TRAPeS

TRAPeS reconstructs T cell receptor (TCR) sequences from paired-end short-read single-cell RNA-sequencing (scRNA-seq) data to enable analysis of TCR diversity and its relationship to T cell states.

Key Features:

• Short-read paired-end compatibility: Reconstructs TCR sequences from paired-end short-read scRNA-seq libraries.
• Efficiency: Extracts TCR sequence information from short-read scRNA-seq libraries to enable analysis of larger cell numbers.
• Accuracy: Demonstrates high accuracy in reconstructing TCR sequences, surpassing existing approaches.
• Sensitivity: Offers greater sensitivity, enabling detection of TCRs across more cells.
• Integration with transcriptome analysis: Pairs reconstructed TCRs with transcriptome profiles to correlate TCR features with cellular phenotypes.
• Applicability: Has been applied to CD8+ T cell datasets from humans and mice.

Scientific Applications:

• CD8+ T cell repertoire analysis: Used to study heterogeneity in CD8+ T cell responses in humans and mice.
• Virus-specific T cell studies (Yellow Fever Virus): Applied to CD8+ T cells specific for Yellow Fever Virus (YFV) epitopes by coupling TCR reconstruction with transcriptome analysis.
• CDR3 and germline divergence analysis across differentiation states: Enabled identification that naive-like memory populations have longer CDR3 regions and greater divergence from germline sequences compared to effector-memory phenotype cells, linking TCR usage to differentiation state.

Methodology:

Reconstructs TCR sequences by extracting TCR sequence information from paired-end short-read scRNA-seq libraries and pairs reconstructed receptors with transcriptome data for downstream correlation analyses.