Question: How do I minimize background RNA during sample prep?
Answer: Cell-free, or background, RNA in single cell suspensions will (in addition to the cells) be captured in single partitions and as a result can significantly increase the background in single cell data. Optimal performance of the 10x Single Cell assay is achieved if free floating cell-free RNA is kept at minimum.
When preparing single cell suspensions, we recommend these best practices to minimize cell-free RNA:
- Wash cells twice before loading.
- Minimize time between generating a single cell suspension and chip loading to prevent cell lysing.
- Cell viability should ideally be > 90% to minimize the amount of RNA from lysed cells.
Products: Single Cell 3', VDJ