[NUCLEUS CAPTURES IMPORTANT GENES]
1. Single cells detect more genes than nuclei but majority of transcripts detected by both.
Genes captured only in cells (ie. cytoplasmic transcripts) are mostly house-keeping genes)
Nuclear genes tend to be good cell type marker genes
2. CAVEAT - Cells have slightly better detection of cell type marker genes which resulted in slightly better cluster separation for two highly similar cell types. Therefore, as the number of nuclei and cells profiled increases, it is possible that finer resolution splits may not be possible with nuclei.
However, there are many benefits to using single nuclei that may outweigh ultimate cell type resolution.