Apoptotic cell exclusion and bias-free single-cell selection are important QC requirements for successful single-cell sequencing applications

Single-cell sequencing experiments are a new mainstay in biology and have been advancing science especially in the biomedical field. The high-pressure to integrate the technology into daily laboratory live requires solid knowledge with respect to potential limitations and precautions to be taken care of before applying it to complex research questions. In the past, we have identified two issues with quality measures neglected by the growing community involving SmartSeq and droplet or micro-well based scRNASeq methods – i) how to ensure that only single-cells are introduced without biasing on light-scattering when handling complex cell mixtures and organ preparations or ii) how best to control for (pro-)apoptotic cell contaminations in single-cell sequencing approaches. Sighting of concurrent literature involving single-cell sequencing technologies revealed that these topics are generally neglected or simply approached in silico but not at the bench before generating single-cell data sets. We fear that those important quality aspects are overlooked due to reduced awareness of their importance for guaranteeing the quality of experiments. In this Cytometry rigour issue, we provide experimentally supported guidance on how to circumvent those critical shortcomings in order to promote a better use of the fantastic single-cell sequencing toolbox in biology.