Question: Why is the distribution of fragments after amplification different between T and B cells?
Answer: Ig transcripts from B cells are enriched by primers amplifying 5 different heavy chain isotypes and 2 light chains. TCR transcripts from T cells are enriched by primers amplifying one alpha and one beta chain. Due to the different isoform sizes, the cDNA profiles on the Bioanalyzer will look very different between T and B V(D)J-enriched libraries. Examples of these profiles can be seen in QC sections of the V(D)J User Guide: