Introduction
In the intricate tapestry of biological systems, every single cell has a story to tell—a narrative of health, disease, development, and function that remains hidden when we study cells in bulk. The emergence of single-cell technologies has revolutionized our ability to decipher these stories, revealing complexities never before imagined.
Among these technological advancements, the BD Rhapsodyâ„¢ Single-Cell Analysis System stands out as a powerful platform that enables researchers to capture multimodal information from thousands of individual cells in parallel. This innovative system allows scientists to simultaneously measure gene expression, protein abundance, and immune receptor specificity, providing unprecedented insights into cellular heterogeneity and function.
From cancer research to immunology and developmental biology, the BD Rhapsody system is helping overcome limitations across various disciplines of life science research, offering a window into the cellular universe that was previously unimaginable 1 .
Key Concepts and Technological Foundations
Microwell-Based Single-Cell Capture
At the heart of the BD Rhapsody system lies a sophisticated microwell-based cartridge technology that represents a significant departure from traditional microfluidic approaches.
Each cartridge contains an array of >220,000 microscopic wells designed to capture individual cells through gravity sedimentation rather than forced fluidic manipulation 2 .
Molecular Barcoding and Multiomics
The system employs a multitier barcoding system that enables simultaneous analysis of multiple molecular modalities from each individual cell.
Using stable magnetic barcoded beads known as BD Rhapsodyâ„¢ Enhanced Cell Capture Beads, the system tags each molecule with unique cellular and molecular identifiers 3 .
Advantages Over Alternative Technologies
Comparative studies have demonstrated distinct advantages of the microwell-based BD Rhapsody system over alternative technologies like droplet-based systems.
The BD Rhapsody system demonstrated superior recovery of cells with low mRNA content (such as T cells), while droplet-based systems recovered more epithelial cells 4 .
The BD Rhapsody Workflow: From Sample to Sequencing Data
Sample Preparation and Staining
The journey begins with careful sample preparation, where researchers may enrich specific cellular phenotypes through cell sorting techniques. The system allows for co-staining with Oligo-conjugated BD® AbSeq antibodies and/or Sample Tag antibodies alongside fluorochrome-conjugated antibodies that share the same clone 5 .
Single-Cell Capture and Barcoding
Cells are loaded into either a BD Rhapsodyâ„¢ Single-Lane Cartridge for lower-throughput needs or a BD Rhapsodyâ„¢ 8-Lane Cartridge for higher-throughput applications. The BD Rhapsodyâ„¢ Scanner provides visual quality control at every step by imaging the cartridge and individual microwells 6 .
Library Preparation and Sequencing
Following cell capture and barcoding, researchers proceed to library preparation using various BD Rhapsodyâ„¢ assay kits tailored to specific applications. Each library type undergoes post-PCR purification through double-sided size selection using AMPure beads to ensure high-quality sequencing ready material 5 .
Data Analysis and Interpretation
The BD Rhapsodyâ„¢ Sequence Analysis Pipeline represents the computational component of the workflow, offering both cloud-based and local installation options. This versatile tool provides primary analysis of single-cell multiomics data by leveraging cutting-edge algorithms to process raw sequencing reads into biologically meaningful information 7 .
| Component | Throughput | Key Features | Best For |
|---|---|---|---|
| BD Rhapsodyâ„¢ Express System | Lower throughput | Single-Lane Cartridge, visual QC with Scanner | Routine use with familiar cell systems |
| BD Rhapsodyâ„¢ HT Xpress System | Higher throughput | 8-Lane Cartridge, scanner-free option possible | Multi-sample workflows, large studies |
| BD Rhapsodyâ„¢ Scanner | N/A | Visual inspection and quality metrics | Workflow QC and troubleshooting |
A Closer Look: Key Experiment Revealing Platform Performance
Experimental Design and Methodology
A crucial study directly compared the performance of the BD Rhapsody system (microwell-based) against the droplet-based 10X Chromium system using paired samples from patients with localized prostate cancer undergoing radical prostatectomy 4 . The study aimed to evaluate how each platform handles different cell types and their ability to provide accurate biological insights from the tumor microenvironment.
