BD Rhapsody Single-Cell Whole Transcriptome Analysis Service
CD Genomics provides a comprehensive BD Rhapsody scWTA (Single-Cell Whole Transcriptome Analysis) service covering every step of your single-cell RNA-seq project: sample processing, single-cell capture on the BD Rhapsody platform, library preparation, high-throughput sequencing, and advanced bioinformatics analysis. With unbiased whole transcriptome amplification and microwell-based single-cell isolation, our service delivers the transcriptome-wide depth and sensitivity needed for gene discovery, rare cell characterization, and high-resolution cell-type annotation.
- Unbiased whole transcriptome profiling at single-cell resolution via BD Rhapsody microwell-based capture
- End-to-end workflow from sample QC to publication-ready bioinformatics — one team, one data structure
- Compatible with immune repertoire and surface proteome multiomic extensions
Services are provided for research use only.
BD Rhapsody scWTA — Technology Overview
BD Rhapsody adopts a microwell-based approach to single-cell isolation. Each cartridge contains over 200,000 microwells — far exceeding the number of input cells — ensuring the vast majority of occupied wells contain a single cell. Cells are loaded by simple gravity sedimentation, which eliminates shear stress and contributes to higher post-capture viability compared with droplet-based microfluidics.
Cell capture and barcoding. A rigid magnetic bead carrying a cell-specific barcode, a transcript-specific molecular tag, and an oligo-dT capture sequence is co-loaded into each well. This enables single-cell indexing of polyadenylated mRNA within the confined microwell environment. A key differentiator is the built-in imaging system, which generates bright-field images of the cartridge after cell loading, allowing direct visualization of cell occupancy, clumping, and debris — reducing experimental risk before committing to library preparation.
Whole Transcriptome Amplification (WTA). The BD Rhapsody WTA kit performs unbiased 3'-based capture and amplification of polyadenylated transcripts. Unlike targeted or 3'-end-only approaches that capture only terminal fragments, WTA amplifies across the full length of captured cDNA, providing broader transcriptome coverage. This is especially advantageous for detecting lowly expressed genes, capturing transcript isoforms, and gene discovery studies where per-cell transcriptome breadth matters more than cell throughput. The recommended input range is 1,000 to 10,000 cells per run.
Library construction and sequencing. Following reverse transcription, barcoded cDNA is pooled, purified, and converted into Illumina-compatible libraries. Captured cDNA on beads remains stable at 4°C for up to three months, enabling re-interrogation of the same material. The platform also supports AbSeq (antibody-based protein detection) and VDJ immune repertoire profiling from the same single-cell suspension, and BD Sample Tag multiplexing allows pooling up to 12 samples per cartridge to reduce per-sample cost and batch effects.
BD Rhapsody scWTA Workflow
CD Genomics delivers a fully managed BD Rhapsody scWTA workflow from sample receipt to bioinformatics report, with built-in quality control at each stage.
- Sample preparation and QC
Upon sample receipt, we assess cell viability, concentration, and purity using automated counters and microscopy. For tissue samples, enzymatic dissociation is performed under optimized conditions. A viability threshold of ≥70% (≥80% for cryopreserved cells) is typically required to proceed.
- Single-cell capture and barcoding
The single-cell suspension is loaded onto the BD Rhapsody cartridge. After gravity sedimentation, the BD Rhapsody Scanner captures bright-field images for cell occupancy analysis. Magnetic barcoded beads are loaded and hybridized to cellular mRNA for on-cartridge reverse transcription. Each cell’s transcriptome is uniquely indexed.
- Library preparation and sequencing
Barcoded cDNA is pooled, purified, and amplified using the BD Rhapsody WTA Amplification Kit. Library quality is verified by Bioanalyzer/TapeStation and Qubit. Sequencing is performed on Illumina platforms (NovaSeq or HiSeq) with paired-end reads at project-tailored depth.
- Bioinformatics data analysis
Raw sequencing data is processed through the BD Rhapsody Analysis Pipeline for sample demultiplexing, read alignment, molecular tag counting, and gene expression matrix generation. Downstream analysis follows our tiered bioinformatics workflow (see below). A comprehensive report with publication-ready figures is delivered within the agreed turnaround time.
scWTA Sample Requirements
Proper sample preparation is critical for high-quality single-cell transcriptome data. Guidelines below apply to BD Rhapsody scWTA; for project-specific consultation, contact our scientific team before shipment.
Cell samples (cryopreserved)
- Minimum cell number: ≥ 5 × 105 viable cells
- Viability: ≥80% after thawing
- Preservation: cell cryopreservation medium, controlled-rate freezing
- Storage and shipping: −80°C; dry ice shipping
- Include viability and count QC data if available; avoid repeated freeze-thaw cycles
Fresh tissue samples
- Sample amount: 200–400 mg; cut into ~0.5 × 0.5 × 0.5 cm pieces (2–3 pieces)
- Immediately immerse in 4°C pre-chilled tissue preservation solution (volume ≥ 5× sample volume)
- Shipping: 4°C cold chain; do NOT freeze, do NOT use dry ice or liquid nitrogen
- Deliver to our facility within 48 hours for optimal viability
Blood samples
- Collection: 3–5 mL peripheral blood in EDTA anticoagulant tube
- Keep on ice or at 4°C; process within 4–6 hours of collection
- Shipping: cold chain at 4°C; alternatively, isolate PBMCs prior to cryopreservation and ship on dry ice
- Avoid hemolysis and clotting; gently invert tube 8–10 times after collection
Bioinformatics Analysis Pipeline
Our bioinformatics team delivers a tiered analysis package that turns BD Rhapsody scWTA data into biological insight. All outputs include publication-quality figures and fully documented analysis code.
