Provides access to a copy of the Human Cell Atlas, but with harmonised metdata. This allows for uniform querying across numerous datasets within the Atlas using common fields such as cell type, tissue type, and patient ethnicity. Usage involves first querying the metadata table for cells of interest, and then downloading the corresponding cells into a anndata object.
Project description
cellNexusPy
Importing the package
from cellnexuspy import get_metadata, get_anndata
Getting the metadata
The get_metadata() function returns a database connection and a DuckDB table.
The table can be used to query the metadata, while the connection's main purpose is to be closed when you are finished:
sample_dataset = "https://object-store.rc.nectar.org.au/v1/AUTH_06d6e008e3e642da99d806ba3ea629c5/cellNexus-metadata/sample_metadata.1.3.0.parquet"
conn, table = get_metadata(parquet_url = sample_dataset)
table
┌──────────────────────────────────────────────────────────────────────────┬──────────────────────────────────────┬────────────────────┬──────────────────────────────────┬────────────────────────────────────┬────────────────────────────┬──────────────────────────────────┬───────────┬────────────────────────┬────────────┬────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┬──────────────────────────────────────┬──────────────────────────────────────┬───────────────────┬─────────────────────────┬────────────────────────────────────┬─────────┬──────────────────────────┬────────────┬───────────────┬──────────────────────────────────────────────────────────────────────────────┬───────────────┬─────────────┬──────────┬─────────────────┬─────────────────────┬──────────────┬───────────────────────────┬────────────────────┬──────────────┬───────────────────┬────────────┬──────────────────┬───────────────────────────────────────────────────────────────────────────────────────────┬────────────────┬────────────────────────────┬──────────────────────────────────────────┬─────────┬──────────────────────┬─────────────────┬─────────────────────────┬─────────────────────────┬─────────────┬─────────────────────────────────────────────────────────────────────────────────────────────────────────────┬───────────┬─────────────────────────────────────────────────────────────────────────────────────┬────────────────────────────┬─────────┬─────────┬──────────┬──────────────────────────┬──────────────────────┬───────────────────────────────────┬────────────────────────────────┬────────────────────────────┬──────────────────────────────┬────────────────────┬───────────────┬───────────────────────────────────┬───────────────────────────────────────────┬───────────────────┬──────────────────────┬────────────────────────────┬───────────┬──────────────────┬───────────────────────┬──────────────────────┬──────────────────────┬────────────────────┬───────────────┬─────────┬───────────────────┬────────────┬────────────┬────────────┬─────────────┬─────────────┬─────────────┬──────────────┬──────────────┬──────────────┬───────────────┬───────────────┬───────────────┬───────────────┬────────────────┬────────────────┬────────────────┬──────────────┬────────────┬─────────────────────────┬───────────────────────────────────────────┬───────────────────────────────────────────┬──────────────────────────┬──────────────────────────┬────────────────────────────┬──────────────────┐
│ cell_id │ dataset_id │ observation_joinid │ sample_id │ cell_type │ cell_type_ontology_term_id │ sample_ │ assay │ assay_ontology_term_id │ cell_count │ citation │ collection_id │ dataset_version_id │ default_embedding │ development_stage │ development_stage_ontology_term_id │ disease │ disease_ontology_term_id │ donor_id │ experiment___ │ explorer_url │ feature_count │ filesize │ filetype │ is_primary_data │ mean_genes_per_cell │ organism │ organism_ontology_term_id │ primary_cell_count │ published_at │ raw_data_location │ revised_at │ run_from_cell_id │ sample_heuristic │ schema_version │ self_reported_ethnicity │ self_reported_ethnicity_ontology_term_id │ sex │ sex_ontology_term_id │ suspension_type │ tissue │ tissue_ontology_term_id │ tissue_type │ title │ tombstone │ url │ x_approximate_distribution │ X_umap1 │ X_umap2 │ age_days │ tissue_groups │ atlas_id │ cell_annotation_blueprint_singler │ cell_annotation_monaco_singler │ cell_annotation_azimuth_l2 │ nFeature_expressed_in_sample │ nCount_RNA │ empty_droplet │ observation_originalid │ ensemble_joinid │ cell_type_unified │ data_driven_ensemble │ cell_type_unified_ensemble │ is_immune │ subsets_Mito_sum │ subsets_Mito_detected │ subsets_Mito_percent │ subsets_Ribo_percent │ high_mitochondrion │ high_ribosome │ alive │ scDblFinder.class │ metacell_2 │ metacell_4 │ metacell_8 │ metacell_16 │ metacell_32 │ metacell_64 │ metacell_128 │ metacell_256 │ metacell_512 │ metacell_1024 │ metacell_2048 │ metacell_4096 │ metacell_8192 │ metacell_16384 │ metacell_32768 │ metacell_65536 │ sample_chunk │ cell_chunk │ sample_pseudobulk_chunk │ file_id_cellNexus_single_cell │ file_id_cellNexus_pseudobulk │ ethnicity_flagging_score │ low_confidence_ethnicity │ imputed_ethnicity │ aggregated_cells │
│ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ int32 │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ int32 │ double │ varchar │ varchar │ double │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ boolean │ varchar │ varchar │ double │ double │ int32 │ varchar │ varchar │ varchar │ varchar │ varchar │ int32 │ double │ boolean │ varchar │ varchar │ varchar │ varchar │ varchar │ boolean │ int32 │ int32 │ int32 │ int32 │ boolean │ boolean │ boolean │ varchar │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ varchar │ varchar │ double │ varchar │ varchar │ int32 │
├──────────────────────────────────────────────────────────────────────────┼──────────────────────────────────────┼────────────────────┼──────────────────────────────────┼────────────────────────────────────┼────────────────────────────┼──────────────────────────────────┼───────────┼────────────────────────┼────────────┼────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┼──────────────────────────────────────┼──────────────────────────────────────┼───────────────────┼─────────────────────────┼────────────────────────────────────┼─────────┼──────────────────────────┼────────────┼───────────────┼──────────────────────────────────────────────────────────────────────────────┼───────────────┼─────────────┼──────────┼─────────────────┼─────────────────────┼──────────────┼───────────────────────────┼────────────────────┼──────────────┼───────────────────┼────────────┼──────────────────┼───────────────────────────────────────────────────────────────────────────────────────────┼────────────────┼────────────────────────────┼──────────────────────────────────────────┼─────────┼──────────────────────┼─────────────────┼─────────────────────────┼─────────────────────────┼─────────────┼─────────────────────────────────────────────────────────────────────────────────────────────────────────────┼───────────┼─────────────────────────────────────────────────────────────────────────────────────┼────────────────────────────┼─────────┼─────────┼──────────┼──────────────────────────┼──────────────────────┼───────────────────────────────────┼────────────────────────────────┼────────────────────────────┼──────────────────────────────┼────────────────────┼───────────────┼───────────────────────────────────┼───────────────────────────────────────────┼───────────────────┼──────────────────────┼────────────────────────────┼───────────┼──────────────────┼───────────────────────┼──────────────────────┼──────────────────────┼────────────────────┼───────────────┼─────────┼───────────────────┼────────────┼────────────┼────────────┼─────────────┼─────────────┼─────────────┼──────────────┼──────────────┼──────────────┼───────────────┼───────────────┼───────────────┼───────────────┼────────────────┼────────────────┼────────────────┼──────────────┼────────────┼─────────────────────────┼───────────────────────────────────────────┼───────────────────────────────────────────┼──────────────────────────┼──────────────────────────┼────────────────────────────┼──────────────────┤
│ 10X389_2:AATCGTGTCTGGGAGA___00476f9f-ebc1-4b72-b541-32f912ce36ea │ 00476f9f-ebc1-4b72-b541-32f912ce36ea │ 6Q`5Q?s8MG │ 9303a73f5d745c5af351a77790608355 │ neuron │ CL:0000540 │ 9303a73f5d745c5af351a77790608355 │ 10x 3' v3 │ EFO:0009922 │ 10099 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/34c82f0d-04a7-4b13-8d4f-ae06065a2b1c.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/283d65eb-dd53-496d-adb7-7570c7caa443 │ 283d65eb-dd53-496d-adb7-7570c7caa443 │ 34c82f0d-04a7-4b13-8d4f-ae06065a2b1c │ NULL │ 42-year-old human stage │ HsapDv:0000136 │ normal │ PATO:0000461 │ H19.30.001 │ │ https://cellxgene.cziscience.com/e/00476f9f-ebc1-4b72-b541-32f912ce36ea.cxg/ │ 59236 │ 132063592.0 │ H5AD │ TRUE │ 5567.875334191504 │ Homo sapiens │ NCBITaxon:9606 │ 10099 │ 2022-12-08 │ X │ 2024-06-11 │ NULL │ H19.30.001___hypothalamus___42-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ nucleus │ hypothalamus │ UBERON:0001898 │ tissue │ Dissection: Hypothalamus (HTH) - mammillary region of HTH (HTHma) │ false │ https://datasets.cellxgene.cziscience.com/34c82f0d-04a7-4b13-8d4f-ae06065a2b1c.h5ad │ NULL │ NULL │ NULL │ 15330 │ limbic and basal systems │ cellxgene/21-08-2025 │ Neurons │ Myeloid dendritic cells │ CD4 TCM │ 1034 │ 2.549410000002595 │ false │ 10X389_2:AATCGTGTCTGGGAGA │ cd4 tcm_non immune_cdc_neuron │ neuron │ non immune │ neuron │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 503 │ 911 │ 550 │ 130 │ 186 │ 110 │ 60 │ 7 │ 7 │ 4 │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 41b6d6f9efa181cf4a2c648cdf479935___1.h5ad │ 5665bf887e0c2e60ffd5f67066496f12___1.h5ad │ NULL │ NULL │ European │ 8673 │
│ 10X389_2:ACCAAACGTCTCAGGC___00476f9f-ebc1-4b72-b541-32f912ce36ea │ 00476f9f-ebc1-4b72-b541-32f912ce36ea │ =rzn8n*;Bt │ 9303a73f5d745c5af351a77790608355 │ neuron │ CL:0000540 │ 9303a73f5d745c5af351a77790608355 │ 10x 3' v3 │ EFO:0009922 │ 10099 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/34c82f0d-04a7-4b13-8d4f-ae06065a2b1c.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/283d65eb-dd53-496d-adb7-7570c7caa443 │ 283d65eb-dd53-496d-adb7-7570c7caa443 │ 34c82f0d-04a7-4b13-8d4f-ae06065a2b1c │ NULL │ 42-year-old human stage │ HsapDv:0000136 │ normal │ PATO:0000461 │ H19.30.001 │ │ https://cellxgene.cziscience.com/e/00476f9f-ebc1-4b72-b541-32f912ce36ea.cxg/ │ 59236 │ 132063592.0 │ H5AD │ TRUE │ 5567.875334191504 │ Homo sapiens │ NCBITaxon:9606 │ 10099 │ 2022-12-08 │ X │ 2024-06-11 │ NULL │ H19.30.001___hypothalamus___42-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ nucleus │ hypothalamus │ UBERON:0001898 │ tissue │ Dissection: Hypothalamus (HTH) - mammillary region of HTH (HTHma) │ false │ https://datasets.cellxgene.cziscience.com/34c82f0d-04a7-4b13-8d4f-ae06065a2b1c.h5ad │ NULL │ NULL │ NULL │ 15330 │ limbic and basal systems │ cellxgene/21-08-2025 │ Neurons │ Myeloid dendritic cells │ HSPC │ 6544 │ 47.12423000001045 │ false │ 10X389_2:ACCAAACGTCTCAGGC │ cd4 tcm_non immune_cdc_neuron │ neuron │ non immune │ neuron │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 54 │ 1565 │ 47 │ 338 │ 224 │ 17 │ 42 │ 2 │ 1 │ 3 │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 41b6d6f9efa181cf4a2c648cdf479935___1.h5ad │ 5665bf887e0c2e60ffd5f67066496f12___1.h5ad │ NULL │ NULL │ European │ 8673 │
│ 10X389_2:TCCGGGACACAGCGCT___00476f9f-ebc1-4b72-b541-32f912ce36ea │ 00476f9f-ebc1-4b72-b541-32f912ce36ea │ {UrC34cLRz │ 9303a73f5d745c5af351a77790608355 │ neuron │ CL:0000540 │ 9303a73f5d745c5af351a77790608355 │ 10x 3' v3 │ EFO:0009922 │ 10099 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/34c82f0d-04a7-4b13-8d4f-ae06065a2b1c.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/283d65eb-dd53-496d-adb7-7570c7caa443 │ 283d65eb-dd53-496d-adb7-7570c7caa443 │ 34c82f0d-04a7-4b13-8d4f-ae06065a2b1c │ NULL │ 42-year-old human stage │ HsapDv:0000136 │ normal │ PATO:0000461 │ H19.30.001 │ │ https://cellxgene.cziscience.com/e/00476f9f-ebc1-4b72-b541-32f912ce36ea.cxg/ │ 59236 │ 132063592.0 │ H5AD │ TRUE │ 5567.875334191504 │ Homo sapiens │ NCBITaxon:9606 │ 10099 │ 2022-12-08 │ X │ 2024-06-11 │ NULL │ H19.30.001___hypothalamus___42-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ nucleus │ hypothalamus │ UBERON:0001898 │ tissue │ Dissection: Hypothalamus (HTH) - mammillary region of HTH (HTHma) │ false │ https://datasets.cellxgene.cziscience.com/34c82f0d-04a7-4b13-8d4f-ae06065a2b1c.h5ad │ NULL │ NULL │ NULL │ 15330 │ limbic and basal systems │ cellxgene/21-08-2025 │ Neurons │ Progenitor cells │ HSPC │ 6332 │ 39.11184000001086 │ false │ 10X389_2:TCCGGGACACAGCGCT │ cd4 tcm_non immune_progenitor_neuron │ neuron │ non immune │ neuron │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 989 │ 1865 │ 199 │ 132 │ 41 │ 60 │ 12 │ 2 │ 1 │ 3 │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 41b6d6f9efa181cf4a2c648cdf479935___1.h5ad │ 5665bf887e0c2e60ffd5f67066496f12___1.h5ad │ NULL │ NULL │ European │ 8673 │
