Dataset Open Access

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

Alma Andersson

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:

count-matrices.zip - processed count matrices formatted as [n_spots]x[n_genes] and named as [PATIENT][SECTION].tsv.gz. 

images.zip - 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).

spot-selection.zip - 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

meta.zip - 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.

code.zip - a clone of the github repository created (2021-05-12).

Files (1.6 GB)
Name Size
code.zip
md5:e80da8ecf87e46a9915e295a8ac10330 		996.9 MB Download
count-matrices.zip
md5:d0dd522b61892435d21ac437af289ae5 		37.2 MB Download
images.zip
md5:383e23ac398790dbdb408ec7b8b5d3b2 		592.1 MB Download
meta.zip
md5:57d358398d7f8cc1410398aa032ff029 		62.6 kB Download
spot-selections.zip
md5:edd47d57c97d9563ca9f3ccc70767c7b 		212.2 kB Download
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Publication date:
September 16, 2021
DOI:
10.5281/zenodo.4751624

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10.5281/zenodo.4751624

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Keyword(s):
spatial transcriptomics single cell breast cancer her2
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License (for files):
Creative Commons Attribution 4.0 International

Versions

Version 3.0 10.5281/zenodo.4751624 Sep 16, 2021
Version 1.0 10.5281/zenodo.3957257 Jul 23, 2020
Cite all versions? You can cite all versions by using the DOI 10.5281/zenodo.3957256. This DOI represents all versions, and will always resolve to the latest one. Read more.

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