Question: What is the minimum number of cells that can be loaded?
Answer: The Single Cell 3' assay allows to capture between 100 and 10,000 cells per sample. In cases where sample is limiting, the following guidelines should be followed:
- If possible, concentrate cells to achieve cell stock concentrations 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 to review 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 for our system compared to primary cells.
Products: Single Cell 3'