Question: Is flow cytometry compatible with the 3’ CellPlex Kit for Cell Multiplexing?
Answer: Yes, CMO-labeled cells or nuclei can be sorted using flow cytometry.
After labeling cells/nuclei with Cell Multiplexing Oligos (CMOs), flow sorting samples can improve Cell Multiplexing data quality by reducing background from debris and unbound CMOs.
- CMO-labeled cells can be sorted using a fluorescent live/dead marker. Cells can also be labeled with both CMOs and fluorescent antibodies and sorted to enrich specific cell populations.
- CMO-labeled nuclei can be sorted based on forward and side-scatter and a fluorescent DNA dye such as 7-AAD.
CMO-labeled cells or nuclei can be pooled before or after flow sorting:
- CMO-labeled samples can be sorted separately and pooled together after sorting.
- Alternatively, CMO-labeled samples can be pooled together first and then sorted together as one sample.
For a demonstration of flow sorting CMO-labeled cells, please refer to our Technical Note on Cell Multiplexing.
After performing CMO-labeling and washing as outlined in our Demonstrated Protocol, CMO-labeled cells/nuclei can be suspended in an appropriate buffer for flow cytometry. For in-house experiments, CMO-labeled cells/nuclei were suspended in the following buffers:
- CMO-labeled nuclei: PBS + 1% BSA + 0.2U/ul RNase inhibitor
- CMO-labeled cells: PBS + 10% FBS
Other buffer types are likely to be compatible and we recommend selecting a buffer that allows for maximal viability of your sample type. Please refer to this article for general guidance on buffers compatible with the Single Cell Gene Expression assay.
For additional guidance, please see: What are the best practices for flow sorting cells for 10x Genomics assays?
Products: Single Cell Gene Expression, CellPlex