Published September 16, 2021 | Version 3.0
Dataset Open

Spatial deconvolution of HER2-positive Breast cancer delineates tumor-associated cell type interactions

  • 1. Royal Institute of Technology (KTH) and Science for Life Laboratory (SciLifeLab)


Processed count matrices, brightfield HE-images (plain and annotated), spot selection files and meta-data associated with the manuscript "Spatial Deconvolution of HER2-positive Breast Tumors Reveals Novel Intercellular Relationships".


The content of the files are: - processed count matrices formatted as [n_spots]x[n_genes] and named as [PATIENT][SECTION].tsv.gz. - contains two folders HE and annotation, the former holds the HE-images for respective section named as [PATIENT][SECTION].jpg, the latter holds the annotated (by the pathologist) images named by patient (only one section from each patient was annotated). - contains .tsv files to map array coordinates to pixel coordinates, allowing the spots and their associated expression values to be visualized jointly. Files are named as [PATIENT][SECTION]_selection.tsv.gz - for all annotated sections, these files are similar to the spot-selection files, but also includes the label of each spot (e.g., breast glands, connective tissue, etc.).

All files are password protected (encrypted), use the passeword zNLXkYk3Q9znUseS do decrypt the data. - a clone of the github repository created (2021-05-12).


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Is source of
Preprint: 10.1101/2020.07.14.200600 (DOI)