Plate-based SMART-Seq single-cell RNA-seq of colorectal cancer patient tumor-resident and circulating 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 plate-based SMART-Seq single-cell RNA-seq libraries from de-identified colorectal cancer patient primary tumor and peripheral blood specimens enriched for tumor-resident and circulating hybrid cells, together with tumor and immune control cells. Fresh colorectal cancer primary tumors and matched peripheral blood specimens were processed to single-cell suspensions. Hybrid cells were FACS-isolated based on EpCAM and/or ECAD with CD45 co-expression. Tumor controls (EpCAM and/or ECAD positive, CD45 negative) and immune controls (CD45 positive) were also collected. Single cells were sorted into 96-well plates containing lysis buffer and profiled using Takara SMART-Seq mRNA Single Cell LP. Methods describe 3 patients total comprising 2 tumor specimens and 4 peripheral blood specimens.