│ 10X389_1:GTGACGCGTATCCCAA___00476f9f-ebc1-4b72-b541-32f912ce36ea │ 00476f9f-ebc1-4b72-b541-32f912ce36ea │ aX=h+H$b%3 │ 9303a73f5d745c5af351a77790608355 │ neuron │ CL:0000540 │ 9303a73f5d745c5af351a77790608355 │ 10x 3' v3 │ EFO:0009922 │ 10099 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/34c82f0d-04a7-4b13-8d4f-ae06065a2b1c.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/283d65eb-dd53-496d-adb7-7570c7caa443 │ 283d65eb-dd53-496d-adb7-7570c7caa443 │ 34c82f0d-04a7-4b13-8d4f-ae06065a2b1c │ NULL │ 42-year-old human stage │ HsapDv:0000136 │ normal │ PATO:0000461 │ H19.30.001 │ │ https://cellxgene.cziscience.com/e/00476f9f-ebc1-4b72-b541-32f912ce36ea.cxg/ │ 59236 │ 132063592.0 │ H5AD │ TRUE │ 5567.875334191504 │ Homo sapiens │ NCBITaxon:9606 │ 10099 │ 2022-12-08 │ X │ 2024-06-11 │ NULL │ H19.30.001___hypothalamus___42-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ nucleus │ hypothalamus │ UBERON:0001898 │ tissue │ Dissection: Hypothalamus (HTH) - mammillary region of HTH (HTHma) │ false │ https://datasets.cellxgene.cziscience.com/34c82f0d-04a7-4b13-8d4f-ae06065a2b1c.h5ad │ NULL │ NULL │ NULL │ 15330 │ limbic and basal systems │ cellxgene/21-08-2025 │ Neurons │ Plasmacytoid dendritic cells │ HSPC │ 6851 │ 58.489660000009906 │ false │ 10X389_1:GTGACGCGTATCCCAA │ cd4 tcm_non immune_pdc_neuron │ neuron │ non immune │ neuron │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 114 │ 1199 │ 981 │ 290 │ 24 │ 59 │ 16 │ 23 │ 1 │ 3 │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 41b6d6f9efa181cf4a2c648cdf479935___1.h5ad │ 5665bf887e0c2e60ffd5f67066496f12___1.h5ad │ NULL │ NULL │ European │ 8673 │
│ 10X389_2:ACTGCAACAAGAGATT___00476f9f-ebc1-4b72-b541-32f912ce36ea │ 00476f9f-ebc1-4b72-b541-32f912ce36ea │ yujwks<ZXP │ 9303a73f5d745c5af351a77790608355 │ neuron │ CL:0000540 │ 9303a73f5d745c5af351a77790608355 │ 10x 3' v3 │ EFO:0009922 │ 10099 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/34c82f0d-04a7-4b13-8d4f-ae06065a2b1c.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/283d65eb-dd53-496d-adb7-7570c7caa443 │ 283d65eb-dd53-496d-adb7-7570c7caa443 │ 34c82f0d-04a7-4b13-8d4f-ae06065a2b1c │ NULL │ 42-year-old human stage │ HsapDv:0000136 │ normal │ PATO:0000461 │ H19.30.001 │ │ https://cellxgene.cziscience.com/e/00476f9f-ebc1-4b72-b541-32f912ce36ea.cxg/ │ 59236 │ 132063592.0 │ H5AD │ TRUE │ 5567.875334191504 │ Homo sapiens │ NCBITaxon:9606 │ 10099 │ 2022-12-08 │ X │ 2024-06-11 │ NULL │ H19.30.001___hypothalamus___42-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ nucleus │ hypothalamus │ UBERON:0001898 │ tissue │ Dissection: Hypothalamus (HTH) - mammillary region of HTH (HTHma) │ false │ https://datasets.cellxgene.cziscience.com/34c82f0d-04a7-4b13-8d4f-ae06065a2b1c.h5ad │ NULL │ NULL │ NULL │ 15330 │ limbic and basal systems │ cellxgene/21-08-2025 │ Neurons │ Plasmacytoid dendritic cells │ HSPC │ 6254 │ 38.74055000000987 │ false │ 10X389_2:ACTGCAACAAGAGATT │ cd4 tcm_non immune_pdc_neuron │ neuron │ non immune │ neuron │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 2585 │ 685 │ 881 │ 202 │ 141 │ 59 │ 16 │ 23 │ 1 │ 3 │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 41b6d6f9efa181cf4a2c648cdf479935___1.h5ad │ 5665bf887e0c2e60ffd5f67066496f12___1.h5ad │ NULL │ NULL │ European │ 8673 │
│ 10X389_2:AGGAGGTAGTTCCGTA___00476f9f-ebc1-4b72-b541-32f912ce36ea │ 00476f9f-ebc1-4b72-b541-32f912ce36ea │ `I`7=IHlhJ │ 9303a73f5d745c5af351a77790608355 │ neuron │ CL:0000540 │ 9303a73f5d745c5af351a77790608355 │ 10x 3' v3 │ EFO:0009922 │ 10099 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/34c82f0d-04a7-4b13-8d4f-ae06065a2b1c.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/283d65eb-dd53-496d-adb7-7570c7caa443 │ 283d65eb-dd53-496d-adb7-7570c7caa443 │ 34c82f0d-04a7-4b13-8d4f-ae06065a2b1c │ NULL │ 42-year-old human stage │ HsapDv:0000136 │ normal │ PATO:0000461 │ H19.30.001 │ │ https://cellxgene.cziscience.com/e/00476f9f-ebc1-4b72-b541-32f912ce36ea.cxg/ │ 59236 │ 132063592.0 │ H5AD │ TRUE │ 5567.875334191504 │ Homo sapiens │ NCBITaxon:9606 │ 10099 │ 2022-12-08 │ X │ 2024-06-11 │ NULL │ H19.30.001___hypothalamus___42-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ nucleus │ hypothalamus │ UBERON:0001898 │ tissue │ Dissection: Hypothalamus (HTH) - mammillary region of HTH (HTHma) │ false │ https://datasets.cellxgene.cziscience.com/34c82f0d-04a7-4b13-8d4f-ae06065a2b1c.h5ad │ NULL │ NULL │ NULL │ 15330 │ limbic and basal systems │ cellxgene/21-08-2025 │ Neurons │ Myeloid dendritic cells │ HSPC │ 5436 │ 27.894660000009644 │ false │ 10X389_2:AGGAGGTAGTTCCGTA │ cd4 tcm_non immune_cdc_neuron │ neuron │ non immune │ neuron │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 1461 │ 12 │ 700 │ 238 │ 144 │ 37 │ 12 │ 2 │ 1 │ 3 │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 41b6d6f9efa181cf4a2c648cdf479935___1.h5ad │ 5665bf887e0c2e60ffd5f67066496f12___1.h5ad │ NULL │ NULL │ European │ 8673 │
│ 10X389_2:GAAGGACGTATGACAA___00476f9f-ebc1-4b72-b541-32f912ce36ea │ 00476f9f-ebc1-4b72-b541-32f912ce36ea │ 9UR&U96Up( │ 9303a73f5d745c5af351a77790608355 │ neuron │ CL:0000540 │ 9303a73f5d745c5af351a77790608355 │ 10x 3' v3 │ EFO:0009922 │ 10099 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/34c82f0d-04a7-4b13-8d4f-ae06065a2b1c.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/283d65eb-dd53-496d-adb7-7570c7caa443 │ 283d65eb-dd53-496d-adb7-7570c7caa443 │ 34c82f0d-04a7-4b13-8d4f-ae06065a2b1c │ NULL │ 42-year-old human stage │ HsapDv:0000136 │ normal │ PATO:0000461 │ H19.30.001 │ │ https://cellxgene.cziscience.com/e/00476f9f-ebc1-4b72-b541-32f912ce36ea.cxg/ │ 59236 │ 132063592.0 │ H5AD │ TRUE │ 5567.875334191504 │ Homo sapiens │ NCBITaxon:9606 │ 10099 │ 2022-12-08 │ X │ 2024-06-11 │ NULL │ H19.30.001___hypothalamus___42-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ nucleus │ hypothalamus │ UBERON:0001898 │ tissue │ Dissection: Hypothalamus (HTH) - mammillary region of HTH (HTHma) │ false │ https://datasets.cellxgene.cziscience.com/34c82f0d-04a7-4b13-8d4f-ae06065a2b1c.h5ad │ NULL │ NULL │ NULL │ 15330 │ limbic and basal systems │ cellxgene/21-08-2025 │ Neurons │ Plasmacytoid dendritic cells │ HSPC │ 6881 │ 48.611990000010685 │ false │ 10X389_2:GAAGGACGTATGACAA │ cd4 tcm_non immune_pdc_neuron │ neuron │ non immune │ neuron │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 1422 │ 1401 │ 349 │ 221 │ 28 │ 37 │ 12 │ 2 │ 1 │ 3 │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 41b6d6f9efa181cf4a2c648cdf479935___1.h5ad │ 5665bf887e0c2e60ffd5f67066496f12___1.h5ad │ NULL │ NULL │ European │ 8673 │
│ 10X389_2:GCCAGGTTCCCGAGAC___00476f9f-ebc1-4b72-b541-32f912ce36ea │ 00476f9f-ebc1-4b72-b541-32f912ce36ea │ GknSduSP`2 │ 9303a73f5d745c5af351a77790608355 │ neuron │ CL:0000540 │ 9303a73f5d745c5af351a77790608355 │ 10x 3' v3 │ EFO:0009922 │ 10099 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/34c82f0d-04a7-4b13-8d4f-ae06065a2b1c.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/283d65eb-dd53-496d-adb7-7570c7caa443 │ 283d65eb-dd53-496d-adb7-7570c7caa443 │ 34c82f0d-04a7-4b13-8d4f-ae06065a2b1c │ NULL │ 42-year-old human stage │ HsapDv:0000136 │ normal │ PATO:0000461 │ H19.30.001 │ │ https://cellxgene.cziscience.com/e/00476f9f-ebc1-4b72-b541-32f912ce36ea.cxg/ │ 59236 │ 132063592.0 │ H5AD │ TRUE │ 5567.875334191504 │ Homo sapiens │ NCBITaxon:9606 │ 10099 │ 2022-12-08 │ X │ 2024-06-11 │ NULL │ H19.30.001___hypothalamus___42-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ nucleus │ hypothalamus │ UBERON:0001898 │ tissue │ Dissection: Hypothalamus (HTH) - mammillary region of HTH (HTHma) │ false │ https://datasets.cellxgene.cziscience.com/34c82f0d-04a7-4b13-8d4f-ae06065a2b1c.h5ad │ NULL │ NULL │ NULL │ 15330 │ limbic and basal systems │ cellxgene/21-08-2025 │ Neurons │ Low-density basophils │ HSPC │ 7277 │ 85.63485000001113 │ false │ 10X389_2:GCCAGGTTCCCGAGAC │ cd4 tcm_non immune_granulocyte_neuron │ neuron │ non immune │ neuron │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 2339 │ 1080 │ 448 │ 116 │ 30 │ 17 │ 42 │ 2 │ 1 │ 3 │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 41b6d6f9efa181cf4a2c648cdf479935___1.h5ad │ 5665bf887e0c2e60ffd5f67066496f12___1.h5ad │ NULL │ NULL │ European │ 8673 │
│ 10X389_1:TTGGATGCAAGCGCAA___00476f9f-ebc1-4b72-b541-32f912ce36ea │ 00476f9f-ebc1-4b72-b541-32f912ce36ea │ U}{>K6!kF$ │ 9303a73f5d745c5af351a77790608355 │ neuron │ CL:0000540 │ 9303a73f5d745c5af351a77790608355 │ 10x 3' v3 │ EFO:0009922 │ 10099 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/34c82f0d-04a7-4b13-8d4f-ae06065a2b1c.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/283d65eb-dd53-496d-adb7-7570c7caa443 │ 283d65eb-dd53-496d-adb7-7570c7caa443 │ 34c82f0d-04a7-4b13-8d4f-ae06065a2b1c │ NULL │ 42-year-old human stage │ HsapDv:0000136 │ normal │ PATO:0000461 │ H19.30.001 │ │ https://cellxgene.cziscience.com/e/00476f9f-ebc1-4b72-b541-32f912ce36ea.cxg/ │ 59236 │ 132063592.0 │ H5AD │ TRUE │ 5567.875334191504 │ Homo sapiens │ NCBITaxon:9606 │ 10099 │ 2022-12-08 │ X │ 2024-06-11 │ NULL │ H19.30.001___hypothalamus___42-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ nucleus │ hypothalamus │ UBERON:0001898 │ tissue │ Dissection: Hypothalamus (HTH) - mammillary region of HTH (HTHma) │ false │ https://datasets.cellxgene.cziscience.com/34c82f0d-04a7-4b13-8d4f-ae06065a2b1c.h5ad │ NULL │ NULL │ NULL │ 15330 │ limbic and basal systems │ cellxgene/21-08-2025 │ Neurons │ Progenitor cells │ HSPC │ 6053 │ 32.747690000010174 │ false │ 10X389_1:TTGGATGCAAGCGCAA │ cd4 tcm_non immune_progenitor_neuron │ neuron │ non immune │ neuron │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 2213 │ 215 │ 773 │ 33 │ 141 │ 59 │ 16 │ 23 │ 1 │ 3 │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 41b6d6f9efa181cf4a2c648cdf479935___1.h5ad │ 5665bf887e0c2e60ffd5f67066496f12___1.h5ad │ NULL │ NULL │ European │ 8673 │
│ 10X389_1:ACACGCGGTCCTGAAT___00476f9f-ebc1-4b72-b541-32f912ce36ea │ 00476f9f-ebc1-4b72-b541-32f912ce36ea │ A;nR~xd6D5 │ 9303a73f5d745c5af351a77790608355 │ neuron │ CL:0000540 │ 9303a73f5d745c5af351a77790608355 │ 10x 3' v3 │ EFO:0009922 │ 10099 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/34c82f0d-04a7-4b13-8d4f-ae06065a2b1c.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/283d65eb-dd53-496d-adb7-7570c7caa443 │ 283d65eb-dd53-496d-adb7-7570c7caa443 │ 34c82f0d-04a7-4b13-8d4f-ae06065a2b1c │ NULL │ 42-year-old human stage │ HsapDv:0000136 │ normal │ PATO:0000461 │ H19.30.001 │ │ https://cellxgene.cziscience.com/e/00476f9f-ebc1-4b72-b541-32f912ce36ea.cxg/ │ 59236 │ 132063592.0 │ H5AD │ TRUE │ 5567.875334191504 │ Homo sapiens │ NCBITaxon:9606 │ 10099 │ 2022-12-08 │ X │ 2024-06-11 │ NULL │ H19.30.001___hypothalamus___42-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ nucleus │ hypothalamus │ UBERON:0001898 │ tissue │ Dissection: Hypothalamus (HTH) - mammillary region of HTH (HTHma) │ false │ https://datasets.cellxgene.cziscience.com/34c82f0d-04a7-4b13-8d4f-ae06065a2b1c.h5ad │ NULL │ NULL │ NULL │ 15330 │ limbic and basal systems │ cellxgene/21-08-2025 │ Neurons │ Myeloid dendritic cells │ HSPC │ 6389 │ 41.608600000010455 │ false │ 10X389_1:ACACGCGGTCCTGAAT │ cd4 tcm_non immune_cdc_neuron │ neuron │ non immune │ neuron │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 2586 │ 685 │ 881 │ 202 │ 141 │ 59 │ 16 │ 23 │ 1 │ 3 │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 41b6d6f9efa181cf4a2c648cdf479935___1.h5ad │ 5665bf887e0c2e60ffd5f67066496f12___1.h5ad │ NULL │ NULL │ European │ 8673 │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
