DOI: 10.5281/zenodo.17153181
title: Healthy Vital Tissue Atlas data for CAR-Machine pipeline

description: 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:



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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&#x2013;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).