Bio-Rad iQ™5 Optical System Software, Version 2.1 - Manual (Page 40)

Section 4 Workshop Module
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4.3 Protocol
Protocol files direct the operation of the iCycler thermal cycler and also specify when optical data
will be collected during the thermal cycling run. iQ5 software protocol files are stored with the
extension .tmo.
•
A protocol is made up of as many as 9 cycles
• A cycle is made up of as many as 9 steps
•
A step is defined by specifying a setpoint temperature and the dwell time at that
temperature
•
A cycle is a collection of steps that are repeated (up to 600 times)
Every protocol must have at least one data collection step. This may be a real-time data
collection step or a melt curve data collection step.
Temperature and Dwell Time Ranges
•
Temperatures between 4.0 and 100.0°C may be entered for any set point temperature
•
Finite dwell times may be as short as 1 second (00:01) or as long as 99 minutes and 59
seconds (99:59)
Minimum Dwell Times for Data Collection
•
1 fluorophore = 10 sec
•
2 fluorophores = 20 sec
• 3 fluorophores = 30sec
•
4 fluorophores = 40 sec
Bio-Rad recommends using a slightly higher dwell time than the minimum values, so that more
data points are collected at each repeat.
4.3.1 Selecting a Protocol
1. With the Protocol tab active, use the browser to locate the folder where the protocol is
located, and then click on the protocol name to select it.
2. The selected protocol appears in the Selected Protocol pane (Figure 4.13).
3. The iQ5 software has a number of sample protocol files you can use.