Question: Why do I see big fragments (2,000- 9,000 bp) after post-target enrichment QC?
Answer: The HMW products in the post-target enrichment QC are non-specific background products that are generated as a result of performing two enrichment reactions for TCRs from the total transcriptome. For the samples we have tested in-house, the high molecular weight product does not affect application performance as long as the library is sequenced to our minimum recommended depth of 5000 read-pairs per cell.
Representative Enriched TCR Trace
These peaks are usually more prevalent in TCR enriched samples than Ig enriched samples because of the lower TRA/TRB expression compared to IGH/IGK/IGL. They are also more prevalent when the percentage of B/T cells is low. We have optimized the double-sided SPRI step after the second target enrichment in the protocol to remove some of the large molecular weight product without losing an excessive amount of on-target product.
Products: Single Cell Immune Profiling Solution