Question: What is the maximum number of cells that can be profiled?
Answer: In each standard 10x Single Cell Gene Expression, Immune Profiling, ATAC, or Multiome library, it is possible to target up to 10,000 cells. Each chip can process eight libraries in parallel, allowing users to target up to 80,000 cells per chip.
In each high-throughput 10X Single Cell Gene Expression or Immune Profiling library, it is possible to target up to 20,000 cells without cell multiplexing. Each chip can process up to sixteen libraries in parallel, allowing users to target up to 320,000 cells per chip.
An important consideration when deciding how many cells to target is the cell multiplet rate. As more cells are loaded on the 10x chip, it becomes more likely that two or more cells will be partitioned together into the same GEM (cell multiplet). Please refer to the Multiplet Rate Table provided in the User Guide for each product, as shown here for the Single Cell 3' Gene Expression v3.1 assay:
You can control the multiplet rate by adjusting the number of loaded cells and, consequently, the number of recovered cells.
Note that for the Single Cell Gene Expression assay, it is possible to target up to 30,000 cells per library if using the 3' CellPlex Kit for Cell Multiplexing. For the Single Cell Gene Expression HT assay, it is possible to target up to 60,000 cells per library if using the 3' CellPlex Kit for Cell Multiplexing. Cell multiplets can be bioinformatically identified and filtered out when using the 3' CellPlex Kit.
Please also refer to the following articles:
Why is the HT multiplet rate lower than our standard assay?
Why is the multiplet rate different for the Next GEM Single Cell 3’ LT v3.1 assay when compared to other single-cell applications?
Products: Single Cell Gene Expression, Single Cell Immune Profiling, Single Cell ATAC, Connect, Single Cell Multiome ATAC+GEX, CellPlex