Robustness of Single-cell RNA-Seq for Identifying Differentially Expressed Genes

We found that single-cell RNA-seq (scRNA-seq)dataneeded to have2,000or more cellsin a cluster to identify the majority of differentially expressed genes (DEGs) with modest differences, while as few as 50-100cells weresufficient for identifying the majority of DEGs withextremely small p values or high abundance.The findings provide a quantitativereference for designing and interpreting studies that usescRNA-seq datato identify DEGs. We performed scRNA-seq and poly(A)-dependent bulk RNA-seq in comparable aliquots of human induced pluripotent stem cells (iPSC)-derived, purifiedvascular endothelial and smooth muscle cells.