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

Zenodo (CERN European Organization for Nuclear Research)

Abstract

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: 10.1016/j.ccell.2025.12.003 The archive comprises the following files: crc_atlas_models.tar.xz: Trained scVI (unsupervised) and scANVI (cell-type aware) models for the global CRC atlas and tissue-specific subsets (normal, tumor, metastasis). Enable projection of external data onto the CRC atlas, expecting Ensembl IDs (e.g. ENSG00000105329) as var_names. Trained with scvi-tools v1.4.1. crc_atlas_models_minified.tar.xz: Lightweight minified models that only retain the weights necessary for downstream inference. Optimized for scArches workflows, including reference mapping and automated cell-type label transfer. 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. downstream_analyses.tar.xz: Fully executed HTML notebooks and corresponding analysis outputs used to generate the main single-cell atlas figures in the paper. 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. remove_ambient_rna.tar.xz: A subset of 24 .h5ad datasets with scAR-denoised counts. The original unfiltered count matrices are available in input_datasets.tar.xz. containers.tar.xz: Singularity .sif images encapsulating all software dependencies required to fully reproduce the workflow. shears_tutorial.tar.xz: Input datasets in .h5ad format required to execute the shears tutorial. Includes the single-cell CRC reference and combined bulk clinical cohorts to demonstrate both the quantitative deconvolution and the single-cell phenotypic modeling (e.g., mapping clinical outcomes to single cells) introduced in this paper. 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 project website and our github repository.

Authors 46

1. Valentin Marteau

   Innsbruck Medical University · Universität Innsbruck

   Affiliation as printed

   Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria

2. Niloofar Nemati

   Innsbruck Medical University · Universität Innsbruck

   Affiliation as printed

   Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria

3. Kristina Handler

   University of Zurich

   Affiliation as printed

   Institute of Experimental Immunology, University of Zurich, Switzerland

4. Deeksha Raju

   University of Zurich

   Affiliation as printed

   Institute of Experimental Immunology, University of Zurich, Switzerland

5. Alexander Kirchmair

   Innsbruck Medical University · Universität Innsbruck

   Affiliation as printed

   Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria

6. Dietmar Rieder

   Innsbruck Medical University · Universität Innsbruck

   Affiliation as printed

   Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria

7. Erika Kvalem Soto

   Innsbruck Medical University · Universität Innsbruck

   Affiliation as printed

   Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria

8. Georgios Fotakis

   Innsbruck Medical University · Universität Innsbruck

   Affiliation as printed

   Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria

9. Sandro Carollo

   Innsbruck Medical University · Universität Innsbruck

   Affiliation as printed

   Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria

10. Nina Boeck

    Innsbruck Medical University · Universität Innsbruck

    Affiliation as printed

    Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria

11. Alessia Rossi

    Innsbruck Medical University · Universität Innsbruck

    Affiliation as printed

    Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria

12. Sophia Daum
    Affiliation as printed

    Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center

13. Alexandra Scheiber
    Affiliation as printed

    Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center

14. Arno Amann
    Affiliation as printed

    Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center

15. Andreas Seeber
    Affiliation as printed

    Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center

16. Elisabeth Gasser

    Innsbruck Medical University · Universität Innsbruck

    Affiliation as printed

    Department of Visceral, Transplant and Thoracic Surgery, Medical University Innsbruck, Austria

17. Steffen Ormanns

    Innsbruck Medical University · Tirol Kliniken

    Affiliation as printed

    Innpath, Tirol Kliniken, Medical University Innsbruck, Austria

18. Michael Günther

    Innsbruck Medical University · Tirol Kliniken

    Affiliation as printed

    Innpath, Tirol Kliniken, Medical University Innsbruck, Austria

19. Agnieszka Martowicz
    Affiliation as printed

    Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center

    Tyrolpath Obrist Brunhuber GmbH, Zams, Austria

20. Zuzana Loncová

    Innsbruck Medical University · Universität Innsbruck

    Affiliation as printed

    Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria

    Institute of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, Austria

21. Giorgia Lamberti

    Innsbruck Medical University · Universität Innsbruck

    Affiliation as printed

    Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria

22. Anne Krogsdam

    Innsbruck Medical University · Universität Innsbruck

    Affiliation as printed

    Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria

23. Michela Carlet

    Innsbruck Medical University · Universität Innsbruck

    Affiliation as printed

    Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria

24. Lena Horvath
    Affiliation as printed

    Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center

25. Marie Theres Eling

    Innsbruck Medical University · Universität Innsbruck

    Affiliation as printed

    Department of Therapeutic Radiology and Oncology, Medical University Innsbruck, Austria

