10x Genomics single-cell RNA-seq of colorectal cancer patient tumor and peripheral blood specimens enriched for hybrid cells

This study profiles tumor-macrophage hybrid cells in colorectal cancer using single-cell transcriptomic and epigenomic approaches. Fusion-derived hybrid cells were generated by co-culture of MC38-H2B-RFP colorectal cancer cells with beta-actin-GFP bone marrow-derived macrophages, and patient-derived hybrid cells were isolated from primary colorectal tumors and peripheral blood by fluorescence-activated cell sorting based on co-expression of epithelial (EpCAM and/or ECAD) and immune (CD45) markers. The study compares hybrid cells with parental tumor and immune controls and includes artificial macrophage-tumor doublets generated on the ICELL8 platform to distinguish bona fide hybrids from technical doublets. This submission contains 10x Genomics single-cell RNA-seq libraries from de-identified colorectal cancer patient tumor and peripheral blood specimens in which pooled cells were enriched for hybrid cells to capture the surrounding cellular landscape. A subset of colorectal cancer patient primary tumor and peripheral blood specimens (n=3) with sufficient hybrid cell yield was profiled by 10x Genomics single-cell RNA-seq (in supplement to plate-based scRNA using SMART seq of isolated hybrid cells). Pooled non-hybrid primary tumor or peripheral blood cells were spiked with an enrichment of EpCAM and/or ECAD positive and CD45 positive hybrid cells. Nuclei were isolated and processed using the 10x Genomics Single Cell 3' Gene Expression kit.