Deconvolution of Bulk RNA Seq

Although bulk RNA-Seq samples lack single cell resolution, such samples are easier to collect and process than scRNA-Seq samples, and the large databases of bulk RNA-Seq for different cancer types (e.g. TCGA) can provide more power to analyze the relationships between tumor gene expression programs and clinical covariates (e.g. patient treatment responses or outcomes). scRNA-Seq performed on a sample biologically similar to the bulk RNA-Seq sample may be used to estimate the cell type composition in the bulk RNA-Seq sample, allowing us to combine advantages of both technologies. Although we have not yet systematically applied such methods to tumor samples, we have applied one such deconvolution method, MuSiC, to COVID-19 lung autopsy tissues.