How can I convert a file from AQ to RQ, or from RQ to AQ file with the 7900HT Fast Real-Time PCR System?
SDS v2.4 and above allow you to convert your AQ files to RQ and vice versa.
To do so, simply go to: Tools then AQ RQ Converter
-Choose from the dropdown which direction you want to go (AQ to RQ, or RQ to AQ).
-Next click on ‘Add' and browse to the plate file location in the new window. and click ‘Open'.
-Click on ‘Convert'. A new file will be created in the same location as the original, but with _AQ or _RQ at the end of the filename.
If you do not have v2.4, you can upgrade your software here (http://www.thermofisher.com/us/en/home/technical-resources/software-downloads/applied-biosystems-7900ht-fast-real-timespcr-system.html).
One benefit of this conversion feature is that it allows you to convert 7900 files to the correct type to do analysis for relative quantification study, for example, if a plate is originally run as AQ instead of RQ, or if you would like to generate a standard curve quantification in the AQ if a plate was originally run as RQ.
Why are there no RQ values for all the samples in my study in the 7900HT Fast Real-Time PCR System software?
The 7900HT Fast Real-Time PCR System software requires that the endogenous control be run on every plate within a study. If not, you will only see RQ values for the plate that contains the endogenous control on it. The other plates will have Ct values for all the wells, but the software will not calculate RQ values. If you designed your experiments in this type of layout, you will want to do your analysis in the free DataAssist Software (https://www.thermofisher.com/us/en/home/technical-resources/software-downloads/dataassist-software.html?icid=fr-realtimesoftware-5) instead, or use the Thermo Fisher Cloud (https://www.thermofisher.com/us/en/home/cloud.html). This program does not have the endogenous control requirement for every plate. Simply export the study results file from the 7900HT software as a *.txt or *.csv file, and use that to create a new study in the DataAssist software. You should now be able to see RQ values for all samples, even those without an endogenous control on the same plate.
Why do I not see any Ct or RQ values from my ddCT experiment in the 7900HT Fast Real-Time PCR System software?
In the 7900HT Fast Real-Time PCR System software, v2.3 or later, CT or RQ values are only provided in the RQ Manager software. RQ Manager is installed on the computer along with SDS v2.x.
What can I use for data analysis on the 7900HT Fast Real-Time PCR System?
For genotyping data, we recommend TaqMan Genotyper Software (https://www.thermofisher.com/us/en/home/technical-resources/software-downloads/taqman-genotyper-software.html?icid=fr-software-1).
For relative quantitation, we recommend ExpressionSuite Software (https://www.thermofisher.com/us/en/home/technical-resources/software-downloads/expressionsuite-software.html). You may also use the Thermo Fisher Cloud for either application. https://www.thermofisher.com/us/en/home/cloud.html
What dyes can I use on the 7900HT Fast Real-Time PCR System?
The Applied Biosystems 7900HT Fast Real-Time PCR Systems use the following dye sets for calibration: FAM, SYBR, VIC, ROX, NED, TAMRA, JOE, TET dyes. Custom dyes can also be used that read between 500 nm and 660 nm, although you will have to calibrate the system first for any new dye.
How do I add detectors to a plate document on the 7900HT Fast Real-Time PCR System?
Detectors can be added to a plate before or after a run is complete. To do so:
-Go to Tools then Detector Manager.
-Find the Detector that you want to add from the list, and select it by clicking on it.
-Click on ‘Copy to Plate Document'. (If you have more than one detector to add, repeat these steps.)
-When finished, click “Done”. You should now see the Detectors you added under the Setup Tab.
-Now highlight the wells that you want and check the box next to the detector you want to use. Repeat for however many detectors you need. Analyze the plate by clicking on the Green Arrow and then ‘Save As' a new file name.
How do I add a melt curve to my experiment on the 7900HT Fast Real-Time PCR System?
In the 7900HT SDS software, you can run a melt curve at the end of an Absolute Quantification plate run, or run a melt curve by itself. You cannot directly add a melt curve to the end of a Relative Quantification (or ddCT plate).
For the former, here are the steps:
-File then New, Assay: Standard Curve (AQ), Click ‘OK'.
-In the new document, click on the ‘Instrument' tab (right hand side). You should now see the thermal profile.
-Click in the box at the last step such that a black line appears. Click on the ‘Add Dissociation Stage' button which should now be active.
If you just want to run a melt curve (no amplification stage), then you will want to highlight the other steps (click and drag across Stages 1-3). Then click on the ‘Delete Step' button. Now you can run just the melt curve.If you want to run a melt curve with a RQ file, you have two options. One, if you have the v2.4 software, you can run the file as demonstrated above as AQ with a melt curve, and then use the conversion tool later to switch to an RQ file. The other option is to run the file as RQ, and then once the run is complete, set up the melt curve run as described above.
Can I use the 7900HT Fast Real-Time PCR System to do a protein thermal melt experiment?
Yes, but the data is not compatible with our Protein Thermal Shift software. Below are instructions on how to program the software and a reference for the analysis.
