Question: Are 10x Single Cell gene expression libraries strand-specific?
Answer: Yes, 10x Single Cell solutions are strand-specific. Cell Ranger 'Count' counts sense-strand reads only. There is a possibility of legitimate antisense transcripts but they are unlikely to follow the same exon structure as the sense transcripts. We do include a measurement of the levels of antisense transcripts detected in Cell Ranger, which typically hovers around 1% of mapped reads. Those antisense transcripts won't contribute any UMI counts since Cell Ranger does not count UMIs from antisense reads.
Products: Single Cell Gene Expression, SIngle Cell Immune Profiling