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│ ACACCAAAGAGCCTAG_Donor1_lung_rest___01209dce-3575-4bed-b1df-129f57fbc031 │ 01209dce-3575-4bed-b1df-129f57fbc031 │ j)WaHcc{DG │ 2eedd5bde16b2bd0724fea31b2c98961 │ CD8-positive, alpha-beta thymocyte │ CL:0000811 │ 2eedd5bde16b2bd0724fea31b2c98961 │ 10x 3' v2 │ EFO:0009899 │ 51876 │ Publication: https://doi.org/10.1038/s41467-019-12464-3 Dataset Version: https://datasets.cellxgene.cziscience.com/71c5026d-9567-4d0f-a808-edf29440df43.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/24d42e5e-ce6d-45ff-a66b-a3b3b715deaf │ 24d42e5e-ce6d-45ff-a66b-a3b3b715deaf │ 71c5026d-9567-4d0f-a808-edf29440df43 │ NULL │ 65-year-old human stage │ HsapDv:0000159 │ normal │ PATO:0000461 │ Donor1 │ │ https://cellxgene.cziscience.com/e/01209dce-3575-4bed-b1df-129f57fbc031.cxg/ │ 54649 │ 314676313.0 │ H5AD │ TRUE │ 1219.6768255069783 │ Homo sapiens │ NCBITaxon:9606 │ 51876 │ 2021-03-09 │ raw.X │ 2024-06-11 │ NULL │ Donor1___lower lobe of left lung___65-year-old human stage___10x 3' v2______normal___TRUE │ 5.1.0 │ Hispanic or Latin American │ HANCESTRO:0014 │ male │ PATO:0000384 │ cell │ lower lobe of left lung │ UBERON:0008953 │ tissue │ Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease │ false │ https://datasets.cellxgene.cziscience.com/71c5026d-9567-4d0f-a808-edf29440df43.h5ad │ NULL │ NULL │ NULL │ 23725 │ respiratory system │ cellxgene/21-08-2025 │ CD8+ Tcm │ Central memory CD8 T cells │ CD4 TCM │ 876 │ 1854.0075000000008 │ false │ ACACCAAAGAGCCTAG_Donor1_lung_rest │ cd4 tcm_cd8 tcm_cd8 tcm_cd8 naive │ cd8 naive │ cd8 tcm │ t cd8 │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 23 │ 25 │ 12 │ 6 │ 2 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ ea7454e0784218aae24af78dd5b31562___1.h5ad │ 139040b951e384864c37af17a0fe5153___1.h5ad │ NULL │ NULL │ Hispanic or Latin American │ 242 │
│ GACTACAAGTGAATTG_Donor1_lung_rest___01209dce-3575-4bed-b1df-129f57fbc031 │ 01209dce-3575-4bed-b1df-129f57fbc031 │ cVC`y!?L{w │ 2eedd5bde16b2bd0724fea31b2c98961 │ CD8-positive, alpha-beta thymocyte │ CL:0000811 │ 2eedd5bde16b2bd0724fea31b2c98961 │ 10x 3' v2 │ EFO:0009899 │ 51876 │ Publication: https://doi.org/10.1038/s41467-019-12464-3 Dataset Version: https://datasets.cellxgene.cziscience.com/71c5026d-9567-4d0f-a808-edf29440df43.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/24d42e5e-ce6d-45ff-a66b-a3b3b715deaf │ 24d42e5e-ce6d-45ff-a66b-a3b3b715deaf │ 71c5026d-9567-4d0f-a808-edf29440df43 │ NULL │ 65-year-old human stage │ HsapDv:0000159 │ normal │ PATO:0000461 │ Donor1 │ │ https://cellxgene.cziscience.com/e/01209dce-3575-4bed-b1df-129f57fbc031.cxg/ │ 54649 │ 314676313.0 │ H5AD │ TRUE │ 1219.6768255069783 │ Homo sapiens │ NCBITaxon:9606 │ 51876 │ 2021-03-09 │ raw.X │ 2024-06-11 │ NULL │ Donor1___lower lobe of left lung___65-year-old human stage___10x 3' v2______normal___TRUE │ 5.1.0 │ Hispanic or Latin American │ HANCESTRO:0014 │ male │ PATO:0000384 │ cell │ lower lobe of left lung │ UBERON:0008953 │ tissue │ Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease │ false │ https://datasets.cellxgene.cziscience.com/71c5026d-9567-4d0f-a808-edf29440df43.h5ad │ NULL │ NULL │ NULL │ 23725 │ respiratory system │ cellxgene/21-08-2025 │ CD8+ Tcm │ Vd2 gd T cells │ CD8 TEM │ 1066 │ 2400.0693000000006 │ false │ GACTACAAGTGAATTG_Donor1_lung_rest │ cd4 tcm_cd8 tcm_tgd_cd8 naive │ cd8 naive │ t │ cd8 naive │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 236 │ 38 │ 86 │ 3 │ 12 │ 1 │ 1 │ 2 │ 2 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ bbec40eb2142a9570836ffed1c4c2bbe___1.h5ad │ 139040b951e384864c37af17a0fe5153___1.h5ad │ NULL │ NULL │ Hispanic or Latin American │ 891 │
│ GGACGTCGTGCTAGCC_Donor1_lung_rest___01209dce-3575-4bed-b1df-129f57fbc031 │ 01209dce-3575-4bed-b1df-129f57fbc031 │ pSmoSMW9^A │ 2eedd5bde16b2bd0724fea31b2c98961 │ CD4-positive, alpha-beta thymocyte │ CL:0000810 │ 2eedd5bde16b2bd0724fea31b2c98961 │ 10x 3' v2 │ EFO:0009899 │ 51876 │ Publication: https://doi.org/10.1038/s41467-019-12464-3 Dataset Version: https://datasets.cellxgene.cziscience.com/71c5026d-9567-4d0f-a808-edf29440df43.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/24d42e5e-ce6d-45ff-a66b-a3b3b715deaf │ 24d42e5e-ce6d-45ff-a66b-a3b3b715deaf │ 71c5026d-9567-4d0f-a808-edf29440df43 │ NULL │ 65-year-old human stage │ HsapDv:0000159 │ normal │ PATO:0000461 │ Donor1 │ │ https://cellxgene.cziscience.com/e/01209dce-3575-4bed-b1df-129f57fbc031.cxg/ │ 54649 │ 314676313.0 │ H5AD │ TRUE │ 1219.6768255069783 │ Homo sapiens │ NCBITaxon:9606 │ 51876 │ 2021-03-09 │ raw.X │ 2024-06-11 │ NULL │ Donor1___lower lobe of left lung___65-year-old human stage___10x 3' v2______normal___TRUE │ 5.1.0 │ Hispanic or Latin American │ HANCESTRO:0014 │ male │ PATO:0000384 │ cell │ lower lobe of left lung │ UBERON:0008953 │ tissue │ Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease │ false │ https://datasets.cellxgene.cziscience.com/71c5026d-9567-4d0f-a808-edf29440df43.h5ad │ NULL │ NULL │ NULL │ 23725 │ respiratory system │ cellxgene/21-08-2025 │ CD4+ Tcm │ Th17 cells │ CD4 TCM │ 928 │ 2021.1804599999998 │ false │ GGACGTCGTGCTAGCC_Donor1_lung_rest │ cd4 tcm_cd4 tcm_cd4 th17 em_cd4 naive │ cd4 naive │ cd4 tcm │ t cd4 │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 11 │ 15 │ 1 │ 21 │ 6 │ 7 │ 2 │ 1 │ 2 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 9dfa71e52562890c138f39095990e085___1.h5ad │ 139040b951e384864c37af17a0fe5153___1.h5ad │ NULL │ NULL │ Hispanic or Latin American │ 856 │
│ GGCGACTAGAGACTTA_Donor1_lung_rest___01209dce-3575-4bed-b1df-129f57fbc031 │ 01209dce-3575-4bed-b1df-129f57fbc031 │ 1LQY~&e2`W │ 2eedd5bde16b2bd0724fea31b2c98961 │ CD4-positive, alpha-beta thymocyte │ CL:0000810 │ 2eedd5bde16b2bd0724fea31b2c98961 │ 10x 3' v2 │ EFO:0009899 │ 51876 │ Publication: https://doi.org/10.1038/s41467-019-12464-3 Dataset Version: https://datasets.cellxgene.cziscience.com/71c5026d-9567-4d0f-a808-edf29440df43.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/24d42e5e-ce6d-45ff-a66b-a3b3b715deaf │ 24d42e5e-ce6d-45ff-a66b-a3b3b715deaf │ 71c5026d-9567-4d0f-a808-edf29440df43 │ NULL │ 65-year-old human stage │ HsapDv:0000159 │ normal │ PATO:0000461 │ Donor1 │ │ https://cellxgene.cziscience.com/e/01209dce-3575-4bed-b1df-129f57fbc031.cxg/ │ 54649 │ 314676313.0 │ H5AD │ TRUE │ 1219.6768255069783 │ Homo sapiens │ NCBITaxon:9606 │ 51876 │ 2021-03-09 │ raw.X │ 2024-06-11 │ NULL │ Donor1___lower lobe of left lung___65-year-old human stage___10x 3' v2______normal___TRUE │ 5.1.0 │ Hispanic or Latin American │ HANCESTRO:0014 │ male │ PATO:0000384 │ cell │ lower lobe of left lung │ UBERON:0008953 │ tissue │ Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease │ false │ https://datasets.cellxgene.cziscience.com/71c5026d-9567-4d0f-a808-edf29440df43.h5ad │ NULL │ NULL │ NULL │ 23725 │ respiratory system │ cellxgene/21-08-2025 │ CD8+ Tcm │ Th1/Th17 cells │ CD4 TCM │ 832 │ 1648.21042 │ false │ GGCGACTAGAGACTTA_Donor1_lung_rest │ cd4 tcm_cd8 tcm_cd4 th1/th17 em_cd4 naive │ cd4 naive │ t cd4 │ cd4 naive │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 114 │ 93 │ 37 │ 19 │ 7 │ 4 │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ e613c33ed7dd9f8400d45cddd2000cbb___1.h5ad │ 139040b951e384864c37af17a0fe5153___1.h5ad │ NULL │ NULL │ Hispanic or Latin American │ 682 │
│ CTAGCCTGTGCTTCTC_Donor1_lung_rest___01209dce-3575-4bed-b1df-129f57fbc031 │ 01209dce-3575-4bed-b1df-129f57fbc031 │ Xu*q-2+W}S │ 2eedd5bde16b2bd0724fea31b2c98961 │ CD8-positive, alpha-beta thymocyte │ CL:0000811 │ 2eedd5bde16b2bd0724fea31b2c98961 │ 10x 3' v2 │ EFO:0009899 │ 51876 │ Publication: https://doi.org/10.1038/s41467-019-12464-3 Dataset Version: https://datasets.cellxgene.cziscience.com/71c5026d-9567-4d0f-a808-edf29440df43.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/24d42e5e-ce6d-45ff-a66b-a3b3b715deaf │ 24d42e5e-ce6d-45ff-a66b-a3b3b715deaf │ 71c5026d-9567-4d0f-a808-edf29440df43 │ NULL │ 65-year-old human stage │ HsapDv:0000159 │ normal │ PATO:0000461 │ Donor1 │ │ https://cellxgene.cziscience.com/e/01209dce-3575-4bed-b1df-129f57fbc031.cxg/ │ 54649 │ 314676313.0 │ H5AD │ TRUE │ 1219.6768255069783 │ Homo sapiens │ NCBITaxon:9606 │ 51876 │ 2021-03-09 │ raw.X │ 2024-06-11 │ NULL │ Donor1___lower lobe of left lung___65-year-old human stage___10x 3' v2______normal___TRUE │ 5.1.0 │ Hispanic or Latin American │ HANCESTRO:0014 │ male │ PATO:0000384 │ cell │ lower lobe of left lung │ UBERON:0008953 │ tissue │ Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease │ false │ https://datasets.cellxgene.cziscience.com/71c5026d-9567-4d0f-a808-edf29440df43.h5ad │ NULL │ NULL │ NULL │ 23725 │ respiratory system │ cellxgene/21-08-2025 │ CD4+ Tem │ Non-Vd2 gd T cells │ CD4 TCM │ 970 │ 1921.0206200000014 │ false │ CTAGCCTGTGCTTCTC_Donor1_lung_rest │ cd4 tcm_cd4 tem_tgd_cd8 naive │ cd8 naive │ Unknown │ cd8 naive │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 223 │ 211 │ 72 │ 33 │ 16 │ 5 │ 5 │ 3 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ bbec40eb2142a9570836ffed1c4c2bbe___1.h5ad │ 139040b951e384864c37af17a0fe5153___1.h5ad │ NULL │ NULL │ Hispanic or Latin American │ 891 │
│ ATCGAGTCATACGCCG_Donor1_lung_rest___01209dce-3575-4bed-b1df-129f57fbc031 │ 01209dce-3575-4bed-b1df-129f57fbc031 │ 1@v2KI3cyI │ 2eedd5bde16b2bd0724fea31b2c98961 │ CD8-positive, alpha-beta thymocyte │ CL:0000811 │ 2eedd5bde16b2bd0724fea31b2c98961 │ 10x 3' v2 │ EFO:0009899 │ 51876 │ Publication: https://doi.org/10.1038/s41467-019-12464-3 Dataset Version: https://datasets.cellxgene.cziscience.com/71c5026d-9567-4d0f-a808-edf29440df43.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/24d42e5e-ce6d-45ff-a66b-a3b3b715deaf │ 24d42e5e-ce6d-45ff-a66b-a3b3b715deaf │ 71c5026d-9567-4d0f-a808-edf29440df43 │ NULL │ 65-year-old human stage │ HsapDv:0000159 │ normal │ PATO:0000461 │ Donor1 │ │ https://cellxgene.cziscience.com/e/01209dce-3575-4bed-b1df-129f57fbc031.cxg/ │ 54649 │ 314676313.0 │ H5AD │ TRUE │ 1219.6768255069783 │ Homo sapiens │ NCBITaxon:9606 │ 51876 │ 2021-03-09 │ raw.X │ 2024-06-11 │ NULL │ Donor1___lower lobe of left lung___65-year-old human stage___10x 3' v2______normal___TRUE │ 5.1.0 │ Hispanic or Latin American │ HANCESTRO:0014 │ male │ PATO:0000384 │ cell │ lower lobe of left lung │ UBERON:0008953 │ tissue │ Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease │ false │ https://datasets.cellxgene.cziscience.com/71c5026d-9567-4d0f-a808-edf29440df43.h5ad │ NULL │ NULL │ NULL │ 23725 │ respiratory system │ cellxgene/21-08-2025 │ CD8+ Tem │ Non-Vd2 gd T cells │ CD4 TCM │ 1041 │ 2079.8513000000003 │ false │ ATCGAGTCATACGCCG_Donor1_lung_rest │ cd4 tcm_cd8 tem_tgd_cd8 naive │ cd8 naive │ t │ cd8 naive │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 322 │ 222 │ 76 │ 4 │ 8 │ 7 │ 1 │ 2 │ 2 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ bbec40eb2142a9570836ffed1c4c2bbe___1.h5ad │ 139040b951e384864c37af17a0fe5153___1.h5ad │ NULL │ NULL │ Hispanic or Latin American │ 891 │
│ GGGTCTGTCGTCCAGG_Donor1_lung_rest___01209dce-3575-4bed-b1df-129f57fbc031 │ 01209dce-3575-4bed-b1df-129f57fbc031 │ 3itcTlIN?= │ 2eedd5bde16b2bd0724fea31b2c98961 │ CD4-positive, alpha-beta thymocyte │ CL:0000810 │ 2eedd5bde16b2bd0724fea31b2c98961 │ 10x 3' v2 │ EFO:0009899 │ 51876 │ Publication: https://doi.org/10.1038/s41467-019-12464-3 Dataset Version: https://datasets.cellxgene.cziscience.com/71c5026d-9567-4d0f-a808-edf29440df43.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/24d42e5e-ce6d-45ff-a66b-a3b3b715deaf │ 24d42e5e-ce6d-45ff-a66b-a3b3b715deaf │ 71c5026d-9567-4d0f-a808-edf29440df43 │ NULL │ 65-year-old human stage │ HsapDv:0000159 │ normal │ PATO:0000461 │ Donor1 │ │ https://cellxgene.cziscience.com/e/01209dce-3575-4bed-b1df-129f57fbc031.cxg/ │ 54649 │ 314676313.0 │ H5AD │ TRUE │ 1219.6768255069783 │ Homo sapiens │ NCBITaxon:9606 │ 51876 │ 2021-03-09 │ raw.X │ 2024-06-11 │ NULL │ Donor1___lower lobe of left lung___65-year-old human stage___10x 3' v2______normal___TRUE │ 5.1.0 │ Hispanic or Latin American │ HANCESTRO:0014 │ male │ PATO:0000384 │ cell │ lower lobe of left lung │ UBERON:0008953 │ tissue │ Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease │ false │ https://datasets.cellxgene.cziscience.com/71c5026d-9567-4d0f-a808-edf29440df43.h5ad │ NULL │ NULL │ NULL │ 23725 │ respiratory system │ cellxgene/21-08-2025 │ CD4+ Tem │ Th17 cells │ CD4 TCM │ 762 │ 1765.2113300000008 │ false │ GGGTCTGTCGTCCAGG_Donor1_lung_rest │ cd4 tcm_cd4 tem_cd4 th17 em_cd4 naive │ cd4 naive │ cd4 th17 em │ t cd4 │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 193 │ 32 │ 1 │ 21 │ 6 │ 7 │ 2 │ 1 │ 2 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 9dfa71e52562890c138f39095990e085___1.h5ad │ 139040b951e384864c37af17a0fe5153___1.h5ad │ NULL │ NULL │ Hispanic or Latin American │ 856 │
