scRNAseq preprocessing, QC filtering and clustering
ADHESION
CellRanger v.6.0.2 was used to align reads to the GRCh38 human genome reference and aggregate all samples into a single feature-barcode matrix. Depth normalization was turned off during the aggregation. Starting with the filtered feature-barcode matrix, cells with gene counts of <200, mitochondrial gene levels of >50% or scrublet-based doublet scores of >0.3 were filtered out, keeping ~90% of cells. Leiden clustering was performed in Scanpy and clusters were manually annotated for major cell types using canonical markers such as epithelial cell adhesion molecule for epithelial cells.