Extended Data Fig. 2: Workflow to test deconvolution performance of CIBERSORTx.
From: An atlas of genetic effects on cellular composition of the tumor microenvironment
Public single-cell RNA sequencing (scRNA-seq) data from 23 tumor and adjacent normal tissues of patients with colorectal cancer (CRC) were applied to build a signature matrix, which could distinguish the abundance of 25 cell subtypes. Additionally, we collected 20 samples from 18 CRC patients to conduct both bulk RNA-seq and scRNA-seq. Using the signature matrix generated above as the reference, we tested the concordance between the deconvolution result estimated by CIBERSORTx for our bulk RNA-seq and ground truth cell proportions measured by scRNA-seq.
