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 project website and our github repository.