Standard analysis
- Raw data QC: read quality, mapping statistics, molecular tag saturation, per-cell metrics
- Normalization and integration: library-size normalization, batch correction (Seurat/Harmony, Scanpy/Scanorama)
- Dimensionality reduction and clustering: PCA, UMAP/t-SNE, graph-based clustering (Louvain/Leiden)
- Cell type annotation: automated (SingleR, CellTypist) plus manual annotation with canonical markers; cell type proportions per sample
- Differential expression: per-cluster and pairwise comparisons with statistical testing (Wilcoxon, DESeq2, MAST); volcano plots and heatmaps
- Marker gene discovery: cluster-specific and condition-specific gene identification with AUC-based or fold-change ranking
Advanced analysis
- Trajectory and pseudotime: Monocle3, Slingshot, or scVelo for developmental and differentiation trajectories; RNA velocity
- Cell–cell communication: ligand–receptor inference using CellChat, CellPhoneDB, or NicheNet
- Gene regulatory networks: transcription factor activity inference (SCENIC/pySCENIC); regulon analysis
- Gene set enrichment: GSEA, GSVA, pathway over-representation (GO, KEGG, Reactome, Hallmark)
- Copy number variation: inferCNV for chromosomal alterations (particularly useful in tumor studies)
- Multiomic integration: co-analysis of transcriptome + surface proteome or transcriptome + immune clonotype when combined with AbSeq/VDJ
Beyond our standard and advanced packages, we offer tailored solutions for cross-species comparative analysis, integration with spatial transcriptomics for cell-type deconvolution, custom gene signature scoring, and machine learning-based classification of disease-associated cell states.
Data Deliverables
Every BD Rhapsody scWTA project includes a comprehensive, structured set of deliverables ready for direct use in analysis and reporting.
- Raw sequencing data
- FASTQ files, demultiplexed per sample
- Processed data
- Gene–cell expression matrix (filtered and unfiltered) in standard formats (.h5, .h5ad, .rds)
- QC report
- Per-sample and per-cell QC metrics, imaging QC snapshots, library QC traces
- Bioinformatics report
- Full analysis report with publication-ready figures (clustering, annotation, differential expression, pathway analysis), methods documentation, and reproducible analysis code
- Custom analysis outputs
- As defined in the project-specific analysis plan
- Data archive
- All intermediate analysis files available for downstream re-analysis upon request
scWTA Applications
BD Rhapsody whole transcriptome scRNA-seq is suited to a broad range of biological questions where maximizing transcriptome coverage per cell is the priority.
Oncology and tumor microenvironment
Characterize intratumoral heterogeneity, map immune and stromal cell populations, identify rare treatment-resistant subclones, and track clonal evolution. WTA's enhanced gene detection is valuable for discovering novel tumor cell states and low-abundance transcriptional programs that targeted approaches may miss. See also: Tumor Microenvironment Solutions.
Immunology and immune profiling
Deconvolve immune cell subsets, profile activation and exhaustion states, map cytokine signaling networks, and reconstruct TCR/BCR repertoires when combined with BD Rhapsody VDJ analysis. Whole transcriptome coverage enables comprehensive characterization of immune functional states beyond surface marker-based definitions. See also: Single-Cell Immune Repertoire Sequencing.
Neuroscience
Resolve neuronal and glial diversity in brain regions and peripheral nervous system. Identify molecularly defined neuronal subtypes and characterize disease-associated microglial and astrocytic states. For frozen brain tissue, see also snRNA Sequencing Services.
Developmental biology
Track cell fate decisions during embryogenesis, organogenesis, and stem cell differentiation. Pseudotime trajectory analysis reveals transitional cell states and gene regulatory cascades driving lineage commitment. WTA's coverage breadth is essential for detecting dynamically regulated genes across developmental windows.
Drug discovery and toxicology
Assess compound-induced transcriptional changes at single-cell resolution, identify sensitive and resistant subpopulations, and characterize on- and off-target effects across heterogeneous cell systems. Whole transcriptome analysis provides a more complete picture of drug mechanism than gene-panel approaches, improving the translatability of preclinical findings.