│ TTAACTCGTTACTGAC_Donor1_lung_rest___01209dce-3575-4bed-b1df-129f57fbc031 │ 01209dce-3575-4bed-b1df-129f57fbc031 │ hRk7OQ5Ph^ │ 2eedd5bde16b2bd0724fea31b2c98961 │ CD8-positive, alpha-beta thymocyte │ CL:0000811 │ 2eedd5bde16b2bd0724fea31b2c98961 │ 10x 3' v2 │ EFO:0009899 │ 51876 │ Publication: https://doi.org/10.1038/s41467-019-12464-3 Dataset Version: https://datasets.cellxgene.cziscience.com/71c5026d-9567-4d0f-a808-edf29440df43.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/24d42e5e-ce6d-45ff-a66b-a3b3b715deaf │ 24d42e5e-ce6d-45ff-a66b-a3b3b715deaf │ 71c5026d-9567-4d0f-a808-edf29440df43 │ NULL │ 65-year-old human stage │ HsapDv:0000159 │ normal │ PATO:0000461 │ Donor1 │ │ https://cellxgene.cziscience.com/e/01209dce-3575-4bed-b1df-129f57fbc031.cxg/ │ 54649 │ 314676313.0 │ H5AD │ TRUE │ 1219.6768255069783 │ Homo sapiens │ NCBITaxon:9606 │ 51876 │ 2021-03-09 │ raw.X │ 2024-06-11 │ NULL │ Donor1___lower lobe of left lung___65-year-old human stage___10x 3' v2______normal___TRUE │ 5.1.0 │ Hispanic or Latin American │ HANCESTRO:0014 │ male │ PATO:0000384 │ cell │ lower lobe of left lung │ UBERON:0008953 │ tissue │ Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease │ false │ https://datasets.cellxgene.cziscience.com/71c5026d-9567-4d0f-a808-edf29440df43.h5ad │ NULL │ NULL │ NULL │ 23725 │ respiratory system │ cellxgene/21-08-2025 │ CD8+ Tcm │ Th1/Th17 cells │ CD4 TCM │ 909 │ 1897.68105 │ false │ TTAACTCGTTACTGAC_Donor1_lung_rest │ cd4 tcm_cd8 tcm_cd4 th1/th17 em_cd8 naive │ cd8 naive │ t cd4 │ cd8 naive │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 209 │ 123 │ 12 │ 9 │ 9 │ 4 │ 2 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ bbec40eb2142a9570836ffed1c4c2bbe___1.h5ad │ 139040b951e384864c37af17a0fe5153___1.h5ad │ NULL │ NULL │ Hispanic or Latin American │ 891 │
│ GTGCATAGTTGACGTT_Donor1_lung_rest___01209dce-3575-4bed-b1df-129f57fbc031 │ 01209dce-3575-4bed-b1df-129f57fbc031 │ Q#-a1ejuu4 │ 2eedd5bde16b2bd0724fea31b2c98961 │ CD8-positive, alpha-beta thymocyte │ CL:0000811 │ 2eedd5bde16b2bd0724fea31b2c98961 │ 10x 3' v2 │ EFO:0009899 │ 51876 │ Publication: https://doi.org/10.1038/s41467-019-12464-3 Dataset Version: https://datasets.cellxgene.cziscience.com/71c5026d-9567-4d0f-a808-edf29440df43.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/24d42e5e-ce6d-45ff-a66b-a3b3b715deaf │ 24d42e5e-ce6d-45ff-a66b-a3b3b715deaf │ 71c5026d-9567-4d0f-a808-edf29440df43 │ NULL │ 65-year-old human stage │ HsapDv:0000159 │ normal │ PATO:0000461 │ Donor1 │ │ https://cellxgene.cziscience.com/e/01209dce-3575-4bed-b1df-129f57fbc031.cxg/ │ 54649 │ 314676313.0 │ H5AD │ TRUE │ 1219.6768255069783 │ Homo sapiens │ NCBITaxon:9606 │ 51876 │ 2021-03-09 │ raw.X │ 2024-06-11 │ NULL │ Donor1___lower lobe of left lung___65-year-old human stage___10x 3' v2______normal___TRUE │ 5.1.0 │ Hispanic or Latin American │ HANCESTRO:0014 │ male │ PATO:0000384 │ cell │ lower lobe of left lung │ UBERON:0008953 │ tissue │ Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease │ false │ https://datasets.cellxgene.cziscience.com/71c5026d-9567-4d0f-a808-edf29440df43.h5ad │ NULL │ NULL │ NULL │ 23725 │ respiratory system │ cellxgene/21-08-2025 │ CD8+ Tcm │ Non-Vd2 gd T cells │ CD8 TCM │ 772 │ 1605.6431800000007 │ false │ GTGCATAGTTGACGTT_Donor1_lung_rest │ cd4 tcm_cd8 tcm_tgd_cd8 naive │ cd8 naive │ t │ cd8 naive │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 248 │ 35 │ 66 │ 1 │ 19 │ 5 │ 5 │ 3 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ bbec40eb2142a9570836ffed1c4c2bbe___1.h5ad │ 139040b951e384864c37af17a0fe5153___1.h5ad │ NULL │ NULL │ Hispanic or Latin American │ 891 │
│ GGCGTGTGTGAGGGTT_Donor1_lung_rest___01209dce-3575-4bed-b1df-129f57fbc031 │ 01209dce-3575-4bed-b1df-129f57fbc031 │ *Ut2cJY<f^ │ 2eedd5bde16b2bd0724fea31b2c98961 │ CD8-positive, alpha-beta thymocyte │ CL:0000811 │ 2eedd5bde16b2bd0724fea31b2c98961 │ 10x 3' v2 │ EFO:0009899 │ 51876 │ Publication: https://doi.org/10.1038/s41467-019-12464-3 Dataset Version: https://datasets.cellxgene.cziscience.com/71c5026d-9567-4d0f-a808-edf29440df43.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/24d42e5e-ce6d-45ff-a66b-a3b3b715deaf │ 24d42e5e-ce6d-45ff-a66b-a3b3b715deaf │ 71c5026d-9567-4d0f-a808-edf29440df43 │ NULL │ 65-year-old human stage │ HsapDv:0000159 │ normal │ PATO:0000461 │ Donor1 │ │ https://cellxgene.cziscience.com/e/01209dce-3575-4bed-b1df-129f57fbc031.cxg/ │ 54649 │ 314676313.0 │ H5AD │ TRUE │ 1219.6768255069783 │ Homo sapiens │ NCBITaxon:9606 │ 51876 │ 2021-03-09 │ raw.X │ 2024-06-11 │ NULL │ Donor1___lower lobe of left lung___65-year-old human stage___10x 3' v2______normal___TRUE │ 5.1.0 │ Hispanic or Latin American │ HANCESTRO:0014 │ male │ PATO:0000384 │ cell │ lower lobe of left lung │ UBERON:0008953 │ tissue │ Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease │ false │ https://datasets.cellxgene.cziscience.com/71c5026d-9567-4d0f-a808-edf29440df43.h5ad │ NULL │ NULL │ NULL │ 23725 │ respiratory system │ cellxgene/21-08-2025 │ CD8+ Tem │ Vd2 gd T cells │ ILC │ 1149 │ 2148.65703 │ false │ GGCGTGTGTGAGGGTT_Donor1_lung_rest │ cd4 tcm_cd8 tem_tgd_cd8 naive │ cd8 naive │ t │ cd8 naive │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 10 │ 161 │ 25 │ 17 │ 14 │ 6 │ 2 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ bbec40eb2142a9570836ffed1c4c2bbe___1.h5ad │ 139040b951e384864c37af17a0fe5153___1.h5ad │ NULL │ NULL │ Hispanic or Latin American │ 891 │
├──────────────────────────────────────────────────────────────────────────┴──────────────────────────────────────┴────────────────────┴──────────────────────────────────┴────────────────────────────────────┴────────────────────────────┴──────────────────────────────────┴───────────┴────────────────────────┴────────────┴────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┴──────────────────────────────────────┴──────────────────────────────────────┴───────────────────┴─────────────────────────┴────────────────────────────────────┴─────────┴──────────────────────────┴────────────┴───────────────┴──────────────────────────────────────────────────────────────────────────────┴───────────────┴─────────────┴──────────┴─────────────────┴─────────────────────┴──────────────┴───────────────────────────┴────────────────────┴──────────────┴───────────────────┴────────────┴──────────────────┴───────────────────────────────────────────────────────────────────────────────────────────┴────────────────┴────────────────────────────┴──────────────────────────────────────────┴─────────┴──────────────────────┴─────────────────┴─────────────────────────┴─────────────────────────┴─────────────┴─────────────────────────────────────────────────────────────────────────────────────────────────────────────┴───────────┴─────────────────────────────────────────────────────────────────────────────────────┴────────────────────────────┴─────────┴─────────┴──────────┴──────────────────────────┴──────────────────────┴───────────────────────────────────┴────────────────────────────────┴────────────────────────────┴──────────────────────────────┴────────────────────┴───────────────┴───────────────────────────────────┴───────────────────────────────────────────┴───────────────────┴──────────────────────┴────────────────────────────┴───────────┴──────────────────┴───────────────────────┴──────────────────────┴──────────────────────┴────────────────────┴───────────────┴─────────┴───────────────────┴────────────┴────────────┴────────────┴─────────────┴─────────────┴─────────────┴──────────────┴──────────────┴──────────────┴───────────────┴───────────────┴───────────────┴───────────────┴────────────────┴────────────────┴────────────────┴──────────────┴────────────┴─────────────────────────┴───────────────────────────────────────────┴───────────────────────────────────────────┴──────────────────────────┴──────────────────────────┴────────────────────────────┴──────────────────┤
│ ? rows (>9999 rows, 20 shown) 97 columns │
└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
Querying the metadata
The DuckDB table can be queried using a number of methods described here. In particular:
.filter(): filters the metadata using a string expression.aggregate(): groups by one or more columns, and calculates some aggregate statistics such as counts.fetchdf(): Executes the query and returns it as a pandas DataFrame
table.aggregate("tissue, cell_type_unified_ensemble, COUNT(*) as n", group_expr="tissue, cell_type_unified_ensemble")
┌─────────────────────┬────────────────────────────┬────────┐
│ tissue │ cell_type_unified_ensemble │ n │
│ varchar │ varchar │ int64 │
├─────────────────────┼────────────────────────────┼────────┤
│ bone marrow │ b naive │ 30605 │
│ lung │ nk │ 91690 │
│ blood │ nk │ 883765 │
│ lamina propria │ cd4 th17 em │ 409 │
│ lung │ cd4 th2 em │ 10577 │
│ jejunal epithelium │ b memory │ 39 │
│ blood │ cd4 th2 em │ 42483 │
│ thoracic lymph node │ macrophage │ 199 │
│ spleen │ progenitor │ 36429 │
│ lamina propria │ cd4 tcm │ 16 │
│ · │ · │ · │
│ · │ · │ · │
│ · │ · │ · │
│ nasopharynx │ dc │ 17 │
│ nasopharynx │ b memory │ 33 │
│ kidney │ epidermal │ 1 │
│ cardiac ventricle │ Unknown │ 5 │
│ adipose tissue │ cdc │ 3 │
│ artery │ b │ 4 │
│ artery │ mait │ 2 │
│ cerebellum │ b naive │ 3 │
│ jejunum │ cytotoxic │ 39 │
│ parietal lobe │ cd4 tem │ 1 │
├─────────────────────┴────────────────────────────┴────────┤
│ 6410 rows (20 shown) 3 columns │
└───────────────────────────────────────────────────────────┘
table.filter("self_reported_ethnicity == 'African'")
┌──────────────────────────────────────────────────────────────────────────────────────────────────┬──────────────────────────────────────┬────────────────────┬──────────────────────────────────────────────────┬─────────────────────────────────────────────────┬────────────────────────────┬──────────────────────────────────┬───────────┬────────────────────────┬────────────┬────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┬──────────────────────────────────────┬──────────────────────────────────────┬───────────────────┬──────────────────────────┬────────────────────────────────────┬─────────┬──────────────────────────┬──────────────────────────────────────────────────────────────────────────────────────┬───────────────┬──────────────────────────────────────────────────────────────────────────────┬───────────────┬───────────────┬──────────┬─────────────────┬─────────────────────┬──────────────┬───────────────────────────┬────────────────────┬──────────────┬───────────────────┬────────────┬──────────────────┬──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┬────────────────┬─────────────────────────┬──────────────────────────────────────────┬─────────┬──────────────────────┬─────────────────┬────────────────────┬─────────────────────────┬─────────────┬─────────────────────────────────────────────────────────────────────────┬───────────┬─────────────────────────────────────────────────────────────────────────────────────┬────────────────────────────┬─────────┬─────────┬──────────┬─────────────────────────────────────┬──────────────────────┬───────────────────────────────────┬────────────────────────────────┬────────────────────────────┬──────────────────────────────┬───────────────────┬───────────────┬───────────────────────────────────────────────────────────┬──────────────────────────────────────────────┬───────────────────┬──────────────────────┬────────────────────────────┬───────────┬──────────────────┬───────────────────────┬──────────────────────┬──────────────────────┬────────────────────┬───────────────┬─────────┬───────────────────┬────────────┬────────────┬────────────┬─────────────┬─────────────┬─────────────┬──────────────┬──────────────┬──────────────┬───────────────┬───────────────┬───────────────┬───────────────┬────────────────┬────────────────┬────────────────┬──────────────┬────────────┬─────────────────────────┬───────────────────────────────────────────┬───────────────────────────────────────────┬──────────────────────────┬──────────────────────────┬───────────────────┬──────────────────┐
│ cell_id │ dataset_id │ observation_joinid │ sample_id │ cell_type │ cell_type_ontology_term_id │ sample_ │ assay │ assay_ontology_term_id │ cell_count │ citation │ collection_id │ dataset_version_id │ default_embedding │ development_stage │ development_stage_ontology_term_id │ disease │ disease_ontology_term_id │ donor_id │ experiment___ │ explorer_url │ feature_count │ filesize │ filetype │ is_primary_data │ mean_genes_per_cell │ organism │ organism_ontology_term_id │ primary_cell_count │ published_at │ raw_data_location │ revised_at │ run_from_cell_id │ sample_heuristic │ schema_version │ self_reported_ethnicity │ self_reported_ethnicity_ontology_term_id │ sex │ sex_ontology_term_id │ suspension_type │ tissue │ tissue_ontology_term_id │ tissue_type │ title │ tombstone │ url │ x_approximate_distribution │ X_umap1 │ X_umap2 │ age_days │ tissue_groups │ atlas_id │ cell_annotation_blueprint_singler │ cell_annotation_monaco_singler │ cell_annotation_azimuth_l2 │ nFeature_expressed_in_sample │ nCount_RNA │ empty_droplet │ observation_originalid │ ensemble_joinid │ cell_type_unified │ data_driven_ensemble │ cell_type_unified_ensemble │ is_immune │ subsets_Mito_sum │ subsets_Mito_detected │ subsets_Mito_percent │ subsets_Ribo_percent │ high_mitochondrion │ high_ribosome │ alive │ scDblFinder.class │ metacell_2 │ metacell_4 │ metacell_8 │ metacell_16 │ metacell_32 │ metacell_64 │ metacell_128 │ metacell_256 │ metacell_512 │ metacell_1024 │ metacell_2048 │ metacell_4096 │ metacell_8192 │ metacell_16384 │ metacell_32768 │ metacell_65536 │ sample_chunk │ cell_chunk │ sample_pseudobulk_chunk │ file_id_cellNexus_single_cell │ file_id_cellNexus_pseudobulk │ ethnicity_flagging_score │ low_confidence_ethnicity │ imputed_ethnicity │ aggregated_cells │
│ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ int32 │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ int32 │ double │ varchar │ varchar │ double │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ boolean │ varchar │ varchar │ double │ double │ int32 │ varchar │ varchar │ varchar │ varchar │ varchar │ int32 │ double │ boolean │ varchar │ varchar │ varchar │ varchar │ varchar │ boolean │ int32 │ int32 │ int32 │ int32 │ boolean │ boolean │ boolean │ varchar │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ varchar │ varchar │ double │ varchar │ varchar │ int32 │
├──────────────────────────────────────────────────────────────────────────────────────────────────┼──────────────────────────────────────┼────────────────────┼──────────────────────────────────────────────────┼─────────────────────────────────────────────────┼────────────────────────────┼──────────────────────────────────┼───────────┼────────────────────────┼────────────┼────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┼──────────────────────────────────────┼──────────────────────────────────────┼───────────────────┼──────────────────────────┼────────────────────────────────────┼─────────┼──────────────────────────┼──────────────────────────────────────────────────────────────────────────────────────┼───────────────┼──────────────────────────────────────────────────────────────────────────────┼───────────────┼───────────────┼──────────┼─────────────────┼─────────────────────┼──────────────┼───────────────────────────┼────────────────────┼──────────────┼───────────────────┼────────────┼──────────────────┼──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┼────────────────┼─────────────────────────┼──────────────────────────────────────────┼─────────┼──────────────────────┼─────────────────┼────────────────────┼─────────────────────────┼─────────────┼─────────────────────────────────────────────────────────────────────────┼───────────┼─────────────────────────────────────────────────────────────────────────────────────┼────────────────────────────┼─────────┼─────────┼──────────┼─────────────────────────────────────┼──────────────────────┼───────────────────────────────────┼────────────────────────────────┼────────────────────────────┼──────────────────────────────┼───────────────────┼───────────────┼───────────────────────────────────────────────────────────┼──────────────────────────────────────────────┼───────────────────┼──────────────────────┼────────────────────────────┼───────────┼──────────────────┼───────────────────────┼──────────────────────┼──────────────────────┼────────────────────┼───────────────┼─────────┼───────────────────┼────────────┼────────────┼────────────┼─────────────┼─────────────┼─────────────┼──────────────┼──────────────┼──────────────┼───────────────┼───────────────┼───────────────┼───────────────┼────────────────┼────────────────┼────────────────┼──────────────┼────────────┼─────────────────────────┼───────────────────────────────────────────┼───────────────────────────────────────────┼──────────────────────────┼──────────────────────────┼───────────────────┼──────────────────┤
│ AAGGCAGTCAAAGACA-CV001_KM8854559-ucl_meyer_nikolic_unpubl___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ f?~%%i=n!= │ ea4ebb456daa39324c8c554aeb54bcee │ unknown │ unknown │ ea4ebb456daa39324c8c554aeb54bcee │ 10x 5' v1 │ EFO:0011025 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 12-year-old human stage │ HsapDv:0000106 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747NP38 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747NP38___respiratory airway___12-year-old human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ NULL │ respiratory airway │ UBERON:0001005 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 4380 │ respiratory system │ cellxgene/21-08-2025 │ Epithelial cells │ Plasmacytoid dendritic cells │ Platelet │ 770 │ 5700.991400000004 │ false │ AAGGCAGTCAAAGACA-CV001_KM8854559-ucl_meyer_nikolic_unpubl │ cd8 naive_non immune_pdc_other │ other │ non immune │ other │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 503 │ 345 │ 30 │ 84 │ 32 │ 26 │ 1 │ 5 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 7 │ 2 │ 0c011c01df7877423d457cb66d49e6f9___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 0.6666666666666666 │ TRUE │ African │ 1977 │
│ ATCGAGTGTTGGTTTG-CV001_KM8854559-ucl_meyer_nikolic_unpubl___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ A6_Gn<9$^V │ ea4ebb456daa39324c8c554aeb54bcee │ nasal mucosa goblet cell │ CL:0002480 │ ea4ebb456daa39324c8c554aeb54bcee │ 10x 5' v1 │ EFO:0011025 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 12-year-old human stage │ HsapDv:0000106 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747NP38 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747NP38___respiratory airway___12-year-old human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ NULL │ respiratory airway │ UBERON:0001005 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 4380 │ respiratory system │ cellxgene/21-08-2025 │ Epithelial cells │ Intermediate monocytes │ Platelet │ 1579 │ 5838.655640000009 │ false │ ATCGAGTGTTGGTTTG-CV001_KM8854559-ucl_meyer_nikolic_unpubl │ cd8 naive_non immune_cd14 mono_secretory │ secretory │ non immune │ secretory │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 193 │ 149 │ 26 │ 15 │ 10 │ 1 │ 4 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 7 │ 2 │ 65429f53581208b81bcd446644f12bb4___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 0.6666666666666666 │ TRUE │ African │ 841 │
│ GGACGTCCAGATCGGA-1-5___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ !i+`j@se%X │ 4b19bc3e7421f9242551a74c72121269 │ club cell │ CL:0000158 │ 4b19bc3e7421f9242551a74c72121269 │ 10x 5' v2 │ EFO:0009900 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_4837472020-3173-NC005 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_4837472020-3173-NC005___nose___37-year-old human stage___10x 5' v2______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ NULL │ nose │ UBERON:0000004 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 13505 │ nasal, oral, and pharyngeal regions │ cellxgene/21-08-2025 │ Keratinocytes │ Myeloid dendritic cells │ Platelet │ 650 │ 6378.251689999999 │ false │ GGACGTCCAGATCGGA-1-5 │ NA_non immune_cdc_epithelial │ epithelial │ non immune │ epithelial │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 838 │ 3 │ 66 │ 48 │ 21 │ 20 │ 1 │ 9 │ 4 │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ 1 │ 11 │ 2 │ 10c4d0e10d3c59cf14469b89aa422bde___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 0.9 │ TRUE │ European │ 4450 │
│ LAP89_TATCTTGGTAGTATAG-1_duong___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ =1uke1lGb} │ b3d27bbec53d4fa905dddf174f974842___LAP89_1_duong │ capillary endothelial cell │ CL:0002144 │ b3d27bbec53d4fa905dddf174f974842 │ 10x 3' v3 │ EFO:0009922 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239___respiratory airway___37-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ respiratory airway │ UBERON:0001005 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 13505 │ respiratory system │ cellxgene/21-08-2025 │ Adipocytes │ Myeloid dendritic cells │ HSPC │ 1675 │ 7536.651880000007 │ false │ LAP89_TATCTTGGTAGTATAG-1_duong │ progenitor_non immune_cdc_endothelial │ endothelial │ non immune │ endothelial │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 84 │ 35 │ 45 │ 12 │ 9 │ 1 │ 4 │ 2 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 9 │ 2 │ d1054da4d0637db9f8ae8e6f9d4e86fb___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 0.875 │ TRUE │ African │ 1297 │
│ LAP89_ATTACTCCAATCGCAT-1_duong___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 36wN0h{KoY │ b3d27bbec53d4fa905dddf174f974842___LAP89_1_duong │ type II pneumocyte │ CL:0002063 │ b3d27bbec53d4fa905dddf174f974842 │ 10x 3' v3 │ EFO:0009922 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239___respiratory airway___37-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ respiratory airway │ UBERON:0001005 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 13505 │ respiratory system │ cellxgene/21-08-2025 │ Adipocytes │ Myeloid dendritic cells │ HSPC │ 2041 │ 7602.483380000011 │ false │ LAP89_ATTACTCCAATCGCAT-1_duong │ progenitor_non immune_cdc_pneumocyte │ pneumocyte │ non immune │ pneumocyte │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 3 │ 207 │ 66 │ 12 │ 7 │ 10 │ 1 │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 9 │ 2 │ 03ce407789f19088b4bd94f7fcb1c018___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 0.875 │ TRUE │ African │ 1137 │
│ LAP89_GTCAGCGAGTCAGAGC-1_duong___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ EHUd}JYqAv │ b3d27bbec53d4fa905dddf174f974842___LAP89_1_duong │ type II pneumocyte │ CL:0002063 │ b3d27bbec53d4fa905dddf174f974842 │ 10x 3' v3 │ EFO:0009922 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239___respiratory airway___37-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ respiratory airway │ UBERON:0001005 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 13505 │ respiratory system │ cellxgene/21-08-2025 │ Adipocytes │ Myeloid dendritic cells │ HSPC │ 1627 │ 7550.186420000004 │ false │ LAP89_GTCAGCGAGTCAGAGC-1_duong │ progenitor_non immune_cdc_pneumocyte │ pneumocyte │ non immune │ pneumocyte │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 536 │ 190 │ 132 │ 8 │ 10 │ 1 │ 1 │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 9 │ 2 │ 03ce407789f19088b4bd94f7fcb1c018___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 0.875 │ TRUE │ African │ 1137 │
│ TACTTGTGTTGAGGTG-1-5___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ E~3Q4ZMGx9 │ 4b19bc3e7421f9242551a74c72121269 │ respiratory hillock cell │ CL:4030023 │ 4b19bc3e7421f9242551a74c72121269 │ 10x 5' v2 │ EFO:0009900 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_4837472020-3173-NC005 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_4837472020-3173-NC005___nose___37-year-old human stage___10x 5' v2______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ NULL │ nose │ UBERON:0000004 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 13505 │ nasal, oral, and pharyngeal regions │ cellxgene/21-08-2025 │ Epithelial cells │ Myeloid dendritic cells │ CD4 Proliferating │ 3860 │ 6153.088149999992 │ false │ TACTTGTGTTGAGGTG-1-5 │ NA_non immune_cdc_epithelial │ epithelial │ non immune │ epithelial │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 135 │ 859 │ 308 │ 12 │ 25 │ 22 │ 4 │ 5 │ 5 │ 2 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ 1 │ 11 │ 2 │ 10c4d0e10d3c59cf14469b89aa422bde___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 0.9 │ TRUE │ European │ 4450 │
│ CTACATTCACGAAATA-1-5___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ GaPe`NvR-P │ 4b19bc3e7421f9242551a74c72121269 │ nasal mucosa goblet cell │ CL:0002480 │ 4b19bc3e7421f9242551a74c72121269 │ 10x 5' v2 │ EFO:0009900 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_4837472020-3173-NC005 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_4837472020-3173-NC005___nose___37-year-old human stage___10x 5' v2______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ NULL │ nose │ UBERON:0000004 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 13505 │ nasal, oral, and pharyngeal regions │ cellxgene/21-08-2025 │ Epithelial cells │ Myeloid dendritic cells │ Platelet │ 1720 │ 6295.899420000004 │ false │ CTACATTCACGAAATA-1-5 │ NA_non immune_cdc_secretory │ secretory │ non immune │ secretory │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 33 │ 84 │ 147 │ 28 │ 13 │ 15 │ 4 │ 2 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 11 │ 2 │ 74206d3aa076189a055d200e84d5b627___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 0.9 │ TRUE │ European │ 1504 │
