The following folders/files are part of this repository: Folder "rna": contains raw data from the RNA & Protein data set Folder "config": .csv file with all the information on the antibody and RNAScope panel Folder "cp_scripts": contains files for the CellProfiler pipeline used to generate single-cell data Folder "cpout": contains results from the CellProfiler pipeline "*_cellmask.tiff": final cell mask used to generate single-cell data "*_full_spillcor.tiff": full .tiff with all channels after spill-over correction "cell.csv": .csv with the channel intensities for all cells "Experiment.csv": .csv containing CellProfiler settings used to export single-cell data "Image.csv": .csv containing information on all single images "Object relationships.csv": .csv containing all cell-cell interactions Folder "tiffs" "*_full.csv": .csv showing channel/metal order of the _full.tiff file "*_full.tiff: .tiff file with all acquired channels "*_cellmask.tiff": initial cell mask (is different to final cell mask stored in "cpout") "*_tumorMask": channel order, probabilities and mask used to define tumor regions Folder "protein": contains raw data from the Protein data set same folder/file structure as the "rna" folder Folder "exhaustion stain": raw data generated for the validation of the exhaustion phenotype of CXCL13+ CD8+ T cells folders are structured according to the steinbock pipeline Folder "12plex_validation": raw data generated for the validation of the new RNAScope 12-plex system for IMC Folder "HeLa": contains raw data of experiments performed with HeLa cells (influence of antibody incubation, house-keeping gene measurement, etc) Folder "overexpression": contains raw data of experiments with PPIB overexpression in A431 cells to quantify unspecific binding of RNAScope probes