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Published July 31, 2025 | Version v1
Dataset Open

Data from "Single-cell integration and multi-modal profiling reveals phenotypes and spatial organization of neutrophils in colorectal cancer"

Authors/Creators

  • 1. Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria
  • 2. Institute of Experimental Immunology, University of Zurich, Switzerland
  • 3. Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center
  • 4. Department of Visceral, Transplant and Thoracic Surgery, Medical University Innsbruck, Austria
  • 5. Innpath, Tirol Kliniken, Medical University Innsbruck, Austria
  • 6. Tyrolpath Obrist Brunhuber GmbH, Zams, Austria
  • 7. Institute of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, Austria
  • 8. Department of Therapeutic Radiology and Oncology, Medical University Innsbruck, Austria
  • 9. Department of Molecular Life Sciences, University of Zürich, Switzerland
  • 10. Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
  • 11. Boehringer Ingelheim International Pharma GmbH & Co KG, Biberach, Germany
  • 12. Department of Dermatology, Venereology and Allergology, Medical University of Innsbruck, Austria
  • 13. Senckenberg Institute of Pathology, Goethe University Frankfurt, Germany
  • 14. University Cancer Center Frankfurt (UCT), Germany
  • 15. Senckenberg Institute of Pathology, Goethe University Frankfurt, GermanySenckenberg Institute of Pathology, Goethe University Frankfurt, Germany
  • 16. Translational Cancer Research and Institute of Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine & Health, Technical University of Munich, Germany
  • 17. Institute of Pathology, Paracelsus Medical University, Salzburg, Austria
  • 18. Department of Internal Medicine III, Paracelsus Medical University, Salzburg, Austria
  • 19. Austrian Breast & Colorectal Cancer Study Group (ABCSG), Vienna, Austria
  • 20. Department of Pathology, Leiden University Medical Center, The Netherlands
  • 21. Comprehensive Cancer Center Zürich, Zürich, Switzerland

Description

This archive provides all datasets needed to reproduce the single‐cell data integration detailed in the paper

Single-cell integration and multi-modal profiling reveals phenotypes and spatial organization of neutrophils in colorectal cancer

DOI: 10.1101/2024.08.26.609563


The archive comprises the following files:

  • MUI_Innsbruck-adata.h5ad: In-house scRNA-seq dataset from CRC cohort I (n = 12) comprising matched peripheral blood, adjacent normal, and tumor samples generated using the BD Rhapsody platform.
  • input_datasets.tar.xz: Preprocessed input datasets in .h5ad format required to build the CRC scRNA-seq atlas.
  • crc_atlas_scanvi_model.tar.xz: Pretrained scArches reference model and matching .h5ad file (highly variable genes only), enabling projection of external data onto the CRC atlas.
  • downstream_analyses_de_analysis.tar.xz: DESeq2-based differential expression analyses on pseudobulked data by cell type for various matched comparisons within the CRC atlas. Includes RDS files, result TSV tables, and short summaries for each comparison.

The CRC atlas is publicly available for download and interactive exploration through a cell-x-gene instance with standardized metadata, which allows custom analyses of the atlas. For more information, check out the

Files

Files (49.3 GB)

Name Size Download all
md5:da056822ea2dcc3a6d2c974f7767177f
7.5 GB Download
md5:8b74a61fc648493ff2c8f2da0c9bb97f
12.0 GB Download
md5:6d73a9c6d9246970e1a02dc39265dd95
27.6 GB Download
md5:4bbe1687d323c735512223df983269e5
2.2 GB Download

Additional details

Related works

Is published in
10.1101/2024.08.26.609563v3 (DOI)

Funding

European Commission
EPIC - Enabling Precision Immuno-oncology in Colorectal cancer 786295
FWF Austrian Science Fund
10.55776/DOC82

Software

Repository URL
https://github.com/icbi-lab/crc-atlas