Applied Biosystems 7900HT - Page 380

DRAFT
September 1, 2004 11:38 am, 4351684AIX.fm
Index-6 Applied Biosystems 7900HT Fast Real-Time PCR System and SDS Enterprise Database User Guide
plate-sensor switch 7-36
replacing the finger pads 7-52
turning ON 2-4
plate queue
adding plate documents (Automation Controller
Software) 4-40
adding plate documents (SDS software) 4-35
adding plate documents (Template Batch
utility) 4-36
removing plate documents 4-40
starting 4-43
stopping 4-44
plate stacks
loading plates 4-41, 4-42
placing in use 4-42
positions 7-36
Plateau Phase of the amplification curve D-5
plates
running batches 4-39, 4-41
running individually 4-25
types, See consumables
plate-sensor switch 7-36
adjusting 7-37 to 7-40
plots
hiding 2-21
maximizing/minimizing 2-22
resizing 2-21, 2-22
showing 2-21
Port Number A-22
Post readout (from the Plate Read tab) 4-27
Pre readout (from the Plate Read tab) 4-27
precision
causes of low precision 8-5 to 8-8
preparing
master mixes B-3
plate for a run 4-6
primer and probe concentrations
optimizing B-3
programming
methods (absolute quantification) 3-21
methods (allelic discrimination) 3-20
methods (dissociation curve analysis) 3-23
methods (relative quantification) 3-21
temperature ramp 3-23
Protocol
preventing contamination 4-6
pure dye plate
constructing for custom dyes 7-27
preparing for use 7-24
pure dye run
about 7-20
creating a plate document 7-21
extracting data 7-25
performing 7-24
troubleshooting 8-11
when to perform 7-20
Q
Quality control, TaqMan Low Density Array 4-12
quantifying
probes and primers B-3
standards for absolute quantification B-6
quantitative RT-PCR
about 6-4
absolute, See absolute quantification
relative, See relative quantification
types of 6-4
quantities, applying to a plate document 3-17
R
R2 readout (from the Standard Curve Plot) 6-13
reagents
custom oligonucleotides C-6
non-Applied Biosystems PCR reagents 8-8
TaqMan Pre-Developed Assays and Reagents C-6
TaqMan RNase P Instrument Verification
Plates C-5
re-connecting the SDS software 4-30
relative quantification
about 6-4, 6-16 to 6-20
analyzing data 6-22 to 6-35
assay development guidelines B-6
procedure checklist 6-22
the Comparative C
T
Method 6-4
the Standard Curve Method 6-4
troubleshooting 8-12
removing
plate documents from the plate queue 4-40
steps from a method 3-21
Rep readout (from the Real Time tab) 4-27
replacing
gripper finger pads 7-52
sample block module 7-6
replicate wells, use of 6-20
reproducible limits 6-19
resizing panes, views, and plots 2-21
restacking plates 4-42
restoring
database connection A-22
RQ Manager Software 1-25
RQ Min/Max Confidence 6-28
running
batches of plates 4-39, 4-41
single plate 4-25
S
sample
calibrator 6-20
sample bars
about 6-31