autoencodix/census-lung

Census Lung

A single-cell RNA-seq dataset of human lung tissue, assembled from the CZ CELLxGENE Census for use with AUTOENCODIX tutorials.

Contents

• 89,030 cells × 8,189 genes, filtered to the gene set used by the Ontix-Dim24-Gemini3ProPreview pretrained model (a chromosome/GO-ontology-informed autoencoder).
• Single file: census_lung.h5ad (AnnData format, load with anndata.read_h5ad / scanpy.read_h5ad).
• Full Census cell metadata retained in .obs (disease, cell_type, sex, donor_id, dataset_id, tissue, assay, etc.) and gene metadata in .var (feature_id, feature_name, feature_type).

Loading

from huggingface_hub import hf_hub_download
import anndata as ad

path = hf_hub_download(repo_id="autoencodix/census-lung", repo_type="dataset", filename="census_lung.h5ad")
adata = ad.read_h5ad(path)

License and attribution

Licensed CC-BY-4.0, per CZ CELLxGENE Discover's data reuse policy - every dataset admitted to Census is contributed under this license by the original authors. Attribution to the original contributing studies (not just CZI) is a term of that license. This dataset draws cells from 23 distinct publications/collections:

• Sikkema et al. (2023) Nat Med — "The integrated Human Lung Cell Atlas" (31,485 cells)
• Salcher et al. (2022) Cancer Cell — "High-resolution single-cell atlas reveals diversity and plasticity of tumor-associated neutrophils in non-small cell lung cancer" (26,179 cells)
• Guo et al. (2023) Nat Commun — "Human CellCards Multi-Study CellRef 1.0 Atlas" (5,191 cells)
• Xu et al. (2025) Nat Genet — "Integrated human endoderm-derived organoids cell atlas (HEOCA)" (4,188 cells)
• "Bronchopulmonary Dysplasia" collection, no citation on file in Census (3,546 cells)
• Natri et al. (2024) Nat Genet — "Single-cell RNA-seq analysis of Interstitial Lung Disease (ILD) subtypes" (2,266 cells)
• Madissoon et al. (2023) Nat Genet — "A spatially resolved atlas of the human lung characterizes a gland-associated immune niche" (2,193 cells)
• Travaglini et al. (2020) Nature — "A molecular cell atlas of the human lung from single cell RNA sequencing" (2,099 cells)
• Lim et al. (2023) Cell Stem Cell — "Organoid modeling of human fetal lung alveolar development reveals mechanisms of cell fate patterning and neonatal respiratory disease" (1,695 cells)
• Lukassen et al. (2020) The EMBO Journal — "SARS-CoV-2 receptor ACE2 and TMPRSS2 are primarily expressed in bronchial transient secretory cells" (1,424 cells)
• Melms et al. (2021) Nature — "A molecular single-cell lung atlas of lethal COVID-19" (1,377 cells)
• Eraslan et al. (2022) Science — "Single-nucleus cross-tissue molecular reference maps to decipher disease gene function" (1,351 cells)
• Wang et al. (2020) eLife — "LungMAP — Human data from a broad age healthy donor group" (1,099 cells)
• The Tabula Sapiens Consortium* et al. (2022) Science — "Tabula Sapiens" (1,027 cells)
• Dong et al. (2024) bioRxiv — "Transcriptome Analysis of Archived Tumor Tissues by Visium, GeoMx DSP, and Chromium Methods Reveals Inter- and Intra-Patient Heterogeneity" (943 cells)
• Domínguez Conde et al. (2022) Science — "Cross-tissue immune cell analysis reveals tissue-specific features in humans" (901 cells)
• Han et al. (2020) Nature — "Construction of a human cell landscape at single-cell level" (667 cells)
• Lim et al. (2025) EMBO J — "A novel human fetal lung-derived alveolar organoid model reveals mechanisms of surfactant protein C maturation relevant to interstitial lung disease" (532 cells)
• Rustam et al. (2023) Am J Respir Crit Care Med — "A Unique Cellular Organization of Human Distal Airways and Its Disarray in Chronic Obstructive Pulmonary Disease" (496 cells)
• Wang et al. (2023) Immunity — "Emphysema Cell Atlas" (199 cells)
• Watanabe et al. (2022) Am J Respir Cell Mol Biol — "Anomalous Epithelial Variations and Ectopic Inflammatory Response in Chronic Obstructive Pulmonary Disease" (125 cells)
• He et al. (2022) Cell — "A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates" (43 cells)
• Barnes et al. (2023) Sci. Immunol. — "Early human lung immune cell development and its role in epithelial cell fate" (4 cells)

Full per-dataset citation and DOI details are also retained in the dataset_id/dataset_id_ontology_term_id-equivalent Census metadata; see the CZ CELLxGENE Discover Census docs to look up any individual dataset_id present in .obs.