Question about Blocker in Paired-seq

[minglu-xie]

Hello Dr. Chen, Thank you for sharing detailed information about single-cell sequencing technologies! I’ve been studying the paired-seq method and have a question regarding blocker design. In the Paired-seq protocol, why are linker-specific blockers essential? Could you clarify their role in preventing unwanted ligation events (e.g., linker self-ligation or dimerization), and how their absence might compromise library integrity? My understanding is that sticky-end ligation is inherently specific, so I’m unclear why blockers are critical here.

Thank you for your time and help.

Best, Minglu