BD Rhapsody™ TCR/BCR Next Multiomic Assays

Overview

Understanding the intricacies of the immune system is crucial to elucidating roles of immune cells in health and disease. This requires profiling T- and B-cell receptors (TCRs and BCRs), key determinants of adaptive immunity. The next generation of BD Rhapsody™ TCR/BCR Multiomic Assays reveal immune repertoire richness with great sensitivity alongside simultaneous single-cell gene and protein expression analyses.

Features

Validated on our new Enhanced Cell Capture Beads V3, BD Rhapsody™ TCR/BCR Next Multiomic Assays enable a highly sensitive analysis of full-length TCR/BCR repertoires with robust workflows for human and mouse. Key features include:

Superior full-length TCR and BCR pairing metrics
Multiomics-enabled for simultaneous immune profiling alongside protein and gene expression analyses in the same cell
Compatibility with preserved cells and BD^® OMICS-Guard Sample Preservation Buffer
Intuitive data analysis pipeline that provides unbiased insights about the biology of your samples

Applications

A single workflow to identify and analyze T and B cell clonotypes with high sensitivity alongside single-cell whole transcriptome or targeted mRNA expression and protein analyses.

In this study, we simultaneously analyzed TCR, BCR, whole transcriptome gene expression as well as cell surface proteins using the BD^® AbSeq Immune Discovery Panel in primary PBMCs. In total, 2,380 complete phenotypes were detected from 6,798 putative cells (out of 7,292 input cells).

Step 1:

Using both protein and gene expression, a UMAP plot was generated, and protein markers were used to identify cell populations.

Step 2:

An unsupervised analysis (phenograph) was performed on CD8⁺ cells where 11 clusters were identified.

Step 3:

Frequencies of unique clonotypes within CD8⁺ were reported.

Step 4:

The top 5 clonotypes were overlaid on the UMAP plot and identified within phenograph clusters.

Clonotype Identification on UMAP Plot within Phenograph Clusters

Step 5:

Using WTA and AbSeq information, differential gene and protein expression analysis of cells with the most frequent clonotype vs the rest of the population were performed.

Differential Gene and Protein Expression Cell Analysis with AbSeq and WTA

Step 6:

Cell IDs and chain information were obtained from the pipeline output files and VDJ and C gene information were determined for the clonotype of interest.

Cell Index	TCR Alpha Gamma V gene dominant	TCR Alpha Gamma J gene dominant	TCR Alpha Gamma CDR3 translation dominant	TCR Beta Delta V gene dominant	TCR Beta Delta D gene dominant	TCR Beta Delta J gene dominant	TCR Beta Delta C gene dominant	TCR Beta Delta CDR3 translation dominant	TCR Paired Chains	Cell type experimental	High quality cell
236563	TRAV41^*01	TRAJ49^*01	AVRSGGDTGNQFY	TRBV5‑6^*01	TRBD2^*02	TRBJ2‑1^*01	TRBC2	ASSLREYNEQF	TRUE	T_CD8_naive	TRUE
638393	TRAV41^*01	TRAJ49^*01	AVRSGGDTGNQFY	TRBV5‑6^*01	TRBD2^*02	TRBJ2‑1^*01	TRBC2	ASSLREYNEQF	TRUE	T_CD8_naive	TRUE
1789392	TRAV41^*01	TRAJ49^*01	AVRSGGDTGNQFY	TRBV5‑6^*01	TRBD2^*02	TRBJ2‑1^*01	TRBC2	ASSLREYNEQF	TRUE	T_CD8_naive	TRUE
2461787	TRAV41^*01	TRAJ49^*01	AVRSGGDTGNQFY	TRBV5‑6^*01	TRBD2^*02	TRBJ2‑1^*01	TRBC2	ASSLREYNEQF	TRUE	T_CD8_naive	TRUE

Step 7:

Full-length sequence of the clonotype was obtained (nucleotide sequence also available) from the pipeline output.

Cell Index	VDJ Translation Trimmed
236563	KNEVEQSPQNLTAQEGEFITINCSYSVGISALHWLQQHPGGGIVSLFMLSSGKKKHGRLIATINIQEKHSSLHITASHPRDSAVYICAVRSGGDTGNQFYFGTGTSLTVIP
236563	DAGVTQSPTHLIKTRGQQVTLRCSPKSGHDTVSWYQQALGQGPQFIFQYYEEEERQRGNFPDRFSGHQFPNYSSELNVNALLLGDSALYLCASSLREYNEQFFGPGTRLTVL
638393	KNEVEQSPQNLTAQEGEFITINCSYSVGISALHWLQQHPGGGIVSLFMLSSGKKKHGRLIATINIQEKHSSLHITASHPRDSAVYICAVRSGGDTGNQFYFGTGTSLTVIP
638393	DAGVTQSPTHLIKTRGQQVTLRCSPKSGHDTVSWYQQALGQGPQFIFQYYEEEERQRGNFPDRFSGHQFPNYSSELNVNALLLGDSALYLCASSLREYNEQFFGPGTRLTVL
1789392	KNEVEQSPQNLTAQEGEFITINCSYSVGISALHWLQQHPGGGIVSLFMLSSGKKKHGRLIATINIQEKHSSLHITASHPRDSAVYICAVRSGGDTGNQFYFGTGTSLTVIP
1789392	DAGVTQSPTHLIKTRGQQVTLRCSPKSGHDTVSWYQQALGQGPQFIFQYYEEEERQRGNFPDRFSGHQFPNYSSELNVNALLLGDSALYLCASSLREYNEQFFGPGTRLTVL
2461787	KNEVEQSPQNLTAQEGEFITINCSYSVGISALHWLQQHPGGGIVSLFMLSSGKKKHGRLIATINIQEKHSSLHITASHPRDSAVYICAVRSGGDTGNQFYFGTGTSLTVIP
2461787	DAGVTQSPTHLIKTRGQQVTLRCSPKSGHDTVSWYQQALGQGPQFIFQYYEEEERQRGNFPDRFSGHQFPNYSSELNVNALLLGDSALYLCASSLREYNEQFFGPGTRLTVL

FR1 CDR1 FR2 CDR2 FR3 CDR3 FR4

TCR_alpha	KNEVEQSPQNLTAQEGEFITINCSYSVGISALHWLQQHPGGGIVSLFMLSSGK KKHGRLIATINIQEKHSSLHITASHPRDSAVYICAVRSGGDTGNQFYFGTGTSLTVIP
TCR_beta	DAGVTQSPTHLIKTRGQQVTLRCSPKSGHDTVSWYQQALGQGPQFIFQYYEEEERQRGNFPDRFSGHQFPNYSSELNVNALLLGDSALYLCASSLREYNEQFFGPGTRLTVL