStudio Design & Analysis Software (v1.x) following the instructions below:
1. Open the data file in the QuantStudio Design & Analysis Software (v1.x).
2. Go to Analysis Settings.
3. Click on the "Standard Curve Settings" tab.
4. Select the option to "Use a standard curve imported from another experiment" and click on "Import".
5. Browse to and highlight the proper data file and click "Select".
6. Click Apply.

Yes. On all of our QuantStudio instruments, the sample names, target names, and other plate layout assignments can be adjusted after the run. The instrument always collects all the data in all filter channels during the run, and uses the plate setup information to know how to analyze the data. When changing the plate layout after a run has been completed, simply make the desired changes and press the "Analyze" button to apply the changes.

Please note that changes to the Experiment Type (outside of shifting between "Standard Curve", "Relative Standard Curve", and "Comparative Ct") and changes to the run method are not possible after a run has completed.

Find additional tips, troubleshooting help, and resources within our Real-Time PCR and Digital PCR Instruments Support Center.

Please review this guided tutorial that explains how to set up an Absolute Quantification/Standard Curve experiment run on your QuantStudio 3 or 5 Real-Time PCR instrument: https://www.brainshark.com/thermofisher/QS35AQSetupTutorial

Find additional tips, troubleshooting help, and resources within our Real-Time PCR and Digital PCR Instruments Support Center.

To set up the QuantStudio 3 or QuantStudio 5 Real-Time PCR System for WiFi capability, we recommend following the instructions in the manual (https://tools.thermofisher.com/content/sfs/manuals/MAN0010407_QuantStudio3_5_InstallUseMaint_UG.pdf). You will also need to purchase the High Power USB WiFi Module (Cat. No. A26774).

Find additional tips, troubleshooting help, and resources within our Real-Time PCR and Digital PCR Instruments Support Center.

Yes, you can use templates from other compatible systems, if you use the Thermo Fisher Cloud Design and Analysis module. Use the function “New Experiment --> From File” to import the .edt file.

Find additional tips, troubleshooting help, and resources within our Real-Time PCR and Digital PCR Instruments Support Center.

Check if the Cloud Monitor is on. Go to Settings, then Maintenance and Service, then Monitoring. Turn CloudSuite Monitor ‘ON'. This needs to be set to ‘ON', otherwise the instrument will not look out to connect to your account even if you are logged in.

Find additional tips, troubleshooting help, and resources within our Real-Time PCR and Digital PCR Instruments Support Center.

No. You can use the QuantStudio Design and Analysis Desktop Software, or for multi-plate analysis of genotyping data, please use the Applied Biosystems qPCR Analysis Module (GT application) with your Thermo Fisher Cloud account.

Find additional tips, troubleshooting help, and resources within our Real-Time PCR and Digital PCR Instruments Support Center.

Yes, ExpressionSuite Software v1.1 is compatible with files from the QuantStudio 3 and 5 Real-Time PCR Systems..

Find additional tips, troubleshooting help, and resources within our Real-Time PCR and Digital PCR Instruments Support Center.

If you are using a master mix that has ROX provided in a separate tube, use a low ROX concentration (50 nM, final well volume).

Find additional tips, troubleshooting help, and resources within our Real-Time PCR and Digital PCR Instruments Support Center.

Use the Applied Biosystems qPCR Analysis Module (RQ application) with your Thermo Fisher Cloud account.

Find additional tips, troubleshooting help, and resources within our Real-Time PCR and Digital PCR Instruments Support Center.

1. Set up the run in the cloud from the Design and Analysis application within the Applied Biosystems qPCR Analysis Modules.
2. Save the experiment before starting a run: The file name was created from the experiment Name entered in the Properties tab. However, changes to the experiment Name in the Properties tab after the first save do not update the file name. To change the file name before a run, select Actions, then Save As.
3. Go to an available cloud-connected instrument, enter your PIN to access this file, and start the run by choosing ‘Open Template'. Following a run, view experiment details, run duration, and instrument and software information in the Run Control screen of the Run tab.

Find additional tips, troubleshooting help, and resources within our Real-Time PCR and Digital PCR Instruments Support Center.

You can set up your run in the Design and Analysis application, but to actually start the run, you will have to go to the instrument touchscreen.

Find additional tips, troubleshooting help, and resources within our Real-Time PCR and Digital PCR Instruments Support Center.

Yes, you have several options for this. You can monitor the run in real time from:

- The instrument touchscreen
- The QuantStudio Design and Analysis Desktop Software
- Online using the Design and Analysis application within Thermo Fisher Connect
- Online using the Instrument Connect App on your Android or Apple mobile device - for more on this, please see here (https://www.thermofisher.com/us/en/home/life-science/pcr/real-time-pcr/real-time-pcr-instruments/quantstudio-3-5-real-time-pcr-system/connectivity-quantstudio-3-5-qpcr-data-analysis-software.html).

Find additional tips, troubleshooting help, and resources within our Real-Time PCR and Digital PCR Instruments Support Center.

Yes. To have the run file automatically upload to your Thermo Fisher Cloud account once complete, you will need to set the file destination on the touchscreen, prior to starting the run:
1. Before you start the run, select the ‘Properties' tab from an open experiment
2. Touch ‘Edit', Data Destination - Choose USB or Cloud
Alternatively, you could use Cloud Connect Utility to have all files from a specific hard drive folder location automatically upload to the cloud (for use with the QuantStudio Design and Analysis Desktop Software).

Find additional tips, troubleshooting help, and resources within our Real-Time PCR and Digital PCR Instruments Support Center.

The block drawer is opened and closed by using the ‘eject' button on the touchscreen. Do not push or pull on the instrument drawer.

Find additional tips, troubleshooting help, and resources within our Real-Time PCR and Digital PCR Instruments Support Center.

When your new QuantStudio 3 or QuantStudio 5 Real-Time PCR System arrives in your lab, it will be factory calibrated. The recommended calibration schedule is to recalibrate every 2 years.

Find additional tips, troubleshooting help, and resources within our Real-Time PCR and Digital PCR Instruments Support Center.

Yes, you can purchase the QuantStudio 3 or QuantStudio 5 Real Time PCR System without a computer. In this configuration, you can run the instrument through the touchscreen or the Design and Analysis application from Thermo Fisher Cloud.

Find additional tips, troubleshooting help, and resources within our Real-Time PCR and Digital PCR Instruments Support Center.

Yes, the QuantStudio 5 Real-Time PCR System has SAE (Security/Auditing/e-Signature) features that can be enabled in the QuantStudio Design and Analysis Desktop Software.

Find additional tips, troubleshooting help, and resources within our Real-Time PCR and Digital PCR Instruments Support Center.

The QuantStudio 3 Real-Time PCR System is a 4-color instrument with a 3-zone VeriFlex block, while the QuantStudio 5 Real-Time PCR System is a 6-color instrument with 6-VeriFlex zones in a 96-well block, (or 5-color format, no VeriFlex with 384-well block).

Find additional tips, troubleshooting help, and resources within ourQuantStudio 3 and QuantStudio 5 Real Time PCR Systems Support Center.