Question: When is deeper sequencing needed for nuclei data?
Answer: Whether there is a need for more data depends on the research question. This can depend on a few reasons such as,
- Biological variability of species and RNA content of tissues (eg: total RNAse, necrotic tumors),
- Variable composition of regions within a tissue or biopsy,
- Storage conditions of different tissue types
Shown below (Fig 1) is the data yield (Fraction of Reads in cells) and complexity and performance (Reads mapped confidently to transcriptome) for some complex tissues (e.g. human tumors) that are complex for many reasons. Despite less-than-ideal metrics, clustering is distinct, and unique cell types are found in each sample (Fig 2).
Related KB articles: Is it required to sequence more for new nuclei protocol compared to cells?
Products: Single Cell Gene Expression, Single Cell ATAC, Single Cell Multiome ATAC + Gene Expression