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Published May 10, 2022 | Version 2022.05.10
Journal article Open

High-resolution single-cell atlas reveals diversity and plasticity of tumor-associated neutrophils in non-small cell lung cancer

Authors/Creators

  • 1. Department of Internal Medicine V (Haematology & Oncology), Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck (MUI), Innsbruck, Austria
  • 2. Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innrain 80, 6020 Innsbruck, Austria
  • 3. Tyrolpath Obrist Brunhuber GmbH, Zams, Austria
  • 4. Department of Visceral, Transplant and Thoracic Surgery, Medical University Innsbruck, Anichstrasse 35, 6020, Innsbruck, Austria
  • 5. Institute of Molecular Biology, Technikerstrasse 25, University of Innsbruck, Austria

Description

This archive contains all data required to reproduce the single-cell data integration and analysis for the paper

High-resolution single-cell atlas reveals diversity and plasticity of tissue-resident neutrophils in non-small cell lung cancer

(https://doi.org/10.1101/2022.05.09.491204 )

In particular, it contains the following files:

  • build_atlas_results.tar.xz contains all intermediate result of the first part of the workflow (data integration and annotation). It is also required to run the second part of the workflow without re-running the data integration steps.
  • containers.tar.xz contains singularity containers that package all software dependencies required to reproduce the analyses
  • core_atlas.h5ad.gz is the main AnnData (h5ad) file of the core atlas
  • core_atlas_scanvi_model.tar.gz contains a scArches model and the corresponding h5ad file (with only highly variable genes). You can use this to project your own data onto the atlas with scArches
  • downstream_anslysis_results.tar.xz contains the results from the second part of the workflow, including an executed HTML version of all jupyter and rmarkdown notebooks that were used to derive the figures from the paper
  • extended_atlas.h5ad.gz is the main AnnData (h5ad) object of the extended atlas. You probably want to use this object for any further analysis.
  • input_data.tar.xz contains the preprocessed input data (e.g. h5ad files for each individual dataset). It is required to run the first part of the analysis workflow.

Files

Files (124.5 GB)

Name Size Download all
md5:723ef242c99d4772bb9ff1a3441b6b1f
56.3 GB Download
md5:8c1b0e0f434e6d5fd3c543afc4c8e1d6
17.9 GB Download
md5:d654d68e315e8e1fb92fa1421ae02d9d
6.4 GB Download
md5:459c8584f5107462f6e43e34aaa6c484
4.2 GB Download
md5:160048abec557efbe4a13c42964d4272
20.6 GB Download
md5:9bcefc27986d351e0b07738ad498b7a5
8.0 GB Download
md5:b344dfe85fdd7c1bebff83e6ae3fb80e
11.1 GB Download

Additional details

Related works

Is published in
Preprint: 10.1101/2022.05.09.491204 (DOI)

Funding

European Commission
EPIC - Enabling Precision Immuno-oncology in Colorectal cancer 786295