Supplementary Materiel to: Tracing colorectal malignancy transformation from cell to tissue scale

WTx CosMx SMI data - results. basenames denote section identifiers(110, 120, 210, 221, 222, 231, 232, 242) .rds files contain SingleCellExperiment objects (R) .h5ad files contain AnnData objects (Python) .zip archives contain alabaster file artifacts metadata thresholds employed during quality control th_fc - false codes th_np - negative probes th_n - total RNA counts th_m - detected RNA species th_d - distance to FOV border (px) alternative experiments AUCell - gene set signature scores COMMOT - cell-cell communication scores, including separate assays for "sender" and "receiver" signals reduced dimensions two slots containing principal components (PCs)based on different feature selections (see next point) "filtered" - all comparments (based on "all" features) "epithelia" - only epithelial cells (based on "epi" features) gene metadata logical flags indicating wether or not features were used for processing (clustering, dimension reduction) all = used for ist/lv1 and "filtered" PCs epi/imm/str = used for jst/lv2,epi = used for "epithelia" PCs cell metadata fil - logical flag indicating whether or not a cell passed quality control typ - histopathological domain annotation roi - region of interest BV = blood vessel, LI = lymphovascular invasion RT/RC/TT/TC = transition crypt between domains i/jst - low-/high-resolution cluster assignments lv1 - annotation into epi(thelia), imm(une), str(omal) compartment lv2 - annotation into 43 subpopulations ctx - spatial niche/context assignment (N1-15) trj - pseudotime from epithelial trajectory inference snPATHO-seq data flex-raw/-fil.zip (un)filtered cellranger outputs including, for each sample,barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz files flex-pbs.zip reference profiles used for InSituType clustering, namely: pbs-lv1.rds - derived from low-res. annotations across all compartments pbs-lv2,epi/imm/str.rds - derived from compartment-wise high-res. annotations