Customize your single-cell experiments with BD
targetedExpress
RNA-Seqand multiplexing technologies
yourself through customized experiments and theBDhelps
Rhapsody
Analysissystem
The BD Rhapsody™ portfolio of products
you answerSingle-Cellbiological questions
with a sensitive,
targeted approach to single-cell
analysis. Researchers can interrogate gene expression from hundreds to tens of thousands of single cells from one or multiple samples
simultaneously.

BD Single-Cell
Multiplexing Kit

BD Rhapsody
Express system

Pool up to 12 samples tominimize batch eﬀects andreduce time to discovery andexperimental costs

Single-cell capture, bead-basedmRNA isolation, and beadretrievalx12BD RhapsodysystemSingle-cell capture, bead-basedmRNA isolation, and beadretrieval with imaging and cell
workﬂow QC

BD Rhapsodytargeted single-cell
RNA-seq panels
Immune Response Panel (Human)
Immune Response Panel (Mouse)
T-cell Panel
Onco-BC (breast cancer) Panel
Custom panel and supplementary
panelsBD Bioinformatics
Alignment and mapping
primary analysis software
BD™ Data View secondary
analysis software for clusteringvisualization and elimination ofmultiplet data for clean
diﬀerential gene expression

The BD Rhapsody Single-Cell Analysis system:
Analyze hundreds of genes across tens of thousandsof single cells in parallel
The system enables high-throughput single-cell RNA-Seq
analyses starting from single-cell suspensions. It supports yourresearch in numerous ways:• Targeted assays provide improved detection sensitivity
at a fraction of the time and cost of whole transcriptome
amplification (WTA)• The optically clear cartridge-based technology allows forvisualization during the workflow to ensure maximal
experimental control• Enhanced data quality due to fewer multiplet events thanequivalent droplet-based WTA assays for a fixed cell load
• BD Molecular Indexing technology counts RNA molecules togive you quantitative gene expression readouts in sequencing• The scanner provides valuable information about cell counts
and viability by simple automatic imaging during the multiple
QC steps of the process• The system is compatible with upstream BD cell-enrichment
technologies, for example, fluorescence-activated cell sortingwith the BD FACSMelody ™ cell sorter

Annotation by cell type

What can the BD Rhapsody scanner do for you?
(1) Dendritic (2.1%)(2) Effector/Effector memory CD4T (4.5%)(3) Effector/memory CD8T (4.1%)(4) Follicular B (49.9%)(5) GC B (3.3%)(6) Granulocyte (0.5%)(7) MM/MZ Macrophage (3.2%)(8) Marginal Zone B (11.2%)(9) NK (1.9%)(10) Naive CD8T (8.1%)(11) Naive/central memory CD4T (8.0%)(12) Plasma (0.8%)(13) Red Pulp Macrophage (2.6%)

Coord 2The BD Rhapsody scanner provides automated cell counting,quality analysis of cell samples, and helps prepare samples atoptimal concentrations for single-cell capture on the BD
Rhapsody cartridge. This is extremely valuable when working
with precious samples as you obtain single-cell capture metrics
in the first step of single-cell sequencing. Some of the featuresof the scanner are:• Automated counts of cells captured with beads onthe cartridge• QC images taken at multiple points in the capture andtagging process• Eliminates tedious manual cell counting with automated cell
calculations that allow you to load correct cell volumes frommultiple samples for multiplexing on the cartridge• Multiplet detection via imaging rather than in sequencing

Coord 1Figure 1. BD Rhapsody and BD Rhapsody Express workflows allow for highquality clustering of primary cell types and reproducibility between methods.
A mouse spleen was mechanically dissociated into a single-cell suspension. ~5000
cells were loaded into two BD Rhapsody cartridges and subjected to the BD
Rhapsody or BD Rhapsody Express workflow in parallel. Single-cell targetedRNA-seq libraries were prepared with the BD Rhapsody Immune Response Targeted
Panel (Mouse) and sequenced with equivalent depth. t-SNE projection of cells fromthe BD Rhapsody and BD Rhapsody Express workflow, annotated by cell type.
Gene-gene correlation for both Rhapsody and BD Rhapsody Express workflows forthis experiment demonstrates no appreciable batch effects, R^2= 0.974.