│ TCGTACCAGACACTAA-1-5___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ Es*y*-1Ex< │ 4b19bc3e7421f9242551a74c72121269 │ club cell │ CL:0000158 │ 4b19bc3e7421f9242551a74c72121269 │ 10x 5' v2 │ EFO:0009900 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_4837472020-3173-NC005 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_4837472020-3173-NC005___nose___37-year-old human stage___10x 5' v2______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ NULL │ nose │ UBERON:0000004 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 13505 │ nasal, oral, and pharyngeal regions │ cellxgene/21-08-2025 │ Epithelial cells │ Myeloid dendritic cells │ Platelet │ 1952 │ 6321.147249999985 │ false │ TCGTACCAGACACTAA-1-5 │ NA_non immune_cdc_epithelial │ epithelial │ non immune │ epithelial │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 105 │ 850 │ 252 │ 52 │ 59 │ 7 │ 12 │ 4 │ 4 │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ 1 │ 11 │ 2 │ 10c4d0e10d3c59cf14469b89aa422bde___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 0.9 │ TRUE │ European │ 4450 │
│ GTATTCTCATCCCACT-1-5___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ xs1MLe*nvg │ 4b19bc3e7421f9242551a74c72121269 │ club cell │ CL:0000158 │ 4b19bc3e7421f9242551a74c72121269 │ 10x 5' v2 │ EFO:0009900 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_4837472020-3173-NC005 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_4837472020-3173-NC005___nose___37-year-old human stage___10x 5' v2______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ NULL │ nose │ UBERON:0000004 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 13505 │ nasal, oral, and pharyngeal regions │ cellxgene/21-08-2025 │ Epithelial cells │ Intermediate monocytes │ Eryth │ 373 │ 6111.819569999998 │ false │ GTATTCTCATCCCACT-1-5 │ NA_non immune_cd14 mono_epithelial │ epithelial │ non immune │ epithelial │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 324 │ 120 │ 35 │ 171 │ 22 │ 14 │ 3 │ 10 │ 2 │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ 1 │ 11 │ 2 │ 10c4d0e10d3c59cf14469b89aa422bde___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 0.9 │ TRUE │ European │ 4450 │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
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│ ATCTACTTCTTTACAC-CV001_KM8853597-ucl_meyer_nikolic_unpubl___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9_ioYKZ4Kq │ 2e6c1fb6624e39411662792e9660e7f6 │ ionocyte │ CL:0005006 │ 2e6c1fb6624e39411662792e9660e7f6 │ 10x 5' v1 │ EFO:0011025 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 12-month-old human stage │ HsapDv:0000185 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747NP18 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747NP18___respiratory airway___12-month-old human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ respiratory airway │ UBERON:0001005 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 360 │ respiratory system │ cellxgene/21-08-2025 │ Epithelial cells │ Myeloid dendritic cells │ HSPC │ 1518 │ 6376.953859999983 │ false │ ATCTACTTCTTTACAC-CV001_KM8853597-ucl_meyer_nikolic_unpubl │ progenitor_non immune_cdc_secretory │ secretory │ non immune │ secretory │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 37 │ 6 │ 3 │ 5 │ 2 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ dc67e8b365ae32ed59044c98ecc880f7___1.h5ad │ a4942dd92de40cc23c6161df7e02ccc7___1.h5ad │ NULL │ NULL │ African │ 131 │
│ CCCAGTTGTGCCTGGT-CV001_KM8853598-ucl_meyer_nikolic_unpubl___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ e150<&h9rZ │ 693c2a06afab5eb9ddafbad9137d295b │ respiratory basal cell │ CL:0002633 │ 693c2a06afab5eb9ddafbad9137d295b │ 10x 5' v1 │ EFO:0011025 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 12-month-old human stage │ HsapDv:0000185 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747NP18 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747NP18___lung___12-month-old human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung │ UBERON:0002048 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 360 │ respiratory system │ cellxgene/21-08-2025 │ Epithelial cells │ Plasmacytoid dendritic cells │ Platelet │ 2015 │ 5466.221970000016 │ false │ CCCAGTTGTGCCTGGT-CV001_KM8853598-ucl_meyer_nikolic_unpubl │ progenitor_non immune_pdc_epithelial │ epithelial │ non immune │ epithelial │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 406 │ 97 │ 77 │ 86 │ 50 │ 27 │ 4 │ 3 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 4 │ 2 │ 9b99f7fe2ba8ce125d526f932eecf327___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ NULL │ NULL │ African │ 1864 │
│ GCAGTTATCGTTACAG-CV001_KM8853597-ucl_meyer_nikolic_unpubl___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ a&`Raa>D1; │ 2e6c1fb6624e39411662792e9660e7f6 │ respiratory basal cell │ CL:0002633 │ 2e6c1fb6624e39411662792e9660e7f6 │ 10x 5' v1 │ EFO:0011025 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 12-month-old human stage │ HsapDv:0000185 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747NP18 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747NP18___respiratory airway___12-month-old human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ respiratory airway │ UBERON:0001005 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 360 │ respiratory system │ cellxgene/21-08-2025 │ Epithelial cells │ Myeloid dendritic cells │ HSPC │ 2324 │ 5497.127409999977 │ false │ GCAGTTATCGTTACAG-CV001_KM8853597-ucl_meyer_nikolic_unpubl │ progenitor_non immune_cdc_epithelial │ epithelial │ non immune │ epithelial │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 71 │ 6 │ 35 │ 30 │ 4 │ 3 │ 2 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 2c6e0353ad4606117ca4c104eacc8f18___1.h5ad │ a4942dd92de40cc23c6161df7e02ccc7___1.h5ad │ NULL │ NULL │ African │ 542 │
│ ACACCCTAGAACAACT-CV001_KM8854508-ucl_meyer_nikolic_unpubl___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ gkLUSQ~a64 │ d59dd0106aca15ba30d72c420799e871 │ ciliated columnar cell of tracheobronchial tree │ CL:0002145 │ d59dd0106aca15ba30d72c420799e871 │ 10x 5' v1 │ EFO:0011025 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 11-month-old human stage │ HsapDv:0000184 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747NP30 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747NP30___respiratory airway___11-month-old human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ NULL │ respiratory airway │ UBERON:0001005 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 330 │ respiratory system │ cellxgene/21-08-2025 │ Epithelial cells │ Plasmacytoid dendritic cells │ HSPC │ 3067 │ 5897.928969999998 │ false │ ACACCCTAGAACAACT-CV001_KM8854508-ucl_meyer_nikolic_unpubl │ progenitor_non immune_pdc_epithelial │ epithelial │ non immune │ epithelial │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 9 │ 175 │ 12 │ 42 │ 3 │ 6 │ 2 │ 3 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 2 │ 1 │ 9a985c2b5d60d1db3095bf5450142956___1.h5ad │ a4942dd92de40cc23c6161df7e02ccc7___1.h5ad │ NULL │ NULL │ African │ 946 │
│ ATTGGACAGCTCAACT_T85___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ -a;E13$C%g │ 15f0b42d719a5e8fbbcbb094a0a48aa1 │ respiratory basal cell │ CL:0002633 │ 15f0b42d719a5e8fbbcbb094a0a48aa1 │ 10x 3' v2 │ EFO:0009899 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 59-year-old human stage │ HsapDv:0000153 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747T85 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747T85___respiratory airway___59-year-old human stage___10x 3' v2______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ respiratory airway │ UBERON:0001005 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 21535 │ respiratory system │ cellxgene/21-08-2025 │ Epithelial cells │ Myeloid dendritic cells │ HSPC │ 2531 │ 4205.862710000011 │ false │ ATTGGACAGCTCAACT_T85 │ cdc_non immune_cdc_epithelial │ epithelial │ non immune │ epithelial │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 248 │ 663 │ 42 │ 40 │ 5 │ 25 │ 15 │ 5 │ 4 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 6 │ 2 │ bed5ce2b45a1b9ffede58a230e1b428a___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ NULL │ NULL │ African │ 3223 │
│ TCGGGACGTGCGGTAA-CV001_KM8853597-ucl_meyer_nikolic_unpubl___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ BgAn|lZY1X │ 2e6c1fb6624e39411662792e9660e7f6 │ respiratory basal cell │ CL:0002633 │ 2e6c1fb6624e39411662792e9660e7f6 │ 10x 5' v1 │ EFO:0011025 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 12-month-old human stage │ HsapDv:0000185 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747NP18 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747NP18___respiratory airway___12-month-old human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ respiratory airway │ UBERON:0001005 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 360 │ respiratory system │ cellxgene/21-08-2025 │ Epithelial cells │ Myeloid dendritic cells │ HSPC │ 2532 │ 5758.978270000038 │ false │ TCGGGACGTGCGGTAA-CV001_KM8853597-ucl_meyer_nikolic_unpubl │ progenitor_non immune_cdc_epithelial │ epithelial │ non immune │ epithelial │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 38 │ 15 │ 20 │ 10 │ 2 │ 4 │ 2 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 2c6e0353ad4606117ca4c104eacc8f18___1.h5ad │ a4942dd92de40cc23c6161df7e02ccc7___1.h5ad │ NULL │ NULL │ African │ 542 │
│ ATCTACTTCTTGAGAC_T85___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ A@U$<4tuKI │ 15f0b42d719a5e8fbbcbb094a0a48aa1 │ respiratory basal cell │ CL:0002633 │ 15f0b42d719a5e8fbbcbb094a0a48aa1 │ 10x 3' v2 │ EFO:0009899 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 59-year-old human stage │ HsapDv:0000153 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747T85 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747T85___respiratory airway___59-year-old human stage___10x 3' v2______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ respiratory airway │ UBERON:0001005 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 21535 │ respiratory system │ cellxgene/21-08-2025 │ Epithelial cells │ Classical monocytes │ HSPC │ 2043 │ 4314.28669999999 │ false │ ATCTACTTCTTGAGAC_T85 │ cdc_non immune_cd14 mono_epithelial │ epithelial │ non immune │ epithelial │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 92 │ 67 │ 292 │ 181 │ 94 │ 47 │ 11 │ 10 │ 3 │ 2 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 6 │ 2 │ bed5ce2b45a1b9ffede58a230e1b428a___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ NULL │ NULL │ African │ 3223 │
│ AGGTCATCACATCCGG-CV001_KM8853598-ucl_meyer_nikolic_unpubl___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ t{J$fe@e%G │ 693c2a06afab5eb9ddafbad9137d295b │ club cell │ CL:0000158 │ 693c2a06afab5eb9ddafbad9137d295b │ 10x 5' v1 │ EFO:0011025 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 12-month-old human stage │ HsapDv:0000185 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747NP18 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747NP18___lung___12-month-old human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung │ UBERON:0002048 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 360 │ respiratory system │ cellxgene/21-08-2025 │ Epithelial cells │ Classical monocytes │ Plasmablast │ 1337 │ 6143.138440000004 │ false │ AGGTCATCACATCCGG-CV001_KM8853598-ucl_meyer_nikolic_unpubl │ progenitor_non immune_cd14 mono_epithelial │ epithelial │ non immune │ epithelial │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 544 │ 189 │ 137 │ 98 │ 11 │ 14 │ 9 │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 4 │ 2 │ 9b99f7fe2ba8ce125d526f932eecf327___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ NULL │ NULL │ African │ 1864 │
│ TTTGTCAGTGCTAGCC_T85___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ GZ0RwefQ-U │ 15f0b42d719a5e8fbbcbb094a0a48aa1 │ nasal mucosa goblet cell │ CL:0002480 │ 15f0b42d719a5e8fbbcbb094a0a48aa1 │ 10x 3' v2 │ EFO:0009899 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 59-year-old human stage │ HsapDv:0000153 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747T85 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747T85___respiratory airway___59-year-old human stage___10x 3' v2______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ respiratory airway │ UBERON:0001005 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 21535 │ respiratory system │ cellxgene/21-08-2025 │ Epithelial cells │ Classical monocytes │ ASDC │ 3857 │ 6059.514770000011 │ false │ TTTGTCAGTGCTAGCC_T85 │ cdc_non immune_cd14 mono_secretory │ secretory │ non immune │ secretory │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 94 │ 18 │ 16 │ 17 │ 4 │ 2 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 6 │ 2 │ c2dd82365ec0a5f01fa0563a35fa7541___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ NULL │ NULL │ African │ 339 │
