Question: How do I create a cluster of cells that express both Gene A and Gene B in Loupe Cell Browser?
Answer: The example below will demonstrate how to create subclusters. This example uses one of our public datasets (http://cf.10xgenomics.com/supp/cell-vdj/LungTumorGEX.cloupe).
We first create a cluster of cells that expressed the gene CD79A. Then we create a subcluster that expressed both CD79A and CDA.
1) Let's start from the complete dataset. Click on the Gene Expression Tab.
2) Select for cells where Gene Expression for CD79A > 0.
- Search for CD79A in the "Search for a gene" text box.
- Click on the filter button (the funnel-shaped icon in the bottom right corner).
- Create a category name and the cluster name. In this example, we name them both 'CD79A'.
3) Go back to the "Gene Expression" tab.
- Search for the gene 'CDA'.
- Ensure that both genes are in the list.
- Ensure neither gene is selected (i.e. neither gene is highlighted in blue color).
- Ensure that the attribute is selected as "Gene Exp Min".
- Click on filter button to create a new cluster within the CD79A category as below.
4) Finally, we see the following screen, where the subset of cells which express both CD79A and CDA are selected in the 'CDA' cluster (orange). The cells that express CD79A but do not express CDA are selected in cluster 'CD79A' (blue color).