WAT3R

WAT3R processes and analyzes T-cell receptor (TCR) variable regions enriched from 3'-based single-cell RNA sequencing (scRNA-seq) data to reconstruct TRA and TRB clonotypes and link nucleotide and amino-acid sequences to cell barcodes for repertoire and differentiation-state analysis.

Key Features:

• TCR Variable Region Enrichment: Processes cDNA from 3' scRNA-seq to capture and analyze TCR α and β chain variable regions encoded by TRA and TRB genes.
• Clonotype Reconstruction: Links nucleotide and amino-acid sequences of TCRs to cell barcodes to reconstruct T-cell clonotypes alongside associated transcriptomes.
• Specificity and Sensitivity: Detects TCR sequences predominantly in single T cells with low detection rates in non-T-cell populations.
• Clonal Analysis: Enables analysis of TCR clone sizes and associations between clonotypes and differentiation states, for example larger clones in CD8 Memory T cells.

Scientific Applications:

• Adaptive immunity profiling: Characterizes T-cell repertoire diversity and composition from 3' scRNA-seq data to study antigen-specific immune responses.
• Clonotype–state association: Correlates TCR clonotypes with immune cell differentiation states and transcriptional phenotypes.
• Immunotherapy research: Provides repertoire-level information relevant to assessing clonal expansion and potential therapeutic targets.

Methodology:

Processes 3' scRNA-seq cDNA to extract and analyze TRA/TRB variable-region sequences, links sequences to cells via barcodes, and reconstructs clonotypes for repertoire and differentiation-state analysis.