1.Create a new experiment using File then New in the 7900HT software. Click ‘OK'.
2.Go to the bottom of the Setup panel, select Passive Reference as None.
3.Click on ‘Add Detector' button on the setup panel.
-If you do not have a preset detector,click on ‘New' from Detector Manager window, so you can define a new detector. Make sure the reporter dye is ROX, and quencher is Non Fluorescent.
-Once you have the desired detector highlighted in the Detector Manager window, click the ‘Copy to Plate Document' button, then click ‘Done'. You will see the detector now in the Setup panel.
4.Next go to Instrument tab, in which you will see the default the thermal profile.
5.Click at the end of the thermal profile, a vertical line will appear.
6.Click the ‘Add Dissociation Stage' button, then highlight and delete the PCR stages.
7.Edit the profile as below, to go from 25 degrees C (2 min) to 95 degrees C (15 sec).
8.Click on the ‘Ramp Rate' tab, and change the ramping to 1%.
9.Save the file, and start the run (or save as a template).
Please note that you will have to perform the data analysis separately from the raw data. You can refer to this reference as a starting point (Nat Protoc 2007;2(9):2212-21).
Where are my files saved to?
On the 7900HT Fast Real-Time PCR System, run files will be saved to a default folder on the connected computer, unless you change it.
To find or change the default folder, go to Tools then Options then General. 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.
Can I collect data at two separate steps for analysis?
No. On the 7900HT Fast Real-Time PCR System, the software will use the last data collection step in the cycling stage for all amplification plots and Ct analysis. So even if you were to set two separate steps with ‘Data Collection On' you would only be able to view and analyze data from the latter step.
What volumes can be used in my plate on the 7900HT Fast Real-Time PCR System?
The following volumes are supported for each 7900HT instrument block:
-Standard 96-well block: 20-50 µL
-Fast 96-well block: 10-30 µL
-384-well block: 5-20 µL
-TaqMan Low Density Array block: approximately 1µL
Can I use the 7900HT Fast Real-Time PCR System instrument computer while a run is in progress?
Using the instrument computer when a run is in progress is not recommended, as this poses a risk of corrupting the data.
How do I add a custom dye to the 7900HT Fast Real-Time PCR System?
The 7900HT Fast Real-Time PCR System can be used to run assays designed with custom dyes (dyes not manufactured by Life Technologies). Custom dyes must fluoresce within the 500-660 nm spectral range measured by the 7900HT instrument. The calibration is done in two steps. In the first step, you will need to obtain an oligo labeled with your dye (no quencher), and then create a plate containing different concentrations of the oligo (approximately 25-3,200 nM). This is done to determine the optimal concentration to use for the actual calibration. In the second step, you will create a plate of the oligo at the concentration determined in the previous step and then run a custom dye calibration. You need to fill at least 3 full columns for adequate data collection. Follow the directions in Appendix B of the 7900HT Fast Real-Time PCR System Maintenance Guide (http://tools.thermofisher.com/content/sfs/manuals/cms_042134.pdf) for more specific instructions.
How do I use tubes in the 7900HT Fast Real-Time PCR System?
Do not use MicroAmp Optical Caps or MicroAmp Optical Tubes with the 7900HT Fast Real-Time PCR System. The instrument is not designed to run MicroAmp Tubes. Please be aware that use of tubes may damage its internal components.
What are the specifications for the 7900HT Fast Real-Time PCR System?
Instrument Specifications
Block Options (Interchangeable)
96-well (standard), 96-well (Fast), 384-well, TaqMan Low Density Array
Sensitivity Down to 1 copy (2-fold discrimination with 99.7% confidence)
Dynamic Range 9 logs of linear dynamic range
Calibrated Dyes FAM, SYBR, VIC, ROX, NED, TAMRA, JOE, TET dyes
Detection Method SYBR dye, primer-probe detection
Resolution Detect changes as little as 1.5-fold
Reaction Volume Range 20-50 µL Standard 96-well, 10-30 µL Fast 96-well block,
5-20 µL 384-well, ~ 1 µL 384-well TaqMan Low Density Array
Reaction Speed 9600 emulation mode, Standard, and Fast
Optics Extended-life 488 nm argon-ion laser excitation source
No filters (CCD acts as spectrograph with continuous detection 500-650 nm)
Temperature Range 4-100 degrees C
Run Time <2 hr (standard mode)
Approximately 35 min (Fast mode)
Temperature Accuracy plus or minus 0.25 degrees C (between 35 degrees C and 95 degrees C, after 3 min)
Temperature Uniformity plus or minu 0.5 degrees C (after 30 sec)
Thermal Cycling System Peltier-based system
Available Applications Gene expression, genotyping, copy number variation, HRM, protein thermal shift, protein detection, mutation detection, miRNA, presence/absence
Dimensions 72 cm (W) x 84 cm (D) x 64 cm (H) (with drawer open)
Weight 82 kg (180 lb) without automation accessory
114 kg (250 lb) with automation accessory
Remote Monitoring No
On-Board Memory No
Setup Configurations PC-controlled only
What do I do if the background calibration fails on the 7900HT Fast Real-Time PCR System?
