How can I export the amplification plot or gene expression plot from the Applied Biosystems™ 7300, 7500, and 7500 Fast Real-Time PCR System’s software?

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With SDS 1.4 software, right-click on the graph, and choose "Export as JPEG" or "Export to Powerpoint". With SDS 2.0.x (for 7500/7500fast only), you can either click on the save icon above the graph "Save as JPEG Image" or click on the Export drop-down arrow (located on the upper toolbar) and choose "Send to Powerpoint"

Answer Id: E2477

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What can I use for data analysis?

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Click on the ‘Group By’ button and choose ‘Well Position’ (Column). Then highlight the plate and print the report.

Answer Id: E7233

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How do I set up a touchdown PCR experiment?

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In a touchdown PCR experiment, you will either change the temperature or the time of a particular PCR step with every cycle. Most commonly, the annealing temperature is adjusted throughout the experiment, such that the specificity is increased in the early cycles and the efficiency in the later cycles.

In this example, we will set the method to do the following:
1. Go to File then New Experiment then Advanced Setup. Fill out the relevant options as you normally would.
2. Go to the Run Method under the ‘Setup’ section and you should see the Graphical View of your thermal profile. Check the box next to ‘Enable AutoDelta’. You should see some grey triangles appear next to the Temperature and Time at every step in the Cycling Stage. (Note: If you want to start the changes at a later cycle, set this here under ‘Starting Cycles’.)
3. A new window called ‘AutoDelta Settings’ will open up. Select the appropriate options. In this example we are decreasing the temperature by 0.4 degrees C per cycle, so choose (“-“) and (0.40). Click ‘Save Setting’. You will then see a green triangle show up next to the parameter you changed, in this case next to the 72 degrees C step. Your new method has now been applied

Answer Id: E7230

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What dyes can be used as a reporter in a multiplex reaction on Applied Biosystems™ 7500 Real-Time PCR System?

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The following dyes can be used as the reporter dye with MGB-NFQ as the quencher on the Applied Biosystems™ 7500 Real-time PCR System or Applied Biosystems™ 7500 Fast Real-Time PCR System when using TaqMan Gene Expression Master Mix (recommended for multiplexing) or any other Applied Biosystems™ TaqMan™ master mix:
FAM™, VIC™, JOE™, NED™, TAMRA™,CY3™, ROX™, TEXAS RED™, CY5™ dyes.

Of these dyes, we recommend a duplex reaction with FAM™ and VIC™ or FAM™ and NED™ dyes; if you are triplexing, we recommend FAM™, VIC™, and Cy5™ or FAM™, VIC™, and TAMRA™ dyes. You must choose dyes that are well separated in emission wavelength. If you are using any probes with a TAMRA™ dye quencher, you cannot use NED™, TAMRA™, or CY3™ dye as one of the reporter dyes in that multiplex reaction. ROX™ or TEXAS RED™ dyes can be used as reporter dyes only when not using an Applied Biosystems™ Master Mix.

Answer Id: E2472

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What should I do if I get “Fatal Error 1420” in SDS 2.0.x software on the 7500 or 7500 Fast Real-Time PCR System?

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You can also Export Data, and the column format will be retained.

Answer Id: E7234

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Can TET ™dye be used on the Applied Biosystems™ real-time PCR instruments?

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Answer

TET™ dye is not recommended to be used on the following real-time PCR instrument models: 7000, 7300, 7500, 7500 FAST, StepOne™, and StepOnePlus™ Systems.

Answer Id: E2571

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Can I use the 7500 or 7500 Fast Real-Time PCR System to do protein thermal shift experiments?

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Yes. If you have the newer version of the software (v2.0.1 or later), which creates *.eds files, your data will be directly compatible with our Protein Thermal Shift™ Software (https://www.thermofisher.com/order/catalog/product/4466038?ICID=search-product). If you have the older software (v 1.x), you will have to program the software differently (see below) and analyze the results independently. For more details on the analysis, you can refer to this paper: “The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability.” Nat Protoc 2007;2(9):2212-21.

