Applied Biosystems 3500 User Manual

Review previously run sequencing samples ....................................... 84
Review sequence quality ........................................................ 84
Review traces ................................................................. 86
Display thumbnails ........................................................ 87
Understand Quality Values (QVs) ................................................. 88
Quality value ranges ....................................................... 88
Pure base versus mixed base QVs ............................................ 88
Quality values (QV) and probability of error (Pe) ................................ 88
Re‑inject samples from Review sequencing results ................................. 89
View, print, and save (.pdf) trace quality reports .................................... 89
View Trace Reports ........................................................ 89
Report options ............................................................ 90
Export sequencing results ...................................................... 90
Modify sequence data ........................................................... 90
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CHAPTER 5 Review fragment/HID analysis results ................. 91
Workflow ..................................................................... 91
Access the View Fragment/HID Results screen ..................................... 92
Review results for the currently running fragment/HID analysis plate ................ 93
Review previously run fragment analysis/HID samples .............................. 94
Review sample quality .......................................................... 94
Review normalized data ......................................................... 96
How normalization is applied ................................................ 96
Normalization factor in secondary analysis ................................... 96
Review plots ................................................................... 97
Zoom on data .............................................................. 97
Change plot settings ....................................................... 97
Overlay samples ........................................................... 98
Label peaks ............................................................... 98
View thumbnails ........................................................... 99
Rename samples .......................................................... 99
Sort by one or multiple columns ............................................ 100
Review sizing ................................................................. 100
Set up the sizing table ..................................................... 100
Examine the size standard plot ............................................. 100
Overlay the sizing curve ................................................... 101
Re-inject samples from Review fragment results ................................. 101
View, print, and save (.pdf) sample quality reports ................................. 101
Report options ........................................................... 101
Export sizing results .......................................................... 102
Modify fragment analysis or HID data ............................................ 102
Contents
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3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1

Applied Biosystems 3500 Specifications

General

Number of capillaries	8
Capillary Length	50 cm
Laser	Solid-state laser
Instrument Type	Capillary electrophoresis system
Technology	Capillary Electrophoresis (CE)
Weight	95 kg
Power Requirements	100–240 V