Question: How does Gene Expression data compare between whole cells and nuclei?
Answer: Nuclei have less mRNA than whole cells, so the total number of genes and UMIs detected may be reduced when profiling gene expression from nuclei versus whole cells. The difference in sensitivity is highly dependent on the sample type. We have observed ~20-40% fewer total genes captured and ~20-60% fewer total UMIs when comparing whole cells to nuclei, and this is highly variable by sample type.
Our internal tests have observed that cell populations recovered between single cell and single nuclei RNA-seq are comparable, and marker expression is maintained. Depending on the sample, the population proportions may differ (i.e., cells in suspension vs. samples requiring harsh dissociation, where sensitive cells may be lost). However, we see similar proportions of cell types recovered when comparing cells vs. nuclei from PBMCs (data below).
In some cases, there are advantages to using single nuclei for RNA-seq, including reducing biases in cell populations caused by cell dissociation, minimizing stress-induced transcriptional artifacts, reducing microfluidic cell capture bias due to cell size, and the potential to capture nascent mRNA for temporal studies. Nuclei also enable single-cell studies of intact frozen whole tissue when isolation of viable whole cells is difficult.
Products: Single Cell Multiome ATAC+GEX, Single Cell Gene Expression