Software Updates User guide

Plates

Plate Size and Type

The software applies these plate settings to all the wells during the run:

• Plate Size. Select a plate size that represents the size of the reaction module block of

your instrument. Choosing the instrument type (CFX96, CFX96 Deep Well, CFX Connect,

or CFX384 instrument) from the pull-down menu option on the Startup Wizard will

change the default plate size loaded in the Plate tab of the Run Settings window. In the

Plate Editor, select the plate size from the Settings menu (Table 15). Plate size cannot be

changed during or after the run

•Plate Type. Select clear or white wells from the Settings menu. Make sure the

fluorophore being used in the run is calibrated for the selected plate type

NOTE: CFX96, CFX96 Deep Well, CFX Connect, and CFX384 instruments are

factory calibrated for many fluorescent dye and plate combinations. Calibration is

specific to the instrument, dye, and plate type. To calibrate a new combination of

dye and plate type on an instrument, select Tools > Calibration Wizard (see

Calibration Wizard on page 151)

Scan Mode

The CFX96 Touch and CFX96 Touch Deep Well systems excite and detect fluorophores in six

channels. The CFX Connect system excites and detects fluorophores in three channels.The

CFX384 Touch system excites and detects fluorophores in five channels. All systems use

multiple data acquisition scan modes to collect fluorescence data during a run.

Select one of these scan modes in the Plate Editor window toolbar:

• All Channels. Includes channels 1 through 5 on the CFX96 Touch and CFX96 Touch

Deep Well systems, channels 1 and 2 on the CFX Connect system, or channels 1 through

4 on the CFX384 Touch system

•SYBR/FAM only. Includes only channel 1 and provides a fast scan

•FRET. Includes only the FRET channel and provides a fast scan

Trace Styles

During plate setup and while a run is in progress, the color of the amplification traces can be

modified. These colors will be displayed as the data are being collected and the traces can be

viewed in the Real-time Status window. For more information on Trace Styles, see page 86.

Setup Wizard

The Setup Wizard can be used to enter plate layout information needed for normalized gene

expression analysis either before, during, or after a run has been completed. Target and

sample name and location on plate, reference gene(s), and control sample can all be entered

from this window.