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_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 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. If you want to download the atlas to perform you own analyses, please refer to the CZI Cell-x-gene portal. From there, you can download h5ad (scverse) and rds (Seurat) files with standardized metadata.