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

in addition, the folder LUNG contains processed data for six lung adenocarcinoma cases from Bischof et al. [doi:10.1038/s41388-021-02054-3.] 

subfolder WGS contains .vcf.gz results from somatic variant calling with mutect2

subfolder cellSNP contains `cellsnp-lite` output: counts of total and alternative alleles observed for somatic variants in scRNAseq data