Fluorescence Detected in Empty Wells on the AriaMx

Answer

This Information Applies To: Agilent AriaMx real-time PCR system

Issue

When running the AriaMx with tube strips, and a tube strip is not present in every well, fluorescence is detected in the wells without plasticware. 

Background

When using the AriaMx, it is expected behaviour that the instrument may detect fluorescence in wells that don't contain plasticware. The AriaMx scans all 96 wells with all optical modules present in the instrument. Fluorescence can reflect off the thermal block and be detected in neighboring wells that are free of plasticware. The following steps will help address this issue.

Steps to Follow

To avoid fluorescence from empty wells impacting the analysis:

• On the Plate Setup screen, on the AriaMx touch screen in the AriaMx computer software, only select the wells that contain samples (see Figure 1 and Figure 2). Leave all empty wells unassigned as well type <Blank>.
• The well assignment of a completed run can also be adjusted from the Plate Setup screen.

Figure 1. Plate Setup: All wells are selected. This is the correct selection if plasticware and samples are present in every well.

Figure 2. Plate Setup: Only columns one, two and three are selected. This is the correct selection if just these threee columns contain plasticware and samples. 

Caution: If not all wells of the same target are selected when the analysis is performed, incorrectly low Cq values or false positive may be detected.

Caution: If wells that are not used for an assay are assigned as ‘Unknown,’ the software will also include the background noise detected in these wells when calculating the threshold for the selected channels.

Learn how to effectively operate your Agilent AriaMx real-time PCR system: AriaMx Real-Time PCR System Setup and User Guide on Agilent.com  Aria Real-Time PCR Software User Manual on Agilent.com

For Research Use Only. Not for use in diagnostic procedures.

PR7001-2944