BD Rhapsody™ Single-Cell Analysis System

Overview

The BD Rhapsody™ Single-Cell Analysis System is a fully integrated, benchtop platform engineered for high-fidelity, multi-omic single-cell analysis. It leverages microfluidic cartridge-based cell capture combined with molecular barcoding technology to enable simultaneous profiling of transcriptome, surface protein expression (via AbSeq), and targeted gene panels from individual cells. The system operates on a combinatorial indexing principle: each cell is uniquely labeled with a cell-specific barcode during encapsulation in nanowell arrays, while mRNA molecules are tagged with unique molecular identifiers (UMIs) and gene-specific primers. This dual-barcode architecture ensures accurate cell-level quantification, minimizes ambient RNA contamination, and supports robust batch correction across samples. Designed for reproducibility in regulated and discovery environments, the BD Rhapsody platform conforms to GLP-aligned workflows and supports audit-ready data traceability through integrated instrument logging and software metadata tagging.

Key Features

• Two-tiered system architecture: BD Rhapsody™ Express (portable, power-free sample loading station) and BD Rhapsody™ Full System (with integrated imaging-based real-time quality control)
• Automated, pre-programmed liquid handling via calibrated electronic pipettors (5000 µL and 1200 µL capacities), eliminating manual variability and reducing hands-on time by >60% versus manual protocols
• BD Rhapsody Scanner delivers in-process QC metrics including viable cell concentration, viability (%), doublet rate (75%), and magnetic bead recovery yield — all visualized pre-library prep
• Cartridge-based nanowell array technology enables scalable throughput (up to 20,000 cells per run) with low doublet rates and high capture efficiency across diverse primary tissues (e.g., PBMCs, tumor digests, dissociated brain, FFPE-derived nuclei)
• Integrated molecular barcoding at three levels: sample index, cell barcode, and UMI — enabling multiplexed sample processing and precise digital gene counting

Sample Compatibility & Compliance

The BD Rhapsody system demonstrates broad compatibility with human and murine samples, including fresh, cryopreserved, and enzymatically dissociated cells. It supports input material ranging from 10,000 to 100,000 total cells per cartridge, with validated performance across immune cell subsets, epithelial populations, and low-input rare cell types (e.g., circulating tumor cells). All reagents—including Rhapsody Cartridges, RT Kits, Whole Transcriptome Amplification Kits, and AbSeq antibody-oligo conjugates—are manufactured under ISO 13485-certified quality systems. The platform supports 21 CFR Part 11-compliant data management when deployed with SeqGeq v4.0+ and BD’s validated instrument control software, ensuring audit readiness for clinical research and translational applications.

Software & Data Management

Data acquisition, alignment, and preliminary quantification are performed using BD’s proprietary Rhapsody Analysis Suite, which integrates STAR aligner, featureCounts, and custom barcode demultiplexing algorithms. Downstream analysis is executed in SeqGeq—a desktop application built on the Bioconductor framework—supporting Seurat v5, Monocle3, and Scanpy-compatible workflows. SeqGeq provides native support for dimensionality reduction (t-SNE, UMAP), differential expression (MAST, DESeq2), trajectory inference, heatmap generation, violin plots, volcano plots, and raincloud visualization. All analyses retain full metadata linkage to original instrument logs, reagent lot numbers, and operator IDs. Raw FASTQ files, BAM alignments, and expression matrices are stored in FAIR-compliant directory structures with MD5 checksum validation.

Applications

• High-parameter immune profiling: simultaneous detection of >100 surface proteins and whole-transcriptome expression in human and mouse immune cells
• Tumor microenvironment mapping: co-profiling of stromal, immune, and malignant subpopulations with spatially agnostic resolution
• Developmental biology studies: lineage tracing and pseudotemporal ordering in stem cell differentiation models
• Biomarker discovery in clinical cohorts: identification of predictive gene–protein signatures in longitudinal PBMC or tissue biopsies
• Targeted panel analysis: focused interrogation of disease-relevant pathways (e.g., T-cell exhaustion, interferon response, breast cancer signaling) using pre-validated primer sets

FAQ

What sample types are validated for use with the BD Rhapsody system?

Primary human and murine cells—including PBMCs, splenocytes, tumor-infiltrating lymphocytes, dissociated solid tissues, and frozen-thawed samples—are extensively validated. Nuclei from FFPE tissues are supported via the BD Rhapsody Nuclear Isolation Kit.
Does the system support multiplexed sample processing?

Yes. Sample Indexing Kits (human/mouse/pan-species) enable up to 12-sample multiplexing per cartridge, with automated deconvolution during bioinformatic processing.
How is data integrity ensured during acquisition and analysis?

Instrument logs record timestamped events for every fluidic step; SeqGeq enforces version-controlled analysis pipelines with immutable parameter snapshots and exportable provenance reports.
Is technical support available globally?

BD provides regional field application scientists and certified service engineers across North America, EMEA, and APAC, with 24/7 remote diagnostics and on-site installation support.
Are reagents supplied as GMP-grade or research-use-only?

All core reagents are manufactured under ISO 13485 and labeled RUO; select kits (e.g., AbSeq Human Immune Panel) are available under investigational use provisions for clinical assay development.