Question: Are targeted cell recoveries greater than 10,000 cells supported using standard throughput kits?
Answer: If you are not performing Cell Multiplexing, we do not recommend or support targeting more than 10,000 cells. The reason is that the cell multiplet rate increases with higher cell loads. When using the 3' CellPlex kit, it is possible to identify and filter out many of the cell multiplets. However, if you are not using the 3' CellPlex kit, it is impossible to identify and filter out cell multiplets in Cell Ranger. Therefore, the cell multiplets will remain in your final data. When targeting more than 10,000 cells, the high cell multiplet rate may compromise the biological interpretation of your data.
Note: The Next GEM Single Cell 3' HT v3.1 kits support cell recovery up to 20,000 cells without cell multiplexing.
Products: Single Cell Gene Expression, CellPlex