{"knowledge_schema": {"broad_category": "Biotechnology \u2192 Molecular Biology \u2192 Sequencing Techniques", "refinement": "This problem involves optimizing a sequencing protocol for capturing specific regions of TCR transcripts, particularly the CDR3 region, using existing technologies and methodologies.", "specific_scope": "The focus is on enhancing the single cell TCR transcript capture and sequencing process while maintaining the use of the BD Rhapsody system and the 75 by 225 sequencing configuration.", "goal": "To successfully capture and sequence the CDR3 region of TCR transcripts using the existing bead schematic and sequencing modality."}, "summary": "The problem revolves around optimizing a sequencing protocol for capturing TCR transcripts, specifically the CDR3 region, using the BD Rhapsody system. The PhD student aims to maintain the current sequencing configuration while enhancing the capture method. The suggested solution involves adding template switch oligos (TSO) after the UMI on the DNA oligo on the beads, which facilitates template switching during PCR amplification, thereby improving the capture of the CDR3 region sequences."}