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