Set up qPCR Run on Thermo Cloud and QuantStudio

Set Up Plate Layout

• 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 file folder icon (on the left side of the screen under the home icon), then New Folder (add your name), and Create.
• Click Create Project, give your project a name, and assign it to your folder.
• Under My Apps on the right hand side click on Design and Analysis Application (qPCR).
• Copy a plate layout file (click Plate and choose Export plate setup from the Action menu) and save it as a CSV file. (to create a template in the program, see addendum below)
  • For each well you are using you need to enter the following:
    • Sample Name
    • Target Name
    • Task (Usually UNKNOWN)
    • Reporter (SYBR)
    • Quencher (NFQ-MGB)
  • Leave the rest of the plate blank
• Click on New under Create new experiment.
• Leave the file name as the default (Date/ID)
  • Change Block type to 384-Well Block.
  • Change Chemistry to SYBR Green Reagents.
  • Click Next or on the Method tab and change volume to 10 uL (or leave at 20 uL if you are using a total volume of 20uL/well)
  • Click Next or on the Plate tab. Click on Actions then Import plate setup and select your plate layout file. Check the visual representation of your plate layout and make sure it is correct.
  • Click Next or on the Run tab. The software will save your plate layout and upload it to thermo cloud for access on the Quant Studio5
• After you plate runs, refer to qPCR Analysis on ThermoCloud protocol.

Addendum

• In the Plate Tab on the plate schematic, outline wells, type in sample number--> Enter to assign (repeat for all samples)-->Outline wells, type in target (primer)-->Enter to assign--> Next