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View additional product information for 7900HT Fast Real-Time PCR System with Fast 96-Well Block Module - FAQs (4351405)
19 product FAQs found
The threshold is the numerical value assigned for each run that reflects the average dRn (change in fluorescence) during the initial cycles of PCR (baseline). The threshold is set by determining a statistically significant point (or value) above the baseline. You can manually adjust the threshold should you desire, to the place in the geometric phase where your replicates are tightest. For more information on how to manually set a threshold, please refer to the tutorial entitled Data Analysis on the ABI PRISM 7700: Setting Baselines and Thresholds (P/N 4370923). While this tutorial is based on the ABI PRISM 7700 system, the concepts are still valid for the Applied Biosystems real-time PCR instruments. You can search the document on our website by using the part number above as the keyword.
If you choose not to manually adjust the baselines and thresholds, the SDS software on the Applied Biosystems real-time PCR instruments has an Auto Ct algorithm that can be used to automatically generate baseline and threshold values for individual detectors. The algorithm calculates baseline and threshold parameters for a detector based on the assumption that the data exhibits the "typical" amplification curve. Experimental error (i.e. contamination, pipetting inaccuracies) can produce amplification curves that deviate significantly from a typical amplification curve. The data from these irregularities can affect the Auto Ct algorithm by causing it to generate incorrect baseline and threshold parameters for the associated detector. Therefore, Applied Biosystems recommends that after analysis of experimental data, you review all baseline and threshold parameters determined by the Auto Ct algorithm.
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You have to run a calibration when a new sample block format is used in the 7900HT Fast Real-Time PCR System, but it is not necessary to run the pure dye calibration if the block has been used before. For example, if you use a 384-well sample block for the first time, then you have to run a 384-well block calibration. Later, should you switch to a 96-well block and then switch back to a 384-well block again, then there is no need to rerun the calibration of the 384-well sample block. We recommend that you run a background run each time you exchange the sample block because dust particles or other contaminants could get into the wells while the block is being stored outside of the instrument. Please consult the 7900HT User Manual, Cat. No. 4317596, for the recommended maintenance procedures.
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The log file tracks events during the course of an instrument run. To locate the log file, open up the hard drive of the instrument computer. Open the Applied Biosystems folder, then the SDS 2.x.x folder, then the log folder. The log file is a Microsoft Word file in .doc format and is saved as the date the run was initiated.
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To program a long-term hold on the Applied Biosystems 7900HT Fast Real-Time PCR System, launch the SDS software and open a new plate. Click on the Instrument tab. Move the cursor to the end of the thermal cycling profile, below the time box, and click. This will create a solid vertical black line. Click on “Add Hold”. Change the temperature to 4.0 and the time to the highest possible time, 98:59. Although an infinity symbol will not appear, the instrument will run for 98 hours and 59 seconds. The run must be aborted when you want to analyze the data.
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While the Applied Biosystems 7900HT Fast Real-Time PCR System is idle, it puts off 6600 BTU/hour. While it is cycling, it puts off 8800 BTU/hour.
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Yes, you can set this as an option. On the Detector Manager for the Applied Biosystems 7900HT Fast Real-Time PCR System, simply set the Quencher to "Non Fluorescent".
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Yes, all of the existing user-interchangeable blocks and the new fast 96-well block can be used on the Applied Biosystems 7900HT Fast Real-Time PCR System.
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No, the ramp rates and thermal cycling profiles on the Applied Biosystems 7900HT Fast Real-Time PCR System are unchanged for the standard 96-well, 384-well and TaqManLow Density Array blocks.
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Yes, the Applied Biosystems 7900HT Fast Real-Time PCR System can be configured with either a fast 96-well, 384-well or standard 96-well block.
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The Applied Biosystems 7900HT Fast Real-Time PCR System has the added capability of being able to thermal cycle in a fast mode. The ABI PRISM 7900HT Sequence Detection System has been renamed and now offers an optional fast 96-well block, which reduces thermal cycling times by up to four fold when compared to the standard 96-well block.
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All SDS files generated on an ABI PRISM 7000, Applied Biosystems 7300 or 7500 or 7900HT Fast Real Time PCR System have a .sds extension (for example, test101.sds). If your computer has more than one version of SDS software, and you double click on the file icon to open the file, it will be opened from the last SDS software version installed. To work around this, simply launch the appropriate version of SDS software, and open the file from within the software.
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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".
There are two main differences between a Fast 96-well and standard 96-well block for the Applied Biosystems real-time PCR systems:
• Reaction well volume: The Fast 96-well blocks have 0.1 mL reaction wells and are compatible with 0.1 mL plates and tubes. The standard 96-well blocks have 0.2 mL reaction wells and are compatible with 0.2 mL plates and tubes.
• Ramp rate: The fast 96-well blocks have a higher maximum ramp rate than standard blocks for the same real-time PCR system. However, both the fast 96-well and standard 96-well blocks are capable of running standard and fast chemistry.
Note: For newer instruments (QuantStudio 3 and 5 Real-Time PCR Systems and later) "0.1 mL" and "0.2 mL" are being used in place of "fast" and "standard" as designations for the two 96-well block formats.
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Signals exceeding 2500 fluorescent intensity units are considered outside the limit of normal background fluorescence and indicate that either the background plate or the sample block module may be contaminated. Please refer to the Applied Biosystems 7900HT Fast Real-Time PCR System's Guide for information on how to determine if the background plate or sample block is contaminated, and how to decontaminate the sample block if the sample block module is contaminated.
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An Applied Biosystems 7900HT Fast Real-Time PCR System with the Zymark Twister Automation Accessory can process 84 standard 96-Well or 384-Well plates or 80 TaqMan Low Density Arrays in a single session. Please note that use of the Fast Optical 96-Well Reaction Plate with Barcodes is not supported on the Automation Accessory.
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Yes, the 7900HT system can create and display multiple standard curves. In order to properly view each standard curve, you must set up separate detectors for each curve. Each standard curve is displayed on a separate graph in the Results tab.
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On the 7900HT system, the data from each run is stored within the .sds plate document, within the directory where it was saved on the hard drive.
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The MicroAmp Optical 384-Well Reaction Plates (with or without barcodes), the MicroAmp Optical 96-Well Reaction Plates (with or without barcode), Fast Optical 96-Well Reaction Plates with Barcodes, and MicroAmp Optical Adhesive Covers may be used in the 7900HT system
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All our real-time PCR instruments are compatible with Thermo Fisher Cloud Apps except the 7500 Fast instrument where the eds files alone are compatible with Thermo Fisher Cloud Apps.
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