Fig. 1: Framework for in silico cell enumeration and purification. | Nature Biotechnology

Fig. 1: Framework for in silico cell enumeration and purification.

From: Determining cell type abundance and expression from bulk tissues with digital cytometry

Fig. 1

A typical CIBERSORTx workflow involves a serial approach, in which molecular profiles of cell subsets are first obtained from a small collection of tissue samples and then repeatedly used to perform systematic analyses of cellular abundance and gene expression signatures from bulk tissue transcriptomes. This process involves: (1) transcriptome profiling of single cells or sorted cell subpopulations to define a signature matrix consisting of barcode genes that can discriminate each cell subset of interest in a given tissue type; (2) applying the signature matrix to bulk tissue RNA profiles in order to infer cell type proportions; (3) representative cell type expression signatures; and (4) purifying multiple transcriptomes for each cell type from a cohort of related tissue samples. Using metastatic melanomas as an example, Fig. 6 illustrates the application of each step.