Question: What is the cell multiplet rate when using the 3’ CellPlex Kit for Cell Multiplexing?
Answer: The cell multiplet rate is dependent on the assay and also the Targeted Cell Recovery.
As the Targeted Cell Recovery increases, it becomes more likely two cells will end up being partitioned together into the same GEM (cell multiplet).
For the standard 3' v3.1 assay, the cell multiplet rate is approximately 0.8% for every 1,000 cells targeted. For example, the expected cell multiplet rate is:
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- ~0.8% at a targeted cell recovery of 1,000
- ~4% at a targeted cell recovery of 5,000
- ~8% at a targeted cell recovery of 10,000
- ~16% at a targeted cell recovery of 20,000
- ~24% at a targeted cell recovery of 30,000
For the high-throughput (HT) 3' v3.1 assay, the cell multiplet rate is approximately 0.4% for every 1,000 cells targeted. For example, the expected cell multiplet rate is:
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- ~0.8% at a targeted cell recovery of 2,000
- ~2% at a targeted cell recovery of 5,000
- ~4% at a targeted cell recovery of 10,000
- ~8% at a targeted cell recovery of 20,000
- ~24% at a targeted cell recovery of 60,000
Note that some, but not all, of these cell multiplets, can be identified and filtered out in Cell Ranger.
See: What affects the cell multiplet rate and cell multiplet filtering?
Products: Single Cell Gene Expression, CellPlex