Question: What is the minimum number of cells that can be profiled?
Answer: The Single Cell Gene Expression and VDJ assays are designed to target between 500 and 10,000 cells per sample*. In cases where the sample is limiting, the following guidelines should be followed:
- If possible, concentrate cells to achieve a cell stock concentration of ~700-1200 cells/ul.
- If concentrating the cells is not an option, load the cell suspension volume to the RT master mix without the addition of water to maximize cell count.
- In order to optimize the target cell count, extra care should be taken when assessing cell viability (>90% healthy) and cell aggregation under the microscope.
- Depending on your cell type of interest you may have very little cDNA going into the library prep. We support a wide range of total RNA and can use as little as 2 ng cDNA for library prep. If needed, the number of PCR cycles during cDNA amplification can be increased by 1-2 cycles to increase cDNA yield.
For sample types with a limited number of cells, we recommend reviewing best practices in the Single Cell Protocols - Cell Preparation Guide (https://support.10xgenomics.com/single-cell-gene-expression/index/doc/demonstrated-protocol-single-cell-protocols-cell-preparation-guide).
The 100 Cell Dataset on our website was performed with cell lines (https://support.10xgenomics.com/single-cell/datasets/hgmm_100), which are generally easier to prepare and handle compared to primary cells.
*The Single Cell LT v3.1 assay efficiently partitions 100–1,000 cells per channel, for up to 8,000 cells per run.
*The Single Cell 3' HT v3.1 and Single Cell 5' HT v2 assays efficiently partition 2,000–20,000 cells per channel, for up to 320,000 cells per run.
Products: Single Cell Gene Expression, Single Cell Immune Profiling