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The BD Rhapsody™ Single-Cell Analysis System includes the BD Rhapsody™ Scanner and BD Rhapsody™ Express Single-Cell Analysis System. The BD Rhapsody™ Express System enables single-cell capture and barcoding of hundreds to thousands of single cells for analysis of genomic and proteomic information, using proprietary, gentle, robust microwell-based single-cell partitioning technology. The BD Rhapsody™ Scanner is designed to visualize all steps in the single-cell capture workflow and provide detailed analysis metrics at every step, enabling the user to make key decisions throughout the workflow.


Get more information from the BD Rhapsody™ System brochure.



The BD Rhapsody™ Scanner provides the ability to visualize single-cell capture and provides key quality metrics at every step

The BD Rhapsody™ Scanner:

  • Enables visual inspection of the cartridge and of each microwell through an optically clear window on the BD Rhapsody™ Cartridge
  • Provides quality control measures such as cell capture rate and cell multiplet rates by direct imaging of the cartridge to analyze quality of the cell preparation. Quality control metrics provide an indication if errors have occurred during the cartridge workflow allowing you to decide whether to proceed to sequencing
  • Can be useful for troubleshooting and provide an estimate of the number of cells expected to be retrieved by sequencing


Number of wells with viable cells at cell load 9118
Cell multiplet rate at cell load 2.4%
Number of wells with viable cells and a bead 7999
Cell multiplet rate 2.0%
Bead loading efficiency
Cell retention rate
Bead retrieval efficiency
Excess bead rate





The BD Rhapsody™ Single-Cell Analysis System provides reliable and reproducible results making it an ideal system for translational studies


The BD Rhapsody™ Single-Cell Analysis System enables simultaneous measurement of surface proteins and mRNA expression, facilitating the identification of distinct subsets of regulatory T cells

Differential gene expression and differential protein expression analysis were performed on three main Treg subsets identified based on manual gating and bivariate analysis of CD45RA and HLA-DR sorted Treg samples. Differential gene expression analysis was performed using the BD Rhapsody™ Targeted Human Immune Response Panel (399 genes). Upregulated genes (>1.25X) are shown in the heat map above. Differential protein expression of 22 proteins was performed simultaneously using BD® AbSeq Oligo-Conjugated Antibodies.


The BD Rhapsody™ Single-Cell Analysis System can be used for deep characterization of exhausted T cells

Expression of 12 proteins and genes that are significantly upregulated at day 14 of chronic simulation of CD8+ T cells. Two populations (red and green boxes) emerged based on the expression level of markers. Co-expression patterns were discerned for CD38, CD39 and CD94. 


The BD Rhapsody™ Single-Cell Analysis System enables resolution of innate lymphoid cell heterogeneity

Differential protein and gene expression at the single-cell level.


Heterogeneity was observed in major ILC subsets.


The BD Rhapsody™ Single-Cell Analysis System enables identification of heterogeneity within CLL samples

Clusters are well defined using simultaneous mRNA and protein analysis. Samples from healthy donors cluster similarly. CLL samples cluster separately and uniquely. 


BD Rhapsody™ Single-Cell Analysis System

A powerful, high-throughput, microwell-based single-cell partitioning system, combined with visual workflow QC
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For Research Use Only. Not for use in diagnostic or therapeutic procedures.

Results shown are not guaranteed and may not be representative.

Dynabeads is a trademark of Thermo Fisher Scientific.