Log into Thermo Cloud (https://apps.thermofisher.com/apps/dashboard using the login information for your lab (the Bridges Lab account data is located on the side of the machine.)
Click on the File Folder icon and find your folder (or the folder in which you saved your run).
Select the file with extension .eds. The program will automatically take you to the Results tab of your run.
Above the graph, use the dropdown box to select Melt Curve.
Click on Target above the plate schematic to select one target at a time.
Verify that there is only one (prominent) peak for each of your targets.
Verify that each of your replicates amplified for each target.
If there is a target that yields 2+ peaks over all samples, mark that target as unusable in the Primer Database.
Exclude samples that did not pass the above criteria by clicking the well (not the plate schematic) and select Omit under the Action dropdown box above the plate schematic.
Check the technical replicates by choosing the Table View and arranging them according to target. Verify that the CT values have <1.5 difference. Omit outliers.
Click Next and Export your results to the appropriate project folder.
Under App Connect on the right hand side click on Relative Quantification (qPCR). Open your run.
Under the Overview tab, assign biological groups to each of your samples (if needed).
If you need to omit samples from the analysis, do so under the Data Review tab by clicking on the affected target, highlighting, and omitting the wells with outliers.
Under the Analysis tab click the blue Analyze button in the top right corner to visualize your adjusted data.