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  3. NanoString nCounter T-cell Receptor (TCR) Diversity

How do I set up my TCR Report?

You can download the TCR walkthrough document here.

Beginning a TCR Analysis on ROSALIND® 

STEP 1: Set up your project library

TCR analysis on ROSALIND requires 5 easy steps and takes less than 10 minutes from the start of the experiment set-up to the final deliverable of the complete TCR report.

After logging in to your account (https://nanostring.rosalind.bio/login) select to "ADD NEW PROJECT" from the main ROSALIND home screen.

Make sure to select "Partner Recommended Analysis" or the "Design a New Experiment" option and choose the NanoString nCounter Data Analysis / NanoString TCR Report options during the experiment set up.



STEP 2: Upload your files

Drag and drop your RCC files (at least 12 files) into the upload area provided, and ROSALIND will validate the data. The validation ensures the panel run was either TCR Diversity or CAR-T Characterization, and all samples were run with the same panel.


STEP 3: Generate your attributes file

The attributes file is a convenient way to inform the analysis of all possible annotations for your samples. A template can be found here, showing the attribute details for samples, including a time course and the panel standard: https://www.rosalind.bio/hubfs/NanoString_TCR_attributes_file.csv

ROSALIND provides a way to create a CSV of defined attributes by clicking "GENERATE ATTRIBUTE FILE". A sample attribute file will be designed and downloaded for your experiment. When your attributes file is ready, click "UPLOAD ATTRIBUTE FILE" to upload your final version of this file.

All sample attributes should be character-based (i.e. non-numerical values) unless you are requesting a time-course assay. Use of ALL “TimeSeries”, “TimeSeriesLabel” and “TimeSeriesID” attributes is required for reports with time series defined. “TimeSeries” is a numerical value that orders the data, “TimeSeriesLabel” is a string that will label the graphs (e.g. 12h, 1d, 24h) and TimeSeriesID connects the data if you have sample replicates. 


STEP 4: Review and launch your experiment

Review your sample annotation table to ensure accuracy and either modify in-line on the table or choose "UPLOAD NEW FILES" to make changes before saving and launching your experiment. Once you have confirmed your data accuracy, select "SAVE ATTRIBUTES".

You will receive an email in 5-10 minutes stating that your TCR report is ready to be unlocked.


STEP 5: "Unlock" and download your TCR Report

While your report is locked, you will notice an “Analysis Locked” navigational item where you can use the Analysis Units provided by NanoString to access your final TCR report.


Once the report is complete and unlocked, a download icon will be present at the top of the screen.

Click on that icon, and then select the option for “TCR Report”. Three TCR reports will be available based on the 3 options for normalization, including the TCR exports of relevant data in a flat csv format. Within each html report, images are available for individual download using a download icon at the side of each figure. Other metrics and values are also available for download on the same page as the TCR report.