Additional file 2 of Increased spatial coupling of integrin and collagen IV in the immunoresistant clear-cell renal-cell carcinoma tumor microenvironment

Additional File 2. Tables S1, S2, S3, S4, S5, S6, S7, S8, S9, S10, S11, S12, S13, S14, S15, S16, S17: Table S1. Number of Cells That Passed Quality Control on Primary Tumor FOV. Abbreviation: FOV, fields of view; Table S2. Differentially Expressed Genes Identified From Subclustering InSituType-Assigned T Cells and Mononucleic Phagocytes; Table S3. Differential Gene Expression Using FindMarkers Between Malignant Proximal Tubule and Normal Proximal Tubule Cells. These cells were used for LASSO regression and genes selected by LASSO for final model. Abbreviation: LASSO, least absolute shrinkage and selection operator; Table S4. Abundance Differences for Cell Phenotypes in the Tumor and Stromal FOV of the Cohorts. Positive estimate indicates lower abundance in IO-naïve nonsarcomatoid. Abbreviations: FOV, fields of view; IO, immunotherapy; Table S5. Association of Ripley’s K Between Cohorts in Tumor and Stromal FOV Tissue at a Radius of 150 px (27 µm). Negative-estimate values indicate lower clustering in IO-naïve nonsarcomatoid samples. Abbreviations: FOV, fields of view; IO, immunotherapy; Table S6. Differential Gene Expression of Primary ccRCC Tumor and Stroma Samples Between Cohorts. Abbreviation: ccRCC, clear-cell renal-cell carcinoma; Table S7. Differential Gene Expression for Each Cell Phenotype in Primary-Tumor FOV Between Pre- and Post-IO. Abbreviations: FOV, fields of view; IO, immunotherapy; Table S8. Differential Gene Expression for Each Phenotype on Primary Tumor FOV Before Undergoing IO With and Without Sarcomatoid Features. Abbreviations: FOV, fields of view; IO, immunotherapy; Table S9. Differential Gene Expression in Stromal FOV, Between Pre- and Post-IO Primary Samples. Abbreviations: FOV, fields of view; IO, immunotherapy; Table S10. Differential Gene Expression for Each Phenotype on Primary Stromal FOV Before Undergoing IO With and Without Sarcomatoid Features. Abbreviations: FOV, fields of view; IO, immunotherapy; Table S2. Results of the Spatial Enrichment of Hallmark Gene Sets in All Samples; Table S12. T-Test Results Comparing Bivariate Moran’s I of Ligand/Receptor Pairs From EMT Gene Set in Tumor and Stromal FOV. Abbreviations: EMT, epithelial-mesenchymal transition; FOV, fields of view; Table S13. T-Test Results Comparing Bivariate Moran’s I of Ligand/Receptor Pairs From IL6/JAK/STAT3 Signaling Gene-Set Tumor and Stromal FOV. Abbreviation: FOV, fields of view; Table S14. Comparisons Between ITGAV and COL4A1 Abundance in the Tumor and Stromal Compartments; Table S15. Results of Beta-Binomial Modeling of Phenotypes Between Cohorts of the Validation mIF. Abbreviation: mIF, multiplex immunofluorescence; Table S16. Nanostrisng CosMx SMI Probe Targets; Table S17. Kidney Cell Atlas Phenotype Names Before (InsituType_Manual) and After (Final) Collapsing Similar Cell Types.