Question: How many cells do I need for CMO labeling when using the 3' CellPlex Kit for Cell Multiplexing?
Answer: The Demonstrated Protocol for Cell Multiplexing Oligo (CMO) labeling was validated for use with 100,000 to 2,000,000 input cells or nuclei. If the number of cells/nuclei is not limited, we recommend using at least 500,000 as input.
We do not recommend or support performing CMO labeling if you have fewer than 100,000 cells/nuclei per sample. Using fewer than 100,000 cells is likely to lead to poor CellPlex assay performance, for two reasons:
- The CMO labeling protocol includes multiple wash steps post CMO labeling, which are essential to reduce background from unbound CMOs. It is absolutely critical to removal all of the supernatant after each wash step. When working with fewer than 100,000 cells/nuclei, the pellet may be difficult to see, which makes it very challenging to fully remove the supernatant. Incomplete removal of the supernatant will lead to high background in the final CellPlex data, which will prevent accurate CMO tag assignment.
- We expect to lose between 30% and 70% of the starting cells/nuclei during the wash steps. If fewer than 100,000 cells/nuclei are used as input, there may not be sufficient cells/nuclei remaining after CMO labeling for accurate cell counting, pooling, and loading onto the chip.
Products: Single Cell Gene Expression, CellPlex