Can I collect data at two separate steps for analysis in the QuantStudio™ 6 and QuantStudio™ 7 Flex Real-Time PCR Systems?

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Answer

Yes, the QuantStudio™ 6 and QuantStudio™ 7 Flex Real-Time PCR Systems can collect data at multiple steps in the amplification stage. You will need to turn on the data collection for every step of interest. In the analysis, only one set of data can be displayed at a time. To change the data set used for analysis, go to Analysis Settings then Ct Settings and change the drop down under ‘Data Step Selection’.

Answer Id: E7148

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Where are my files saved on the QuantStudio™ 6 and QuantStudio™ 7 Flex Real-Time PCR Systems?

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Answer

Run files will be saved to both the instrument and the connected computer. On the connected computer, files will be saved to the default data folder, unless you change it.

To find or change the default folder, go to then Tools then Preferences then Defaults. Here you will see a Data Folder and an Import Folder. The default location is shown. If you want files to be saved to (or open from) a different location, click ‘Browse’, and choose the new folder.

Answer Id: E7149

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How do I transfer a QuantStudio™ software license to another computer?

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Answer

Follow the directions in this blog post (http://solid.community.appliedbiosystems.com/community/real-time_pcr/blog/2013/03/26/transferring-a-quantstudio-12k-flex-software-license-to-another-computer) to transfer your license to another computer. (Please note that the instructions here still apply, although they are written for the QuantStudio™ 12K Flex Real-Time PCR System.)

Answer Id: E7150

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Is it possible to see the traces in an allelic discrimination experiment on the QuantStudio™ 6 and QuantStudio™ 7 Flex Real-Time PCR Systems

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Answer

The ‘reveal traces’ feature for genotyping runs allows you to trace the clusters throughout the PCR process. For some assays you may find better cluster discrimination at, say, cycle 40, as opposed to cycle 50. To use this feature, the amplification data needs to have been collected for the run.

- Go to ‘Analysis Settings’
- Under the default ‘Call Settings’ tab, Choose ‘Analyze Real-Time Rn Data’
- Click ‘Apply Analysis Settings’
- Under the Allelic Discrimination Plot, check the box next to ‘Reveal Traces’. You can then move the slide bar to see how the data changes with the cycles number.
In the example below, the image on the left shows the data at a full 40 cycles. The image on the right is the same data after revealing traces (grey lines). The clusters can be traced back by moving the cycle bar. Notice that one point is no longer called at the earlier cycle set point.

Answer Id: E7152

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How many QuantStudio™ 3D Digital PCR Chips can be cycled at one time on the GeneAmp™ 9700 PCR System?

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Answer

Using the Chip Carrier on the GeneAmp™ 9700 Dual Flat Block, up to 24 QuantStudio™ 3D Digital Chips can be run at one time. Please refer to Chapter 3 in the QuantStudio™ 3D Digital PCR System User Guide (http://tools.thermofisher.com/content/sfs/manuals/MAN0007720.pdf) for more details on loading the chips for thermal cycling.

Answer Id: E7169

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What does “Error - Calibration file already exists” mean?

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Answer

The calibration files are stored on the QuantStudio™ instrument itself; therefore, when you need to perform a new calibration, you will have to delete the old calibration files. From the instrument console, go to the QuantStudio™ instrument touchscreen and select ‘Collect Results’. You should then see a list of files stored on the instrument. Manually select a calibration file such as “Fast-96-cal”, and press the ‘Delete’ button to remove the old calibration file. Occasionally, users cannot delete the file off the instrument and may encounter this error: “Some experiments did not collect results therefore cannot be deleted.”. In these situations, launch the software, go to ‘maintenance’, manage files, and download the calibration file. The status of the experiment should be displayed as ‘complete’. Next, delete the old calibration file and rerun the calibration.

Answer Id: E7153

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How soon do I have to read the QuantStudio™ 3D Digital Chip after cycling is complete?