Follow the directions in the 7900HT Fast Real-Time PCR System Maintenance Guide, Chapter 7 (http://tools.thermofisher.com/content/sfs/manuals/cms_042134.pdf), to decontaminate the sample block.
When do I need to run the RNaseP calibration on the 7900HT Fast Real-Time PCR System?
The RNaseP verification plate contains template, master mix, and a TaqMan assay for RNaseP. It is used to verify that the instrument is performing to specifications. If you have reason to suspect there is something wrong with the instrument, or if you want to rule out a chemistry issue, the RNaseP plate is a good way to test the system. The RNaseP verification plate is a single-use plate.
Can I reuse my calibration plates on the 7900HT Fast Real-Time PCR System?
The calibration plates can be stored and reused three times for up to 12 months after you first open them, so make sure to return them to their original packaging and return them to -20 degrees C storage until the next use. (Note: Due to the small volumes, calibration array cards cannot be reused. Please discard them after use.) If needed, you can make your own background plate using deionized water.
When do I need to calibrate the 7900HT Fast Real-Time PCR System?
Recommended Maintenance Schedule
Power on/off the computer controlling the instrument: Weekly
Check computer disk space. If necessary, archive or back up your experiment files and instrument settings: Weekly
Run disk cleanup and disk defragmentation: Every month
Background calibration: Every month
Perform an instrument self test: Every month
Pure dye calibrations: Every 6 months
RNaseP instrument verification: After the instrument has been moved, or as needed to verify instrument performance
I cannot open the QuantStudio 3/5 Design & Analysis 2 (DA2) software on my Mac. What are the software requirements for Mac?
To open the software download on your Mac, you will need to adjust your security settings using the following instructions from Apple support:
Safely open apps on your mac
Please note, the software should run on Mac OS 10.10 or later.
Does the StepOnePlus Real-Time PCR System (Cat. No.: 4376600) include an RNAse P calibration plate?
Yes, it does. It is the TaqMan RNase P Instrument Verification Plate, Fast 96-well (Cat. No. 4351979). Please note that this verification plate is required to verify the performance of the instrument just once (see page 42 of this link: https://assets.thermofisher.com/TFS-Assets/LSG/manuals/4376782.pdf).
Can I use my 7900HT System RNase P instrument verification plates with both the 7900HT System and the QuantStudio 6 and 7 Flex Real-Time PCR Systems?
Only the TaqMan RNase P Instrument Verification Plate, Fast 96-well (for 0.1 mL block) (Cat. No. 4351979) is compatible with both the 7900HT System and the QuantStudio 6 and 7 Flex Real-Time PCR Systems. The following RNase P instrument verification plates can be used on the 7900HT System, but not on the QuantStudio 6 and 7 Flex Real-Time PCR Systems:
• TaqMan RNase P Instrument Verification Plate, 96-well (Cat. No. 4310982) (for 96-well standard block)
• TaqMan RNase P Instrument Verification Plate for 7900HT System, 384-well (Cat. No. 4323306) (for 384-well block)
• 7900HT TaqMan Low Density Array Instrument Verification RNase P Kit (Cat. No. 4351468) (for TaqMan Array Card block)
The following RNase P instrument verification plates can be used on the QuantStudio 6 and 7 Flex Real-Time PCR Systems, but not on the 7900HT System:
• TaqMan RNase P Instrument Verification Plate for ViiA7 System, 96-well (Cat. No. 4432382) (for 96-well standard block)
• TaqMan RNase P Instrument Verification Plate for ViiA7 System, 384-well (Cat. No. 4455280) (for 384-well block)
• ViiA7 Array Card RNase P Verification Kit (Cat. No. 4432265) (for TaqMan Array Card block)
How can I get a summary of the calibrations performed on the QuantStudio 6 and 7 Flex Real-Time PCR Systems?
You can get a summary of the calibrations from the QuantStudio Software by going to Instrument > Instrument Console > Manage Instrument > Information > Print Calibration Log.
Do I need to back up my calibration files before I upgrade the software for the ViiA7 Real-Time PCR System?
No, you do not need to back up the calibration files as all of the calibration files are stored on the ViiA7 Real-Time PCR instrument. Once the computer software is properly installed and the computer is connected to the instrument, the calibration information will automatically update in the QuantStudio Software.
Can I still start a run on the ViiA7 Real-Time PCR System if the "Calibration is expired" notification is displayed?
Yes, you can still start a run on the ViiA7 Real-Time PCR System if the expired calibration notice displays. This is just a reminder and you can close it to proceed with the run. Additionally, you can change when you want the notifications to show up and how frequently you want to be notified to calibrate the instrument. To do this, go to the toolbar in the QuantStudio Software and select Instrument > Instrument Console. Select your instrument icon and click on Manager Instrument > Maintenance > Calibration Reminders. From the Calibration reminders Settings page you can update when the calibrations expire, turn expiration reminders on/off, and set when the reminders show up.