Results and Interpretation
The study revealed that while both platforms showed high technical consistency in unraveling the whole transcriptome, they exhibited significant differences in cell population recovery. The BD Rhapsody system demonstrated superior recovery of T cells and other immune cells with low mRNA content, attributed to its higher RNA capture rates. In contrast, the droplet-based system recovered more epithelial cells 4 .
| Performance Metric | BD Rhapsodyâ„¢ System | Droplet-Based System | Implications |
|---|---|---|---|
| T cell recovery | Higher | Lower | Better for immunology studies |
| Epithelial cell recovery | Lower | Higher | Better for epithelial-focused studies |
| RNA capture efficiency | Higher | Lower | Improved detection of low-expression genes |
| Technical consistency | High | High | Both platforms reliable |
| Cell type annotation variability | Platform-dependent | Platform-dependent | Cross-platform comparisons challenging |
Research Reagent Solutions: The Scientist's Toolkit
The BD Rhapsodyâ„¢ ecosystem encompasses a comprehensive suite of reagents and tools designed to support every step of the single-cell multiomics workflow. These specialized materials enable researchers to extract maximum biological information from precious samples while maintaining experimental quality and reproducibility.
| Reagent/Tool | Function | Key Applications |
|---|---|---|
| BD Rhapsodyâ„¢ Cartridges (Single-Lane or 8-Lane) | Microwell array for single-cell capture | All application areas |
| BD Rhapsodyâ„¢ Enhanced Cell Capture Beads | Magnetic barcoded beads for molecular tagging | All application areas |
| BD® AbSeq Oligo-Conjugated Antibodies | Protein detection alongside mRNA measurement | Immune cell profiling, surface protein analysis |
| BD® Single-Cell Multiplexing Kit | Sample multiplexing to reduce costs | Large cohort studies, multiple conditions |
| BD Rhapsodyâ„¢ Targeted mRNA Panels | Focused analysis of specific gene sets | High-sensitivity transcript detection, large cohorts |
| dCODE Dextramer® | Antigen-specific cell identification | T-cell and B-cell antigen specificity studies |
| BD Rhapsodyâ„¢ WTA Amplification Kit | Whole transcriptome library preparation | Discovery biology, novel cell type identification |
BD® AbSeq Assays
These oligo-conjugated antibodies enable researchers to quantify surface protein abundance alongside transcriptomic measurements using sequencing as the readout, rather than traditional fluorescence-based detection 8 .
Barcoded Magnetic Beads
These beads remain intact throughout the workflow and can be stored for several months after cDNA synthesis. Studies have shown high correlation in gene expression with minimal batch effects in data obtained from beads stored up to 12 weeks 2 .
Conclusion
The BD Rhapsodyâ„¢ Single-Cell Analysis System represents a significant milestone in the evolution of single-cell technologies, offering researchers a comprehensive solution for multimodal single-cell analysis from sample preparation through data visualization. Its innovative microwell-based approach, combined with extensive quality control capabilities and flexible analytical options, addresses critical challenges in single-cell research while maintaining accessibility for users with varying levels of computational expertise.
As single-cell technologies continue to transform our understanding of biology and disease, platforms like the BD Rhapsody system are pushing the boundaries of what's possible by enabling deeper characterization of cellular heterogeneity, function, and relationships. The technology's demonstrated applications across oncology, immunology, developmental biology, and neuroscience highlight its versatility and power to uncover new biological insights that were previously inaccessible.
With ongoing advancements in both wet-lab methodologies and computational approaches, the BD Rhapsody ecosystem continues to evolve, offering researchers ever more powerful tools to explore the complex universe of cellular diversity.