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Answer

After thermal cycling, the QuantStudio™ 3D Digital PCR 20K Chips can remain on the sample block for up to 24 hours. Read the QuantStudio™ 3D Digital PCR 20K Chips within 1 hour after you remove them from the GeneAmp™ 9700 PCR System sample block.

Answer Id: E7170

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What can I do if there are no predesigned assays to my SNP?

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Answer

You can use our Custom Assay Design Tool (https://www.thermofisher.com/us/en/home/life-science/pcr/real-time-pcr/real-time-pcr-assays/snp-genotyping-taqman-assays/custom-snp-assays.html?ICID=ta-lm-custom%20taqman%20snp%20assay-Single%20Tube%20Custom%20TaqMan%C2%AE%20SNP%20Genotyping%20Assays) to submit your SNP sequence for an assay design. Alternatively, you can also use Primer Express™ Software to design an assay.

Answer Id: E7517

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What can I do when I get an error message related to “...JVM...”?

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Answer

This error can occur due to allocation of the computer’s virtual memory. If you see this message, try the following:

1. Click ‘OK’ to the error, close any unnecessary programs, and re-launch the software (you may have to do this several times).
2. Using the Task Manager (Control+Alt+Delete), look for a process called ‘javaw.exe’. Select this line and end the process. Then re-launch the software.

Answer Id: E7154

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How quickly can the QuantStudio™ 3D Digital PCR System read a chip?

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Answer

The QuantStudio™ 3D Digital PCR System can read the digital chip in less than 1 minute. In fact, if you are running multiple chips, you can run the next chip in the series when the instrument touch screen displays the Analyzing Chip screen.

Answer Id: E7171

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What is the maximum size of insertion/deletion that can be detected by a TaqMan™ SNP Genotyping Assay?

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Answer

Assays can detect an insertion/deletion of up to 6 bases. If you desire an assay to detect a larger insertion or deletion you may want to consider our Custom Design Service (https://www.thermofisher.com/us/en/home/life-science/pcr/real-time-pcr/custom-services-reagents-real-time-pcr-qpcr/custom-services-real-time-pcr-assays.html).

Answer Id: E7518

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What should I do if the software will not connect to the QuantStudio™ 6 or QuantStudio™ 7 Real-Time PCR System?

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Answer

After launching the QuantStudio™ software, go to the Maintenance Manager. Check if the QuantStudio™ system icon is present in the “On the Network” window. If not, click on the ‘Refresh’ button to the left of ‘Remove from My Instruments’. If you still do not see the QuantStudio™ system icon for the following reasons:

- There is an icon but you cannot add it into the "My Instruments" area
- There is a red “X” on the instrument
- A message says "Disconnected" at the bottom of the window with a red “X” in it
then you will need to add the Instrument into the ‘My Instruments’ area. Click on the wrench icon in the upper right-hand corner of the icon as pictured below. You may get a message that says the firmware is older than the one you're trying to run. If appropriate, choose to download the new firmware and let it progress to finish. Do not turn off the instrument during this update. After the firmware update is completed, restart the instrument and check for the QuantStudio™ system icon in ‘On the Network’ area.

Answer Id: E7155

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How many files can the ViiA™ 7 Real-Time PCR System hold?

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Answer

The ViiA™ 7 Real-Time PCR System can store up to 100 runs on the instrument itself.

Answer Id: E7190

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How do I connect the QuantStudio™ 3D Digital PCR System to a network?

Product FAQ

Answer

Please follow the procedures described starting in Appendix B of the QuantStudio™ 3D Digital PCR System User Guide (http://tools.thermofisher.com/content/sfs/manuals/MAN0007720.pdf) to connect the instrument to a network.

Answer Id: E7172

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Will the DSS crosslinked product become unlinked as a result of boiling, incubation with SDS, high salt, high or low pH or any other means?

Product FAQ

Answer

No. DSS crosslinks are amide bonds (same as peptide bonds).

Answer Id: E8578

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