26. Hassan Fazilaty

    University of Zurich

    Affiliation as printed

    Department of Molecular Life Sciences, University of Zürich, Switzerland

27. Tomáš Valenta

    University of Zurich · Czech Academy of Sciences, Institute of Molecular Genetics

    Affiliation as printed

    Department of Molecular Life Sciences, University of Zürich, Switzerland

    Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic

28. Gregor Sturm

    Boehringer Ingelheim (Germany) · Innsbruck Medical University · Universität Innsbruck

    Affiliation as printed

    Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria

    Boehringer Ingelheim International Pharma GmbH & Co KG, Biberach, Germany

29. Sieghart Sopper
    Affiliation as printed

    Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center

30. Andreas Pircher
    Affiliation as printed

    Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center

31. Patrizia Stoitzner

    Innsbruck Medical University · Universität Innsbruck

    Affiliation as printed

    Department of Dermatology, Venereology and Allergology, Medical University of Innsbruck, Austria

32. PJ Wild

    Goethe University Frankfurt

    Affiliation as printed

    Senckenberg Institute of Pathology, Goethe University Frankfurt, Germany

    University Cancer Center Frankfurt (UCT), Germany

33. Patrick Welker

    Goethe University Frankfurt

    Affiliation as printed

    Senckenberg Institute of Pathology, Goethe University Frankfurt, Germany

34. Pascal J. May

    Goethe University Frankfurt

    Affiliation as printed

    Senckenberg Institute of Pathology, Goethe University Frankfurt, GermanySenckenberg Institute of Pathology, Goethe University Frankfurt, Germany

35. Paul K. Ziegler

    Goethe University Frankfurt

    Affiliation as printed

    Senckenberg Institute of Pathology, Goethe University Frankfurt, Germany

    University Cancer Center Frankfurt (UCT), Germany

36. Markus Tschurtschenthaler

    TUM Klinikum · Technical University of Munich

    Affiliation as printed

    Translational Cancer Research and Institute of Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine & Health, Technical University of Munich, Germany

37. Daniel Neureiter

    Paracelsus Medical University

    Affiliation as printed

    Institute of Pathology, Paracelsus Medical University, Salzburg, Austria

38. Florian Huemer

    Paracelsus Medical University

    Affiliation as printed

    Department of Internal Medicine III, Paracelsus Medical University, Salzburg, Austria

39. Richard Greil

    Paracelsus Medical University

    Affiliation as printed

    Department of Internal Medicine III, Paracelsus Medical University, Salzburg, Austria

40. Lukas Weiss

    Paracelsus Medical University · Austrian Breast & Colorectal Cancer Study Group

    Affiliation as printed

    Department of Internal Medicine III, Paracelsus Medical University, Salzburg, Austria

    Austrian Breast & Colorectal Cancer Study Group (ABCSG), Vienna, Austria

41. Marieke E. Ijsselsteijn Aachen Department of Pathology, Leiden University Medical Centre

    Leiden University · Leiden University Medical Center

    Affiliation as printed

    Department of Pathology, Leiden University Medical Center, The Netherlands

42. Noel F.C.C. de Miranda Aachen Department of Pathology, Leiden University Medical Centre

    Leiden University · Leiden University Medical Center

    Affiliation as printed

    Department of Pathology, Leiden University Medical Center, The Netherlands

43. Dominik Wolf
    Affiliation as printed

    Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center

44. Isabelle Catherine Arnold

    University of Zurich

    Affiliation as printed

    Institute of Experimental Immunology, University of Zurich, Switzerland

    Comprehensive Cancer Center Zürich, Zürich, Switzerland

45. Stefan Salcher
    Affiliation as printed

    Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center

46. Zlatko Trajanoski

    Innsbruck Medical University · Universität Innsbruck

    Affiliation as printed

    Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria