Question: Why is the number of cells called in Cell Ranger less than the Targeted Cell Recovery?
Answer: The number of "cells" called by Cell Ranger will be less than the Targeted Cell Recovery, given that some cells will be partitioned together into the same GEMs (cell multiplets).
As shown in the example below, 6 cells were partitioned into GEMs. However, given that two cells were incorporated into the same GEM, there are only 5 GEMs that are associated with cells. Therefore, Cell Ranger would only call 5 cell barcodes.
This graph shows the expected number of cell barcodes called in Cell Ranger (purple). This number is less than the Targeted Cell Recovery (red).
Using the 3' CellPlex Kit for Cell Multiplexing, we support a Targeted Cell Recovery of up to 30,000 cells.
If we consider the maximum Targeted Cell Recovery of 30,000 cells:
- ~49,500 cells will be loaded onto the chip
- ~30,000 cells will be incorporated into GEMs
- ~23,300 GEMs will contain one or more cells (this is the total number of “cells” called in Cell Ranger, also referred to as "cell barcodes detected")
- Of these ~23,300 GEMs, we expect ~17,700 to contain one cell (singlet) and ~5,600 to contain more than one cell (multiplet)
- Note that this is a multiplet rate of ~24%
- 5,600 multiplets / 23,300 cell-associated GEMs = ~24% multiplets
Please note that for the high-throughput (HT) assay, we anticipate the number of cells to be called in Cell Ranger to equal the Targeted Cell Recovery. Please refer to Why is the number of cells called in Cell Ranger equal to the Targeted Cell Recovery for HT?
Please also refer to the Cell Multiplexing User Guide, which contains a table that lists the expected number of Cell Barcodes Detected at different Targeted Cell Recoveries.
Products: Single Cell Gene Expression, CellPlex