Single-Cell Multiplexing

BD® Single-Cell Multiplexing Kits enable multiplexing samples on a single run of the BD Rhapsody™ Single-Cell Analysis System to reduce single-cell sequencing reagent cost and improve data quality in single-cell sequencing analysis.

Start here for a filtered table containing only single-cell multiplexing FAQ from the master document. Easily searchable with CMD+F on a Mac or CTRL+F on a PC.

Is there any cross reactivity between human and mouse clones used in the BD® Single-Cell Multiplexing Kits (SMK)?

The clone in the BD® Human SMK has been reported to cross-react with non-human primates but may react more weakly. It does not cross-react with mouse. The BD® Mouse SMK does not cross-react with other species.

For which cell types can I use the BD® Mouse SMK?

You can use the BD® Mouse SMK for all cell types that express CD45. The Sample Tag in the BD® Mouse SMK is conjugated to an anti-mouse CD45, clone 30-F11 antibody. The CD45 antibody is a lymphocyte and leukocyte marker, expressed on cells including T cells, Pro-B cells, B cells, NK cells, eosinophils, macrophages, LT-HSCs, monocytes, innate lymphoid cells, granulocytes, basophils and mast cells. If you are unsure that your sample expresses the BD® Mouse SMK marker, contact us at

For which cell types can I use the BD® Human SMK?

The BD® Human SMK marker is a universal marker expressed on a wide range of cell types, including but not limited to PBMCs, MSCs and different cancer cell lines. If you are unsure if your sample expresses the BD® Human SMK marker, contact us at

For BD® SMK libraries, why do I need more reads for different types of cells rather than for the same type?

The Sample Tag targets have different expression levels among different cell types. Most of the reads will go to the predominant cell type if there are various cell types within a sample. We have validated that 600 reads/cell should be enough to recover most of the cells within a sample having various cell types. When you are working with samples with one cell type such as cell lines or samples for which the expression level of the Sample Tag target among the different cell types is similar, 120 reads/cell should be enough to recover most of the cells within the sample.

Can we multiplex samples that have a varying number of antibodies per sample?

Yes, internally, we have tested a 10-plex Ab-oligo multiplexed with a 40-plex sample and saw minimal residual jumping. Ensure that each sample is washed well for best results.

For Research Use Only. Not for use in diagnostic or therapeutic procedures.


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