Supplementary material for Integrative spatial omics reveals distinct tumor-promoting multicellular niches and immunosuppressive mechanisms in Black American and White American patients with TNBC (Imaging Mass Cytometry portion)

Main article: Integrative spatial omics reveals distinct tumor-promoting multicellular niches and immunosuppressive mechanisms in Black American and White American patients with TNBC There are three cohorts of IMC data: BSW-Discovery, BSW-Validation, and Roswell Park. Raw Data Imaging Mass Cytometry (IMC): BSW-Discovery IMC data (MCD files): TMA-1.mcd, TMA-2.mcd, TMA-4.mcd, TMA-6.mcd, TMA-7.mcd, TMA-8.mcd, TMA-9.mcd, TMA-10.mcd, where TMAs 7, 8, 10, 4 denote White American, and TMAs 1, 2, 6, 9 denote Black American. BSW-Validation IMC data (MCD files): T1-EA1.mcd, T2-EA2.mcd, T5-EA5.mcd, T6-EA6.mcd, T7-EA7.mcd, T9-AA1.mcd, T10-AA2.mcd, T14-AA6.mcd, T16-AA8.mcd, T17-AA9.mcd, where AA denotes Black American and EA denotes White American. Roswell Park IMC data (MCD files): B1Ca57b.mcd (all Black American), B1Ca71b.mcd (all White American) Roswell.excluded.ROI.txt: list of ROIs being excluded and their reasons. Important as this Roswell TMA contains non-breast control tissues. Processed Data Imaging Mass Cytometry (IMC): roswell_deepCell.RDS: A Giotto object containing the raw expression, scaled expression, and cell centroid. roswell.processing.R: An R script showing how the roswell_deepCell.RDS is derived roswell.raw.expr.txt: Roswell raw cell-by-protein intensity matrix quantified by Steinbock roswell.cell.centroid.txt: X- and Y-coordinates of cells in Roswell, quantified by Steinbock roswell_panel.csv: Panel.csv file used for cell segmentation by Steinbock bsw_validation_deepCell.RDS: A Giotto object containing the raw expression, scaled expression, and cell centroid. bsw_validation_processing.R: An R script showing how the bsw_validation_deepCell.RDS is derived bsw_validation_raw_expr.txt: BSW validation raw cell-by-protein intensity matrix quantified by Steinbock bsw_validation_cell_centroid.txt: X- and Y-coordinates of cells in BSW validation, quantified by Steinbock bsw_validation_panel.csv: Panel.csv file used for cell segmentation by Steinbock bsw_discovery_cytof_test.RData: A Giotto object containing the scaled expression and cell centroid for BSW-Discovery cohort bsw_discovery_cell_centroid.txt: X- and Y-coordinates of cells in BSW-discovery bsw_discovery_zscored_expr.txt: Z-scored cell-by-protein intensity matrix quantified by Histocat bsw_discovery_processing.R: processing script Data processing information: BSW-Discovery: Segmentation and quantification was done using Histocat. BSW-Validation & Roswell Park: Segmentation and quantification was done using Steinbock pipeline, choosing DeepCell as segmentation tool. Other File list: GSM_giotto_processed.tar.gz: Bassiouni et al Cancer Research TNBC ST datasets, Giotto normalized and processed cytof_test.aug13.RData: An RData object for the BSW-discovery IMC dataset, used for generating Figure 1e, Figure 1f, i.e., the clustering analysis. Tutorial referring to this analysis is available at: https://qianzhulab.github.io/suppl/TNBC.scripts/table_of_content.html. cytof_test.RData: An RData object for the BSW-discovery IMC dataset, used for generating Figure 1d, i.e., the clustering analysis. Tutorial referring to this analysis is available at: https://qianzhulab.github.io/suppl/TNBC.scripts/table_of_content.html.