Case Study: Multimodal Single-Cell Profiling of Alpha-Gal Syndrome Immune Cells
Source: Single-cell mRNA analysis and surface marker expression profiling of circulating immune cells in humans with alpha-gal syndrome (Choudhary SK, Commins SP. Frontiers in Immunology, 2025)
Background
Alpha-gal syndrome (AGS) is a tick-bite-induced food allergy to the oligosaccharide galactose-alpha-1,3-galactose, affecting an estimated 450,000 individuals in the United States. The specific immune cells, their interactions, and signaling cascades triggered by tick bites — including the identity of IgE-secreting cells and rare circulating progenitor populations — were poorly understood. Bulk approaches could not resolve these rare cell populations or their functional states at single-cell resolution.
Methods
The study used the BD Rhapsody platform with BD AbSeq oligo-conjugated antibodies for simultaneous transcriptome and surface proteome profiling of peripheral blood mononuclear cells from AGS subjects and healthy controls. B cells were enriched and sequentially labeled with sample tags and AbSeq antibodies, enabling multimodal single-cell analysis that captured both gene expression and surface marker panels from the same individual cells.
Results
The multimodal analysis identified several cell clusters unique to AGS subjects, including circulating mast cell progenitors, natural killer B (NKB) cells, and natural killer T (NKT) cells. Alpha-gal-specific memory B cells and IgE-secreting cells were identified and characterized. The study further revealed a unique pattern of immunoglobulin class switching, with IgE-secreting transcripts and other immunoglobulin classes co-expressed in the same B cells, distinguishing heterogeneous B cell populations including CCR6-proficient and CCR6-deficient plasmablast/plasma cells.
Conclusion
BD Rhapsody single-cell multiomic profiling enabled the discovery of rare immune cell populations and their transcriptomic and surface proteomic signatures in a human allergic disease. The identification of circulating mast cell progenitors and innate-like cells provides new mechanistic insight into tick-bite-induced sensitization, demonstrating the value of combining transcriptome-wide analysis with surface protein readouts at single-cell resolution.
BD Rhapsody scWTA vs 10x scRNA-seq — Choosing the Right Platform
Both BD Rhapsody and 10x Genomics Chromium are high-throughput single-cell RNA-seq platforms, built on fundamentally different capture technologies and serving partially different research needs. The choice depends on your biological question and experimental constraints. For further context, see our 10x Genomics Chromium scRNA-Seq Service.
| Dimension | BD Rhapsody scWTA | 10x Chromium scRNA-seq |
|---|---|---|
| Capture method | Microwell-based, gravity sedimentation | Droplet-based microfluidics |
| Transcript coverage | Unbiased whole transcriptome (3'-WTA amplification across transcript body) | 3' or 5' end-focused gene expression |
| Genes detected per cell | Higher — broader coverage, better detection of longer genes and low-abundance transcripts1 | Moderate — optimized for high-throughput cell counting |
| Cell throughput (per run) | ~200,000 microwells; practical input 1,000–10,000 cells | Up to ~10,000+ cells recovered per channel; eight channels per chip |
| Low-expression gene sensitivity | Superior — WTA chemistry provides more uniform coverage1 | Moderate — may miss very low-abundance transcripts |
| Cell capture QC | Built-in imaging system — direct visualization before library prep | No direct imaging — QC relies on post-sequencing metrics |
| Sample multiplexing | BD Sample Tag — up to 12 samples per cartridge | Cell Multiplexing (Feature Barcode) — up to 12 samples per lane |
| Multiomics extension | AbSeq (protein) and VDJ (immune repertoire) on the same platform | CITE-seq, V(D)J, ATAC-seq — broader ecosystem, separate consumables |
| Sample flexibility | Fresh and cryopreserved single-cell suspensions; FFPE not compatible with WTA | Fresh and cryopreserved cells; FFPE-compatible Fixed RNA Profiling available |
| Best for | Maximizing transcriptome coverage per cell; rare cell characterization; gene discovery | Large-scale cell atlasing; high-throughput screening; profiling many cells across many samples |
1 Based on Woeste et al. (Heliyon, 2024), comparing 10X Chromium and BD Rhapsody whole transcriptome scRNA-seq using paired localized prostate cancer samples.
How to decide
If your primary goal is discovering novel transcriptional programs, characterizing rare cell populations, or maximizing gene detection per cell, BD Rhapsody scWTA is the recommended starting point. If you are building a large cell atlas, screening many conditions in parallel, or need to profile hundreds of thousands of cells, 10x Chromium may be more practical due to higher cell throughput. For projects benefiting from both, CD Genomics offers both platforms and can advise on a staged experimental design. See also: Single-Cell Full-Length RNA Sequencing Service.
Frequently asked questions (FAQ)
References
- Woeste MR, et al. "Comparative analysis of 10X Chromium vs. BD Rhapsody whole transcriptome single-cell sequencing technologies using localized prostate cancer samples." Heliyon, vol. 10, no. 7, 2024, e29032.
- Gao C, Zhang M, Chen L. "Analytical Workflows for Single-Cell Multiomic Data Using the BD Rhapsody Platform." Current Protocols, vol. 4, no. 2, 2024, e963.
- Choudhary SK, Commins SP. "Single-cell mRNA analysis and surface marker expression profiling of circulating immune cells in humans with alpha-gal syndrome." Frontiers in Immunology, vol. 16, 2025, 1629310.
