Wei et al. 2024

Processed data for Wei et al. "High-confidence calling of normal epithelial cells allows identification of a novel stem-like cell state in the colorectal cancer microenvironment"

the scanpy object contains raw (cellbender) and normalized counts, two UMAPs for all cells and epithelial cells only, respectively, and the following meta-data columns:

• sample: sample ID
• sample_origin: tumour or normal
• patient: patient ID
• MS_status: MSI or MSS
• n_counts: # of UMIs per cell
• n_genes: # of gnes per cells
• S_score: score for S phase
• G2M_score: score of G2/M phase
• cell_type_coarse: low-resolution cell type annotation (epithelial vs. immune vs. stromal)
• cell_type_fine: high-resolution cell type annotation (by label transfer from Uhlitz et al.)
• CCISM_call: cell assignment by CCISM
• CCISM_score: score from CCISM
• numbat_call: assignment by numbat
• numbat_score: score from numbat
• inferCNV_call:  assignment from inferCNV
• iCMS_call: assignment using iCMS signatures
• consensus_call: numbat/CCISM consensus identity
• cell_type_epi: epithelial cell type (combining TC1-4 from Uhlitz et al., and labeling cells defined here as genomically cancer as Tumour)
• cytotrace_pseudotime: pseudotime from cytotrace
• louvain: louvain clusters for epithelial cells

list of processed data used to create this object

• folder cellranger contains raw feature barcode matrices for single-cell RNAseq data of 10 patients
• folder cellbender contains filtered feature barcode matrices after background removal
• folder WGS contains vcf.gz results from somatic variant calling with mutect2
• folder cellSNP contains `cellsnp-lite` output: counts of total and alternative alleles observed for somatic variants in scRNAseq data; subfolder downsampled contains results after downsampling bam files to 5, 10, 20 or 50% of reads
• folder numbat contains final clone assignments by Numbat