│ LAP91_GACTCTCAGATTAGAC-1_duong___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ ;icMsP?lx@ │ 9c8fa5a8d2ae37179b579a0217670512___LAP91_1_duong │ classical monocyte │ CL:0000860 │ 9c8fa5a8d2ae37179b579a0217670512 │ 10x 3' v3 │ EFO:0009922 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239___lung parenchyma___37-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 13505 │ respiratory system │ cellxgene/21-08-2025 │ Neutrophils │ Low-density neutrophils │ CD14 Mono │ 464 │ 7582.985489999997 │ false │ LAP91_GACTCTCAGATTAGAC-1_duong │ progenitor_granulocyte_granulocyte_monocytic │ monocytic │ granulocyte │ Unknown │ true │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ false │ singlet │ 4 │ 26 │ 10 │ 6 │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 12 │ 2 │ 7477a838ce5baf4278da7e47da91069b___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 1.0 │ FALSE │ African │ NULL │
├──────────────────────────────────────────────────────────────────────────────────────────────────┴──────────────────────────────────────┴────────────────────┴──────────────────────────────────────────────────┴─────────────────────────────────────────────────┴────────────────────────────┴──────────────────────────────────┴───────────┴────────────────────────┴────────────┴────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┴──────────────────────────────────────┴──────────────────────────────────────┴───────────────────┴──────────────────────────┴────────────────────────────────────┴─────────┴──────────────────────────┴──────────────────────────────────────────────────────────────────────────────────────┴───────────────┴──────────────────────────────────────────────────────────────────────────────┴───────────────┴───────────────┴──────────┴─────────────────┴─────────────────────┴──────────────┴───────────────────────────┴────────────────────┴──────────────┴───────────────────┴────────────┴──────────────────┴──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┴────────────────┴─────────────────────────┴──────────────────────────────────────────┴─────────┴──────────────────────┴─────────────────┴────────────────────┴─────────────────────────┴─────────────┴─────────────────────────────────────────────────────────────────────────┴───────────┴─────────────────────────────────────────────────────────────────────────────────────┴────────────────────────────┴─────────┴─────────┴──────────┴─────────────────────────────────────┴──────────────────────┴───────────────────────────────────┴────────────────────────────────┴────────────────────────────┴──────────────────────────────┴───────────────────┴───────────────┴───────────────────────────────────────────────────────────┴──────────────────────────────────────────────┴───────────────────┴──────────────────────┴────────────────────────────┴───────────┴──────────────────┴───────────────────────┴──────────────────────┴──────────────────────┴────────────────────┴───────────────┴─────────┴───────────────────┴────────────┴────────────┴────────────┴─────────────┴─────────────┴─────────────┴──────────────┴──────────────┴──────────────┴───────────────┴───────────────┴───────────────┴───────────────┴────────────────┴────────────────┴────────────────┴──────────────┴────────────┴─────────────────────────┴───────────────────────────────────────────┴───────────────────────────────────────────┴──────────────────────────┴──────────────────────────┴───────────────────┴──────────────────┤
│ ? rows (>9999 rows, 20 shown) 97 columns │
└───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
Quality control
cellNexusPy metadata provides quality control records such as empty droplets, inoperable cells (death or damaged), doublets, and samples with low gene counts:
table = table.filter("""
empty_droplet = 'false'
AND alive = 'true'
AND "scDblFinder.class" != 'doublet'
AND feature_count >= 5000
""")
query = table.filter("""
self_reported_ethnicity = 'African'
AND assay LIKE '%10%'
AND tissue = 'lung parenchyma'
AND cell_type LIKE '%CD4%'
AND feature_count >= 5000
""")
query
┌───────────────────────────────────────────────────────────────────────┬──────────────────────────────────────┬────────────────────┬──────────────────────────────────────────────────┬─────────────────────────────────┬────────────────────────────┬──────────────────────────────────┬───────────┬────────────────────────┬────────────┬────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┬──────────────────────────────────────┬──────────────────────────────────────┬───────────────────┬─────────────────────────┬────────────────────────────────────┬─────────┬──────────────────────────┬───────────────────────────────────────────────────────────────────────────────┬───────────────┬──────────────────────────────────────────────────────────────────────────────┬───────────────┬───────────────┬──────────┬─────────────────┬─────────────────────┬──────────────┬───────────────────────────┬────────────────────┬──────────────┬───────────────────┬────────────┬──────────────────┬──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┬────────────────┬─────────────────────────┬──────────────────────────────────────────┬─────────┬──────────────────────┬─────────────────┬─────────────────┬─────────────────────────┬─────────────┬─────────────────────────────────────────────────────────────────────────┬───────────┬─────────────────────────────────────────────────────────────────────────────────────┬────────────────────────────┬─────────┬─────────┬──────────┬────────────────────┬──────────────────────┬───────────────────────────────────┬────────────────────────────────┬────────────────────────────┬──────────────────────────────┬────────────────────┬───────────────┬────────────────────────────────┬──────────────────────────────────────────┬───────────────────┬──────────────────────┬────────────────────────────┬───────────┬──────────────────┬───────────────────────┬──────────────────────┬──────────────────────┬────────────────────┬───────────────┬─────────┬───────────────────┬────────────┬────────────┬────────────┬─────────────┬─────────────┬─────────────┬──────────────┬──────────────┬──────────────┬───────────────┬───────────────┬───────────────┬───────────────┬────────────────┬────────────────┬────────────────┬──────────────┬────────────┬─────────────────────────┬───────────────────────────────────────────┬───────────────────────────────────────────┬──────────────────────────┬──────────────────────────┬───────────────────┬──────────────────┐
│ cell_id │ dataset_id │ observation_joinid │ sample_id │ cell_type │ cell_type_ontology_term_id │ sample_ │ assay │ assay_ontology_term_id │ cell_count │ citation │ collection_id │ dataset_version_id │ default_embedding │ development_stage │ development_stage_ontology_term_id │ disease │ disease_ontology_term_id │ donor_id │ experiment___ │ explorer_url │ feature_count │ filesize │ filetype │ is_primary_data │ mean_genes_per_cell │ organism │ organism_ontology_term_id │ primary_cell_count │ published_at │ raw_data_location │ revised_at │ run_from_cell_id │ sample_heuristic │ schema_version │ self_reported_ethnicity │ self_reported_ethnicity_ontology_term_id │ sex │ sex_ontology_term_id │ suspension_type │ tissue │ tissue_ontology_term_id │ tissue_type │ title │ tombstone │ url │ x_approximate_distribution │ X_umap1 │ X_umap2 │ age_days │ tissue_groups │ atlas_id │ cell_annotation_blueprint_singler │ cell_annotation_monaco_singler │ cell_annotation_azimuth_l2 │ nFeature_expressed_in_sample │ nCount_RNA │ empty_droplet │ observation_originalid │ ensemble_joinid │ cell_type_unified │ data_driven_ensemble │ cell_type_unified_ensemble │ is_immune │ subsets_Mito_sum │ subsets_Mito_detected │ subsets_Mito_percent │ subsets_Ribo_percent │ high_mitochondrion │ high_ribosome │ alive │ scDblFinder.class │ metacell_2 │ metacell_4 │ metacell_8 │ metacell_16 │ metacell_32 │ metacell_64 │ metacell_128 │ metacell_256 │ metacell_512 │ metacell_1024 │ metacell_2048 │ metacell_4096 │ metacell_8192 │ metacell_16384 │ metacell_32768 │ metacell_65536 │ sample_chunk │ cell_chunk │ sample_pseudobulk_chunk │ file_id_cellNexus_single_cell │ file_id_cellNexus_pseudobulk │ ethnicity_flagging_score │ low_confidence_ethnicity │ imputed_ethnicity │ aggregated_cells │
│ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ int32 │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ int32 │ double │ varchar │ varchar │ double │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ boolean │ varchar │ varchar │ double │ double │ int32 │ varchar │ varchar │ varchar │ varchar │ varchar │ int32 │ double │ boolean │ varchar │ varchar │ varchar │ varchar │ varchar │ boolean │ int32 │ int32 │ int32 │ int32 │ boolean │ boolean │ boolean │ varchar │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ varchar │ varchar │ double │ varchar │ varchar │ int32 │
├───────────────────────────────────────────────────────────────────────┼──────────────────────────────────────┼────────────────────┼──────────────────────────────────────────────────┼─────────────────────────────────┼────────────────────────────┼──────────────────────────────────┼───────────┼────────────────────────┼────────────┼────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┼──────────────────────────────────────┼──────────────────────────────────────┼───────────────────┼─────────────────────────┼────────────────────────────────────┼─────────┼──────────────────────────┼───────────────────────────────────────────────────────────────────────────────┼───────────────┼──────────────────────────────────────────────────────────────────────────────┼───────────────┼───────────────┼──────────┼─────────────────┼─────────────────────┼──────────────┼───────────────────────────┼────────────────────┼──────────────┼───────────────────┼────────────┼──────────────────┼──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┼────────────────┼─────────────────────────┼──────────────────────────────────────────┼─────────┼──────────────────────┼─────────────────┼─────────────────┼─────────────────────────┼─────────────┼─────────────────────────────────────────────────────────────────────────┼───────────┼─────────────────────────────────────────────────────────────────────────────────────┼────────────────────────────┼─────────┼─────────┼──────────┼────────────────────┼──────────────────────┼───────────────────────────────────┼────────────────────────────────┼────────────────────────────┼──────────────────────────────┼────────────────────┼───────────────┼────────────────────────────────┼──────────────────────────────────────────┼───────────────────┼──────────────────────┼────────────────────────────┼───────────┼──────────────────┼───────────────────────┼──────────────────────┼──────────────────────┼────────────────────┼───────────────┼─────────┼───────────────────┼────────────┼────────────┼────────────┼─────────────┼─────────────┼─────────────┼──────────────┼──────────────┼──────────────┼───────────────┼───────────────┼───────────────┼───────────────┼────────────────┼────────────────┼────────────────┼──────────────┼────────────┼─────────────────────────┼───────────────────────────────────────────┼───────────────────────────────────────────┼──────────────────────────┼──────────────────────────┼───────────────────┼──────────────────┤
│ CTGTTTAGTGACTACT_SC24___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ WNfm2B*T#b │ 270eb221dd0456cc063240404aec74cd │ CD4-positive, alpha-beta T cell │ CL:0000624 │ 270eb221dd0456cc063240404aec74cd │ 10x 3' v2 │ EFO:0009899 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 22-year-old human stage │ HsapDv:0000116 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747Donor_06 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747Donor_06___lung parenchyma___22-year-old human stage___10x 3' v2______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 8030 │ respiratory system │ cellxgene/21-08-2025 │ CD4+ T-cells │ Naive CD8 T cells │ CD4 Naive │ 723 │ 3414.5829899999985 │ false │ CTGTTTAGTGACTACT_SC24 │ cd16 mono_t cd4_cd8 naive_t cd4 │ t cd4 │ t cd4 │ t cd4 │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 13 │ 1 │ 4 │ 3 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 7 │ 2 │ 8e1c12bf9a1d3ad7e805ac1a66fff5da___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 0.5 │ TRUE │ South Asian │ 43 │