For an experiment using SDS v1.x, follow the directions below:
1.Create a new experiment, choosing Absolute Quantification assay type. Click ‘Next’.
2.Go to ‘Select Detectors’. If there is no predefined detector for this application, create a new one. Make sure the Reporter Dye is ROX, and Quencher Dye is none.
3.Assign the detector to the plate. Select none for the Passive Reference

Answer Id: E7231

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I lost my user manuals for the 7300 and 7500 Fast Real-Time PCR Systems. How can I get an additional copy?

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Answer

Please contact Technical Support for Real-Time PCR, and provide the serial number of your instrument. We will email you a copy of the user manual upon request.

Answer Id: E2470

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What is the maximum thermal output for the Applied Biosystems™ 7500 / 7500 Fast Sequence Detection System in BTU/h?

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The maximum thermal output for the Applied Biosystems™ 7500/7500 Fast Sequence Detection System is 3241.5 BTU/h (950W).

Answer Id: E2503

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If I were to upgrade my existing 7500 System standard unit to the a 7500 Fast configuration, can I still open my old data files?

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Answer

Yes, older 7500 or 7500 fast data files are compatible with the current version of the SDS software. However, there is one exception: please note that the SDS v1.3 software will not allow RQ Studies to be created from RQ Plates from different instrument types, different thermal modes (i.e., fast and standard modes) or different numbers of thermal cycles.

Answer Id: E2341

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Can I run slower, standard thermal cycling experiments on a 7500 Fast Real-Time PCR System?

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Answer

Yes. you can choose either standard or fast ramp on the 7500 Fast System for software versions 2x or greater, and a 9600 emulation thermal cycling mode is available for customers who wish to run assays based on adjusted ramp rate. However, you should be aware that we cannot guarantee identical performance to the same modes run on a standard 7500 system block.

Answer Id: E2343

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To analyze an RQ Study, can I import RQ plates from a combination of Fast and Standard mode runs on a 7500 Fast Real-Time PCR System?

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Answer

We do not recommend this as the current and previous versions of SDS software will not allow RQ Studies to be created from RQ Plates from different instrument types, different thermal modes/profiles or different numbers of thermal cycles. It is important to reduce variability among RQ plates in an RQ study by importing RQ plates from the same instrument type, with the same thermal profile and mode, as well as the same block type and sample volume.

Answer Id: E2319

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What dyes can I use on the 7500 and 7500 Fast Real-Time PCR Systems?

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Answer

The Applied Biosystems™ 7500 and 7500 Fast Real-Time PCR Systems use the following dye sets for calibration: Cy™3, Cy™5, FAM™, JOE™, NED™, ROX™, SYBR™ Green, TAMRA™, Texas Red™, and VIC™ dyes. Custom dyes that are read between 520 and 650 nm can also be used, although you will have to calibrate the system first for any new dye.

Answer Id: E7224

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What are the extensions of files generated by the ABI PRISM™ 7000 Sequence Detection System, Applied Biosystems™ 7300, 7500, 7500Fast, 7900HT Fast Real-Time PCR System, StepOnePlus™ Real-Time PCR System, and ViiA™ 7 Real-Time PCR Systems?

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Answer

All run files have an .SDS or .EDS extension. A Relative Quantification study will have an .SDM or .EDM extension and a template will have an .SDT or .EDT extension. The software for StepOnePlus™, ViiA™ 7, and 7500 2.0.x software have .EDS, .EDT, or .EDM extensions; all other software have .SDS, .SDT, or .SDM extensions.

Answer Id: E2473

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What can I do when I get the error message “Time too short” on the 7500 or 7500 Fast Real-Time PCR System?

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Answer

You may encounter this error message, which will abort the run before it even starts. If so, go into the software under Setup then Run Method and check how much time has been set for the data collection step. The instrument has a minimum collection time, which is dependent on the number of filters being used. (This is true in both the 1.x and 2.0.x versions of the 7500 software.) Increase the extension time to 30 sec and restart the run. It should now proceed as normal. If the error persists, please contact us at techsupport@thermofisher.com for further assistance.

Answer Id: E7239

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