Multiplexed Imaging Mass Cytometry of Chemokine Milieus in Metastatic Melanoma - Raw Data

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