Question: Can I identify differentially expressed genes between cells in two different clonotypes?
Answer: Yes. If you have generated 5' gene expression data along with V(D)J data for your sample, you can identify differentially expressed genes between clonotypes.
Start by opening your .cloupe file in Loupe Cell Browser and importing your .vloupe file to get the clonotypes.
To import the .vloupe file Click on "VDJ Clonotypes" tab in Loupe Cell Browser:
A new window will open that asks you to import a file containing V(D)J clonotypes. Click "Click here" to upload the .vloupe file for this sample:
Now you should see the clonotypes identified by Cell Ranger V(D)J in the right panel. Colored in blue in the t-SNE view are the cells that Cell Ranger V(D)J identified as cells based on TCRs/BCRs:
Right click your clonotype of interest in the right panel. Then click "Assign to Category" to create a separate category of cells that express this clonotype:
Here we called the category "Clonotypes" and named the cluster "clonotype1":
Follow the same procedure to create another cluster with another clonotype. Use the same "Clonoypes" category and give the cluster a unique name. Here we called it "clonotype2":
Now we can identify genes that are differentially expressed between our two clonotype clusters.
Switch from the "V(D)J Clonotypes" view to the "Categories" view. Select our new "Clonotypes" category and select our two new clusters as shown below:
Click on the "Significant Genes" button at bottom right of the screen, and then on "Locally distinguishing":
Once the analysis is complete, click the the gene table icon in the lower left corner of the screen to see a list of differentially expressed genes: