Healthy Vital Tissue Atlas data for CAR-Machine pipeline

Healthy Vital Tissue Atlas compiled for CAR-T identification pipeline project. 1. Files: File Name Description hema_genes.csv Feature names for the hematopoietic subset. hema_obs.csv Cell metadata for the hematopoietic subset. hema_sparse_matrix.p Sparse expression matrix (pickle format) for hematopoietic subset. Log-transformed counts (computed with scanpy normalize_total, log1p functions). hvta_celltype_weights.csv Example weights for HVTA cell-types. hvta_celltypes_category.csv Broad categories for cell-types in HVTA. hvta_tissue_weights.csv Example weights for HVTA tissues. nonhema_genes.csv Feature names for the non-hematopoietic subset. nonhema_obs.csv Cell metadata for the non-hematopoietic subset. nonhema_sparse_matrix.p Sparse expression matrix (pickle format) for non-hematopoietic subset. Log-transformed counts (computed with scanpy normalize_total, log1p functions). 2. Made up of 29 tissue types, encompassing over 1.5 million cells, and retrieved from the following 18 sources: Kim, N. et al. Single-cell RNA sequencing demonstrates the molecular and cellular reprogramming of metastatic lung adenocarcinoma. Nature Communications 11, 2285, doi:10.1038/s41467-020-16164-1 (2020). Eraslan, G. et al. Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function. Science 376, eabl4290, doi:doi:10.1126/science.abl4290 (2022). Han, X. et al. Construction of a human cell landscape at single-cell level. Nature 581, 303-309, doi:10.1038/s41586-020-2157-4 (2020). Habib, N. et al. Massively parallel single-nucleus RNA-seq with DroNc-seq. Nature Methods 14, 955-958, doi:10.1038/nmeth.4407 (2017). Regev, A. et al. The Human Cell Atlas. eLife 6, e27041, doi:10.7554/eLife.27041 (2017). Madissoon, E. et al. scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation. Genome Biology 21, 1, doi:10.1186/s13059-019-1906-x (2019). Ramachandran, P. et al. Resolving the fibrotic niche of human liver cirrhosis at single-cell level. Nature 575, 512-518, doi:10.1038/s41586-019-1631-3 (2019). James, K. R. et al. Distinct microbial and immune niches of the human colon. Nature Immunology 21, 343-353, doi:10.1038/s41590-020-0602-z (2020). Ma, F. et al. Single cell and spatial sequencing define processes by which keratinocytes and fibroblasts amplify inflammatory responses in psoriasis. Nature Communications 14, 3455, doi:10.1038/s41467-023-39020-4 (2023). Siletti, K. et al. Transcriptomic diversity of cell types across the adult human brain. Science 382, eadd7046, doi:doi:10.1126/science.add7046 (2023). Tosti, L. et al. Single-Nucleus and In Situ RNA–Sequencing Reveal Cell Topographies in the Human Pancreas. Gastroenterology 160, 1330-1344.e1311, doi:10.1053/j.gastro.2020.11.010 (2021). Gray, G. K. et al. A human breast atlas integrating single-cell proteomics and transcriptomics. Developmental Cell 57, 1400-1420.e1407, doi:10.1016/j.devcel.2022.05.003 (2022). Li, J. et al. Integrated multi-omics single cell atlas of the human retina. bioRxiv, 2023.2011.2007.566105, doi:10.1101/2023.11.07.566105 (2023). Guo, J. et al. The adult human testis transcriptional cell atlas. Cell Research 28, 1141-1157, doi:10.1038/s41422-018-0099-2 (2018). Elmentaite, R. et al. Cells of the human intestinal tract mapped across space and time. Nature 597, 250-255, doi:10.1038/s41586-021-03852-1 (2021). Jin, C. et al. Molecular and genetic insights into human ovarian aging from single-nuclei multi-omics analyses. Nature Aging, doi:10.1038/s43587-024-00762-5 (2024). Williams, D. W. et al. Human oral mucosa cell atlas reveals a stromal-neutrophil axis regulating tissue immunity. Cell 184, 4090-4104.e4015, doi:10.1016/j.cell.2021.05.013 (2021). Park, J.-E. et al. A cell atlas of human thymic development defines T cell repertoire formation. Science 367, eaay3224, doi:doi:10.1126/science.aay3224 (2020).