Single-cell immune profiling via hybridisation-capture enrichment and Oxford Nanopore sequencing

This poster presents a hybridisation-capture workflow for enriching and sequencing full-length T-cell receptor (TCR) transcripts on the Oxford Nanopore PromethION device. In a human PBMC single-cell cDNA library (~5,000 cells), a compact hybridisation probe panel increases TCR raw read count per PromethION Flow Cell by >1,000-fold and recovers more unique functional clonotypes. Enriched TCR reads support full-length paired-chain reconstruction and clonotype-network analysis at single-cell level. We map the expanded T-cell clones onto the transcriptomic landscape, where gene expression analysis identifies a cytotoxic CD8+/TEMRA (terminally differentiated effector memory cells re-expressing CD45RA) programme. Full-length Oxford Nanopore reads also reveal differential CD45 (PTPRC) isoform usage between expanded T-cell clones and singletons.

Download this poster to discover:

• How hybridisation capture enriches full-length TCR transcripts directly from a 10x Genomics single-cell 3’ cDNA library
• Sequencing of the enriched library on a PromethION Flow Cell results in >1,000-fold more TCR raw reads, improving chain pairing and clonotype detection
• Clonotype recovery remains stable after substantial data subsampling, supporting sample multiplexing on a single PromethION Flow Cell
• Oxford Nanopore full-length TCR cDNA reads resolve V(D)J and constant-region assignments for TCR clonotype-network analysis
• Expanded clonotypes are mapped to transcriptomic landscape, unveiling cytotoxic CD8+ and TEMRA programmes in the expanded T-cell clones
• Oxford Nanopore full-length TCR cDNA reads detect differential CD45 (PTPRC) isoform usage between the expanded T-cell clones and singletons