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  2. Experiment Setup
  3. NanoString nCounter Gene Expression

How do I set up my NanoString nCounter Experiment?

On ROSALIND you can set up your experiment within minutes. On average, it takes ROSALIND 8-10 minutes to process your RCCs or nSolver normalized counts.

Step-by-step guide: 

1. Create an experiment in ROSALIND by selecting "Add New Experiment" to an existing project folder or by selecting "Add New Project". You can find either button at the bottom of your screen; "Add New Project" at the bottom of the All Projects view and "Add New Experiment" if you're in a specific project folder. 


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2. Enter a Title and Description for your Project.

3. Select "Partner Recommended Analysis" from the menu below. 


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4. Select "NanoString nCounter Data Analysis" from the menu below. 


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5. Select which datasets you are looking to upload. ROSALIND is compatible with either RCCs directly from your nCounter or nSolver normalized counts. 


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6. Enter a Title and Description for your Experiment.

7. Drag and drop your RCC files to upload them to ROSALIND.


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8. ROSALIND intelligently auto-detects the species and panel of your RCC files, but if your samples are of a different species or a different panel you can select the correct species and panel from the dropdown menu. 


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9. Specify attributes for each of your samples or upload an attribute file. You can find further instructions on how to create an attribute file here


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10. ROSALIND provides you with a sample sheet based on your specified attributes. You may make any changes you need directly on the sample sheet or, if all your attributes look correct, you can select "Next" to continue. 


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11. You may next set up your comparisons by selecting "Create New Comparison".  Then drag and drop different attribute values into the condition and control boxes on the right hand side of your screen. This is an optional step as you may create an unlimited number of comparisons before or after your experiment has been launched.  Once you're satisfied with your comparisons, you can hit "Save" and then "Next". Your experiment design is complete and your analysis will start its processing. 


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