The BD Rhapsody Express system: Personal, bench-side
assays for targeted single-cell RNA-Seq analysis.
• The BD Rhapsody Express system provides a decentralized,
portable option that eliminates the need to move to a corelab or wait in a queue for an instrument to prepare precious
primary samples

SEQUENCING READS PER CELL
267,064

Droplet WTA
BD Rhapsody targeted

19,044• No electronics required, lightweight, and dependable• The technology is the same as the BD Rhapsody system, but
the workflow is designed and optimized without the need forthe scanner hardware, providing a low-cost way for
researchers to enter the single-cell RNA world or supplement
and round out their RNA-Seq research tools

SEQUENCING SATURATION
Droplet WTA

68.2

Rhapsody targeted

84.3

SEQUENCING READ ALIGNMENT

Regardless of the option you choose,
you can be assured of high quality
data between the two BD Rhapsodysystem workflow options (Figure 1).
BD Rhapsody targeted panels
Targeted gene expression assays are an efficient way to screen
hundreds of genes at once that provide a cost-effective, moresensitive detection of low abundant transcripts than WTA
assays (Figure 2). With this targeted approach you can remove
high expressers to eliminate excessive, costly sequencing reads.
• BD Rhapsody pre-designed targeted panels include:

Droplet WTA

58.7%

BD Rhapsody targeted

91.2%

MEDIAN TRANSCRIPTS PER CELL
Droplet WTA
BD Rhapsody targeted

1470
1688

GENES DETECTED IN BD RHAPSODY
ONCO-BC PANEL
Droplet WTA
Rhapsody targeted

305
323

• Onco-BC panel (human) for breast cancer
oncology research• Immune response panels (human or mouse)• T-cell panel (human)• Custom panels: Request a panel for up to 500 of your genetargets of interest; the BD Bioinformatics service cangenerate a custom panel from your WTA findings orfavorite gene lists• Supplemental panels: Add up to 100 targets to any BD
predesigned panels or custom panel

Figure 2: The BD Rhapsody targeted assays provide higher sensitivity with lower
sequencing cost BT549 and Ramos cells were mixed at a 1:1 ratio and pooled intoeither a BD Rhapsody system or a commercially available WTA droplet-basedsystem. The cells captured from the BD Rhapsody system were subsampled tomatch the number of cells captured in the droplet-based capture system prior tolibrary preparation. NGS libraries were generated from the BD Rhapsody systemusing the BD Rhapsody Targeted Onco-BC panel and compared with WTA libraries
derived from the droplet-based method. The WTA libraries were sequenced to~250,000 reads per cell and the BD Rhapsody libraries were sequenced to ~20,000
reads per cell. With significantly fewer reads per cell, the targeted workflow
achieved higher sequencing saturation and outperformed the WTA workflow inpercentage read alignment, number of transcripts per cell and number of genes
identified. Genes of interest were identified more readily and with less sequencing
requirement with a targeted approach as compared to a WTA method.

BD Rhapsody targeted, customizable panels allow you to focus on the genes thatreally matter, including rare transcripts.

Cell hash with the BD Single-Cell Multiplexing kit to reduce experimentcosts and enhance data quality
BD™ Single-Cell Multiplexing Kit
Instead of running one sample per single-cell capture, researchers can now run up to 12 in one using the BD
Single-Cell Multiplexing kit. This kit allows you to customize your experiments by choosing between 1 to 12samples at once on a BD Rhapsody cartridge or other compatible system using an antibody-oligo conjugate tostain each individual sample. Multiplexing samples allows you to not only improve data quality, but drasticallyreduce cost per run.
Benefits of the kit include:• Allows for inter-sample multiplet detection and removal in analysis• Pools up to 12 samples together to reduce experiment costs• Lowers technical errors between samples by reducing batch effects• Integrates easily into standard RNA-Seq workflow via the upstream antibody-labeling step• Compatible with the 10X Genomics® Chromium™ system and other droplet-based 3’ solutions

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www.bd.com/genomics
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