Question: Can I use more than one CMO tag per sample when using the 3’ CellPlex Kit for Cell Multiplexing?
Answer: When using the 3’ CellPlex Kit for Cell Multiplexing, it is possible to take a cell/nuclei sample, split it into aliquots, and stain each aliquot separately with a different CMO. These CMO-labeled aliquots can then be pooled together to load onto the same well of a 10x chip.
The benefit of this approach is that it can improve cell multiplet detection. For example, if you only have 2 cell samples to use for Cell Multiplexing, you could split each sample into two aliquots and stain each aliquot with a different CMO tag. When pooling the cells together, you will now have a total of 4 CMO tags instead of 2 CMO tags. Using a greater number of CMO tags will improve cell multiplet detection.
When analyzing data in Cell Ranger, you can specify which CMO-labeled samples belong to the same sample. Cell Ranger will combine the data for these samples when producing the final output files.
Note that we only support splitting the cell sample into aliquots and staining each aliquot separately with a single CMO tag. We do not support staining the same aliquot simultaneously with multiple CMO tags. In Cell Ranger, if a cell is identified as being labeled with more than one CMO tag, it will be classified as a cell multiplet and will be filtered out.
Products: Single Cell Gene Expression, CellPlex