Question: Can I identify differentially expressed genes between cells in two different clonotypes?
Answer: Yes. If you generated 5' gene expression data and V(D)J data from the same 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 the VDJ Clonotypes tab in Loupe Cell Browser as shown here:
A pop-up window asks you to import a file containing the V(D)J clonotypes. Click the "Click here" hyperlink to upload your .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 named 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 the bottom right of the screen, and then on Locally distinguishing:
Once the analysis is complete, click the gene table icon in the lower-left corner of the screen to see a list of differentially expressed genes:
Click here for more information on creating categories from clonotypes, and here for differential expression between categories.