Applied Biosystems 7900HT User Manual page 369

background
baseline
calibrator
cDNA
(complementary
DNA)
clipped data
command line
consumable
container type
cycle set-point
delta C
T
delta delta C
T
delta R
n
Applied Biosystems 7900HT Fast Real-Time PCR System and SDS Enterprise Database User Guide
An inherent spectral component of the signal generated by a fluorescence assay that
is attributed to the Applied Biosystems 7900HT Fast Real-Time PCR System.
Uncorrected background signal can interfere with the sensitivity of the SDS software
and its ability to determine C
calibration and is removed mathematically during multicompoenting.
In terms of the Amplification plot, the baseline is a line fit to defined range of cycles
before the sequence detection system detects the amplification of the PCR product.
For standard PCR assays, the SDS software uses a default range of cycles 3-15 to
establish the baseline for a PCR assay.
In relative quantification analysis a sample to which all other samples are referenced
on a detector-by-detector basis.
A DNA molecule with a nucleotide sequence that is complementary to an RNA
molecule. cDNA is made from RNA through the action of the enzyme Reverse
Transcriptase. RNA is converted to cDNA because cDNA is more robust than fragile
RNA, and because DNA templates are required for many applications, including PCR.
In real time mode, fluorescent signal intensity is collected for the entire plate every
8.5 seconds. Clipped data points are calculated by averaging the last three computed
R (normalized reporter signal) data points collected during the extension phase of
n
each cycle repetition. Clipped data are presented as baseline uncompensated data
(R vs. cycle data) and baseline compensated data (∆R
n
Some executable programs can be invoked in a DOS Command Prompt window
and/or from within a.bat script file, to run usually without a graphic user interface
(GUI). Such programs may support user specification of parameters via a command
line, where those parameters would be entered after the name of the executable
program. Often these command line parameters are filenames, directory paths, or flag
settings.
(1) A vessel used to contain reactions run on the 7900HT instrument (a microplate or
a TaqMan ® Low Density Array). (2) A reagent kit, chemical, or disposable labware
used as part of an assay.
The type of plate to be analyzed by the 7900HT instrument. The types are:
ABI P ™ 96-Well Optical Reaction Plates, ABI P
RISM
Reaction Plates, Optical 96-Well Fast Thermal Cycling Plates, and TaqMan
Density Arrays.
(1) A cycle set-point is any temperature desired for a sample block or heated cover.
(2) In the context of thermal cycling, cycle set-point could represent one or more
temperatures in a step or stage.
∆
See C .
T
∆∆
See C .
T
∆
See R .
n
s. For this reason background signal is measured during
T
DRAFT
September 1, 2004 11:39 am, Glossary.fm
vs. cycle data).
n
™ 384-Well Optical
RISM
® Low
Glossary-3