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View additional product information for 7900HT Fast Real-Time PCR System with 384-Well Block Module - FAQs (4329001)
14 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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No. The current version of the Zymark Twister Instrument and SDS Automation Controller software is NOT compatible with MicroAmp Fast 96-Well Optical Plates with Barcode. The Zymark Twister Instrument is compatible with MicroAmp Optical 96-Well Reaction Plate with Barcode, MicroAmp Optical 384-Well Reaction Plate with Barcode, as well as TaqMan Low Density Arrays.
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The file remains "read only" due to the status of the SDS Automation Controller Queue. The SDS run file in question still remains in the queue and must be cleared by the user within the SDS Automation Controller Software. To do this, the customer must open the SDS Automation Controller software, highlight the plate in question, select File -> Clear Selected Plates.
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When launching the SDS 2.3 software, you will be prompted for a user name and password. The default user name will be administrator and the default password field can be left blank. The user can simply click "OK" to launch the SDS 2.3 software. User accounts are configured by selecting TOOLS and then clicking LOCAL USER ACCOUNT MANAGER. Additional information regarding the LOCAL USER ACCOUNT MANAGER can be found by searching SDS 2.3 Online Help from the HELP pull down menu in the SDS 2.3 software.
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For detailed instructions on performing Fast TaqMan Real-Time PCR using the 384-well block on Applied Biosystems 7900HT, please refer to User Bulletin for Performing Fast TaqMan Gene Quantitation using 384 well plates on the Applied Biosytems 7900HT Fast-Real-Time PCR System with the 384 well Block Module. (P/N 4369584)
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The older versions of the software did not include this feature for all assay types. For the 7500 and 7500fast instruments, the latest software 2.0.5 allows a melt curve to be added to the PCR experiment. The other instruments/software require a separate program for melt curves. To run a Dissociation Curve after running a Relative Quantification Plate (ddCt) Assay, you will need to open a new assay from File -> New, select DISSOCIATION from the assay pull-down menu and run the Dissociation Curve as a separate assay. This will generate a separate SDS file for the Dissociation Run.
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The sample ramp rates for the 7900HT Fast Real-Time PCR system are as follows:
- Standard Mode: 1.6 deg C/sec up and 1.6 deg C/sec down
- Fast Mode: Average is about 3.0 deg C/sec up and 3.0 deg C/sec down
- 9600 Emulation Mode: 0.8 deg C/sec up and 1.6 deg C/sec down. This matches the sample ramp rate achieved for the ABI PRISM 7700 Sequence Detection System.
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You can export the graph as a “. jpeg” file. Right click on the graph and choose the “Save plot to image file” option. This will open a window where you can choose a location to save your image. These images can then be imported into other applications. This allows you limited cosmetic manipulation of the graph. Alternatively, you can export the results table into Excel and use it to plot your graph for greater flexibility with graph manipulation
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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.
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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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All Applied Biosystems instrument systems are qualified to detect a two-fold change. Scientifically speaking, there is a statistical calculation that predicts the probability of detecting one molecule in any given sample called the Poisson Distribution. The Poisson Distribution predicts that one molecule will be detected 66% of the time. This is assuming that the assay has been optimized to the fullest capacity and that there are no aliquoting or pipetting errors involved. Please refer to the following paper concerning one-copy detection: Lockey, C., E. Otto, and Z. Long. "Real-time fluorescence detection of a single DNA molecule." BioTechniques 24 (1998): 744-746.
Each assay designed on one of our platforms needs to be optimized to determine the Linear Dynamic Range of the assay. An Applied Biosystems Sequence Detection System (Real-Time PCR instrument) may be able to detect one copy in a fully optimized assay. As stated above, one copy can only be detected 66% of the time in a fully optimized system.
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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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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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