Single cell 3' RNA sequencing of 6 Belgian colorectal cancer patients

For the understanding of intrinsic cancer cell signatures and the surrounding microenvironment, we provide single-cell 3’ RNA sequencing data on 27,414 cells from 6 CRC patients in core and border tumor regions, as well as in matched normal mucosa. Analysis of primary colorectal cancer and normal mucosa samples depicts a comprehensive cellular landscape of colorectal cancer and potential cellular interactions, which would be a valuable resource for the development of therapeutic strategies. Single-cell 3' mRNA sequencing data were obtained from 6 Belgian patients in core and border tumor regions, as well as in matched normal mucosa. To remove low-quality cells, we applied filtering criteria using nUMI, nGene and percent of mitochondrial genes. 29,003 cells have passed the criteria. To eliminate cells of an ambiguous identity, we combined the Seurat multiCCA and RCA pipelines for initial clustering and cell type identification, and removed discordant cells from 2 methods. After defining the global cell type, cells with a number of genes exceeding the outliers were removed to eliminate potential doublets. 27,414 cells have passed the final criteria. Raw data was deposited at ArrayExpress, accession number : E-MTAB-8410