Question: How can I reduce background from unbound CMOs using the 3’ CellPlex kit for Cell Multiplexing?
Answer: When using the 3’ CellPlex kit for Cell Multiplexing, it is important to follow our Demonstrated Protocol for CMO labeling and washing to ensure optimal signal to noise ratios in the final CellPlex data. This article highlights best practices for CMO labeling and washing.
For examples of how insufficient washing can negatively impact Cell Multiplexing metrics, please refer to this article.
1) Fully remove the supernatant after each wash step
It is extremely important to remove as much supernatant as possible after each wash step post CMO labeling. If the supernatant is not completely removed, unbound CMOs remaining in the sample will lead to high background noise levels in the final CellPlex data. This will prevent Cell Ranger from accurately distinguishing true signal from noise, leading to inaccurate CMO tag assignment.
We recommend leaving no more than 10 ul of supernatant after each wash step, as illustrated here:
2) Do not reduce the number or volume of wash steps
We recommend performing 3 total wash steps post CMO-labeling. This includes adding 1.9 ml wash buffer immediately after CMO incubation (wash 1), followed by two additional wash steps with 2 ml wash buffer (wash 2 & 3).
We do not recommend performing fewer wash steps or reducing the volume of wash buffer, as this may lead to insufficient removal of background from unbound CMOs.
3) Use at least 100,000 cells/nuclei as input into CMO labeling, or 500,000 if possible
When working with low cell/nuclei numbers, a pellet may not be visible after centrifugation, making it challenging to fully remove the supernatant after each wash step. We do not recommend or support using fewer than 100,000 cells/nuclei as input into CMO labeling. Furthermore, if the sample is not limited, we recommend using at least 500,000 cells/nuclei as input into CMO labeling.
4) Use a swinging bucket centrifuge
It may be preferable to use a centrifuge with a swinging bucket rotor, especially when working with nuclei or lower cell numbers. Using a swinging bucket rotor, the cell/nuclei pellet will be more compact and easier to see. This will make it easier to fully remove the supernatant after each wash step.
5) Remove debris before or after CMO labeling
If your sample contains debris consisting of cell/nuclei fragments, the CMO lipids may bind to the debris. If these debris are not removed before loading the cells/nuclei onto the 10x Genomics chip, these debris can lead to high background noise levels in the Gene Expression data and CellPlex data.
Therefore, we recommend fully removing debris before loading the sample on the 10x chip. An excellent method for removing debris is to perform flow sorting, which can be performed on cells or nuclei after CMO labeling, as described here. During in-house tests, we found that using FACS to remove debris and dead/dying cells improved signal to noise ratios in CellPlex data and improved Gene Expression data.
6) Use 1% BSA in the wash buffer post CMO labeling
As outlined in our Demonstrated Protocol, the 3’ CellPlex assay was validated using the following buffers to wash cells/nuclei after CMO labeling:
|Wash buffer post CMO labeling||Sample type|
|PBS + 1% BSA||PBMCs, cell lines, dissociated tumor cells|
|NbActiv-1 + 1% BSA||Dissociated brain tissue|
|PBS + 1% BSA + RNase Inhibitor (0.2 U/μl)||Nuclei|
We recommend including 1% BSA in the wash buffer post CMO labeling. We do not recommend decreasing the percentage of BSA in the wash buffer. During in-house experiments, we found that using 1% BSA, compared to various other wash buffers tested (including 0.04% BSA), produces the best signal to noise ratios in CellPlex data and also minimizes cell/nuclei loss and aggregation.
1% BSA should be diluted in PBS or a cell culture media appropriate for your cell type. Primary cells, stem cells, and other sensitive cell types may have improved viability when diluting BSA in an appropriate cell culture media instead of PBS. Please refer to this article for general guidance on selecting cell culture media compatible with the downstream Single Cell 3’ Gene Expression assay.
For sensitive cell types, it is also possible to use 10% FBS instead of 1% BSA in the wash buffer post CMO labeling.
7) Before CMO labeling, suspend cells/nuclei in the appropriate buffer
For in-house experiments, cells/nuclei were suspended in the following buffers before CMO labeling:
- PBS + 0.04% BSA -- for cells
- PBS + 1% BSA + RNase Inhibitor -- for nuclei
If you use alternative cell/nuclei isolation protocols that include different resuspension buffers, we recommend washing and resuspending the cells/nuclei in our recommended buffers before CMO labeling.
For example, if detergents are used during nuclei isolation, wash steps should be performed with PBS + 1% BSA + RNase Inhibitor to remove detergents before CMO labeling. Similarly, if cell culture media + 10% FBS is used for cell isolation, cells should be resuspended in PBS + 0.04% BSA immediately before CMO labeling. This will avoid introducing components that may interfere with the CMO labeling reaction.
Products: Single Cell Gene Expression, CellPlex