Question: What is the minimum number of cells that can be profiled?
Answer: The Single Cell Gene Expression and VDJ assay is designed to target between 500 and 10,000 cells per sample. In cases where 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.
Products: Single Cell 3', VDJ