│ AAGCCGCGTGTCCTCT_F02607___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ _$G0w7n|j@ │ e4d7f8162faf68a85f61bdbd81dae627 │ CD4-positive, alpha-beta T cell │ CL:0000624 │ e4d7f8162faf68a85f61bdbd81dae627 │ 10x 5' v1 │ EFO:0011025 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 29-year-old human stage │ HsapDv:0000123 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD104 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD104___lung parenchyma___29-year-old human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 10585 │ respiratory system │ cellxgene/21-08-2025 │ Adipocytes │ Th17 cells │ CD4 TCM │ 471 │ 4780.512520000001 │ false │ AAGCCGCGTGTCCTCT_F02607 │ NA_non immune_cd4 th17 em_t cd4 │ t cd4 │ non immune │ other │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 9 │ 3 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 11 │ 2 │ 1334018aa2e484043b9780895420dfe8___2.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___2.h5ad │ 0.0 │ TRUE │ European │ 22 │
│ AGGTCCGTCCAGTAGT_F02526___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ UC?pUPL1GZ │ d0a8856647d20b1fa1e83edb4bb9313e │ CD4-positive, alpha-beta T cell │ CL:0000624 │ d0a8856647d20b1fa1e83edb4bb9313e │ 10x 5' v1 │ EFO:0011025 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 55-year-old human stage │ HsapDv:0000149 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD92 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD92___lung parenchyma___55-year-old human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 20075 │ respiratory system │ cellxgene/21-08-2025 │ CD8+ Tem │ Effector memory CD8 T cells │ CD8 TEM │ 700 │ 5443.884920000003 │ false │ AGGTCCGTCCAGTAGT_F02526 │ progenitor_cd8 tem_cd8 tem_t cd4 │ t cd4 │ cd8 tem │ t cd4 │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 28 │ 50 │ 5 │ 3 │ 1 │ 1 │ 2 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 5 │ 2 │ e52795dec7b626b6276b867d55328d9f___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 0.6666666666666666 │ TRUE │ European │ 336 │
│ AGACGTTAGAGAACAG_F02526___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ V43m=xZrYN │ d0a8856647d20b1fa1e83edb4bb9313e │ CD4-positive, alpha-beta T cell │ CL:0000624 │ d0a8856647d20b1fa1e83edb4bb9313e │ 10x 5' v1 │ EFO:0011025 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 55-year-old human stage │ HsapDv:0000149 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD92 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD92___lung parenchyma___55-year-old human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 20075 │ respiratory system │ cellxgene/21-08-2025 │ CD4+ Tem │ Effector memory CD8 T cells │ CD4 TCM │ 446 │ 6417.487769999994 │ false │ AGACGTTAGAGAACAG_F02526 │ progenitor_cd4 tem_cd8 tem_t cd4 │ t cd4 │ Unknown │ t cd4 │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 6 │ 31 │ 36 │ 12 │ 2 │ 4 │ 3 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 5 │ 2 │ e52795dec7b626b6276b867d55328d9f___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 0.6666666666666666 │ TRUE │ European │ 336 │
│ TCACGAACACACCGAC_F02526___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ <UB2cuB(-R │ d0a8856647d20b1fa1e83edb4bb9313e │ CD4-positive, alpha-beta T cell │ CL:0000624 │ d0a8856647d20b1fa1e83edb4bb9313e │ 10x 5' v1 │ EFO:0011025 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 55-year-old human stage │ HsapDv:0000149 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD92 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD92___lung parenchyma___55-year-old human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 20075 │ respiratory system │ cellxgene/21-08-2025 │ CD4+ Tem │ Th1/Th17 cells │ CD4 TCM │ 661 │ 5140.212969999999 │ false │ TCACGAACACACCGAC_F02526 │ progenitor_cd4 tem_cd4 th1/th17 em_t cd4 │ t cd4 │ cd4 th1/th17 em │ cd4 th1/th17 em │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 50 │ 44 │ 7 │ 10 │ 3 │ 2 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 5 │ 2 │ 05caaf5f714b928ffe4f831211f30cf9___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 0.6666666666666666 │ TRUE │ European │ 186 │
│ GGCTCGATCACTTACT_F00409___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 98x(9Fs4Q< │ bfe624d44f7e5868cc22e11ad0f13866 │ CD4-positive, alpha-beta T cell │ CL:0000624 │ bfe624d44f7e5868cc22e11ad0f13866 │ 10x 5' v1 │ EFO:0011025 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 31-year-old human stage │ HsapDv:0000125 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD69 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD69___lung parenchyma___31-year-old human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 11315 │ respiratory system │ cellxgene/21-08-2025 │ CD4+ Tem │ Th1/Th17 cells │ CD4 TCM │ 1514 │ 5529.080849999984 │ false │ GGCTCGATCACTTACT_F00409 │ cd4 tcm_cd4 tem_cd4 th1/th17 em_t cd4 │ t cd4 │ cd4 th1/th17 em │ cd4 th1/th17 em │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 14 │ 5 │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 3cef5b6aa0f5772485bb710f71e69456___1.h5ad │ a4942dd92de40cc23c6161df7e02ccc7___1.h5ad │ 1.0 │ FALSE │ African │ 47 │
│ ACGATGTAGAGCCTAG_F02526___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ <zRFt{z~mX │ d0a8856647d20b1fa1e83edb4bb9313e │ CD4-positive, alpha-beta T cell │ CL:0000624 │ d0a8856647d20b1fa1e83edb4bb9313e │ 10x 5' v1 │ EFO:0011025 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 55-year-old human stage │ HsapDv:0000149 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD92 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD92___lung parenchyma___55-year-old human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 20075 │ respiratory system │ cellxgene/21-08-2025 │ CD8+ Tcm │ Effector memory CD8 T cells │ CD8 TEM │ 806 │ 5137.590340000002 │ false │ ACGATGTAGAGCCTAG_F02526 │ progenitor_cd8 tcm_cd8 tem_t cd4 │ t cd4 │ t cd8 │ t cd4 │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 28 │ 50 │ 5 │ 3 │ 1 │ 1 │ 2 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 5 │ 2 │ e52795dec7b626b6276b867d55328d9f___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 0.6666666666666666 │ TRUE │ European │ 336 │
│ TTCGAAGCAGCTGCTG_F01853___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ Agz|pY8y5T │ a2459ad4272363e6eb775e8e99607c3e │ CD4-positive, alpha-beta T cell │ CL:0000624 │ a2459ad4272363e6eb775e8e99607c3e │ 10x 5' v1 │ EFO:0011025 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 53-year-old human stage │ HsapDv:0000147 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD85 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD85___lung parenchyma___53-year-old human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 19345 │ respiratory system │ cellxgene/21-08-2025 │ CD8+ Tcm │ T regulatory cells │ CD4 TCM │ 695 │ 6153.737810000003 │ false │ TTCGAAGCAGCTGCTG_F01853 │ NA_cd8 tcm_treg_t cd4 │ t cd4 │ Unknown │ treg │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 9e62207287ebeaa020d3e92d17b01f8e___1.h5ad │ a4942dd92de40cc23c6161df7e02ccc7___1.h5ad │ 1.0 │ FALSE │ African │ 1 │
│ GCAGCCAAGCCTATGT_F02526___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ Dj{h@$MwO8 │ d0a8856647d20b1fa1e83edb4bb9313e │ CD4-positive, alpha-beta T cell │ CL:0000624 │ d0a8856647d20b1fa1e83edb4bb9313e │ 10x 5' v1 │ EFO:0011025 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 55-year-old human stage │ HsapDv:0000149 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD92 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD92___lung parenchyma___55-year-old human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 20075 │ respiratory system │ cellxgene/21-08-2025 │ CD8+ Tem │ MAIT cells │ MAIT │ 952 │ 5727.74044 │ false │ GCAGCCAAGCCTATGT_F02526 │ progenitor_cd8 tem_mait_t cd4 │ t cd4 │ progenitor │ t cd4 │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 4 │ 48 │ 6 │ 14 │ 5 │ 2 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 5 │ 2 │ e52795dec7b626b6276b867d55328d9f___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 0.6666666666666666 │ TRUE │ European │ 336 │
│ CCGTTCAAGATCCTGT_F02607___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ N;qgpZ@z91 │ e4d7f8162faf68a85f61bdbd81dae627 │ CD4-positive, alpha-beta T cell │ CL:0000624 │ e4d7f8162faf68a85f61bdbd81dae627 │ 10x 5' v1 │ EFO:0011025 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 29-year-old human stage │ HsapDv:0000123 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD104 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD104___lung parenchyma___29-year-old human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 10585 │ respiratory system │ cellxgene/21-08-2025 │ CD4+ Tem │ Th1/Th17 cells │ CD4 TCM │ 1234 │ 4164.975309999998 │ false │ CCGTTCAAGATCCTGT_F02607 │ NA_cd4 tem_cd4 th1/th17 em_t cd4 │ t cd4 │ cd4 th1/th17 em │ cd4 th1/th17 em │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 11 │ 2 │ 505f851988e91eb226d9542ec5870881___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 0.0 │ TRUE │ European │ 14 │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ GAGCAGAAGTGGAGTC_F02526___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 6Wbx$vHfdA │ d0a8856647d20b1fa1e83edb4bb9313e │ CD4-positive, alpha-beta T cell │ CL:0000624 │ d0a8856647d20b1fa1e83edb4bb9313e │ 10x 5' v1 │ EFO:0011025 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 55-year-old human stage │ HsapDv:0000149 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD92 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD92___lung parenchyma___55-year-old human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 20075 │ respiratory system │ cellxgene/21-08-2025 │ Tregs │ Th17 cells │ CD4 TCM │ 744 │ 5116.505849999994 │ false │ GAGCAGAAGTGGAGTC_F02526 │ progenitor_treg_cd4 th17 em_t cd4 │ t cd4 │ progenitor │ t cd4 │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 50 │ 19 │ 2 │ 3 │ 1 │ 1 │ 2 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 5 │ 2 │ e52795dec7b626b6276b867d55328d9f___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 0.6666666666666666 │ TRUE │ European │ 336 │
│ AGCTTCCCATGACTGT_SC84___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ aW$eYv!nw6 │ 4f067f7e5f960bc72b0710684a521e84____SC84 │ CD4-positive, alpha-beta T cell │ CL:0000624 │ 4f067f7e5f960bc72b0710684a521e84 │ 10x 3' v3 │ EFO:0009922 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 52-year-old human stage │ HsapDv:0000146 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747NU_CZI01 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747NU_CZI01___lung parenchyma___52-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 18980 │ respiratory system │ cellxgene/21-08-2025 │ Tregs │ T regulatory cells │ CD4 TCM │ 1244 │ 4855.224029999997 │ false │ AGCTTCCCATGACTGT_SC84 │ cd14 mono_treg_treg_t cd4 │ t cd4 │ treg │ treg │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 15 │ 1 │ 5 │ 2 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 14 │ 2 │ 5dcd68cc5017f513da840caaa6e9fc8f___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 0.5 │ TRUE │ European │ 52 │
│ TGACAGTGTACCAATC_SC84___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ MW$lt=VxZM │ 4f067f7e5f960bc72b0710684a521e84____SC84 │ CD4-positive, alpha-beta T cell │ CL:0000624 │ 4f067f7e5f960bc72b0710684a521e84 │ 10x 3' v3 │ EFO:0009922 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 52-year-old human stage │ HsapDv:0000146 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747NU_CZI01 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747NU_CZI01___lung parenchyma___52-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 18980 │ respiratory system │ cellxgene/21-08-2025 │ CD4+ Tcm │ T regulatory cells │ CD4 TCM │ 1204 │ 5285.411519999998 │ false │ TGACAGTGTACCAATC_SC84 │ cd14 mono_cd4 tcm_treg_t cd4 │ t cd4 │ t cd4 │ t cd4 │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 28 │ 20 │ 4 │ 4 │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 14 │ 2 │ 68aa23f4bbaaa7ff1068447055a7cec8___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 0.5 │ TRUE │ European │ 133 │
│ TTTCCTCTCAAAGTAG_F02526___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ p>fW<SCE$j │ d0a8856647d20b1fa1e83edb4bb9313e │ CD4-positive, alpha-beta T cell │ CL:0000624 │ d0a8856647d20b1fa1e83edb4bb9313e │ 10x 5' v1 │ EFO:0011025 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 55-year-old human stage │ HsapDv:0000149 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD92 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD92___lung parenchyma___55-year-old human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 20075 │ respiratory system │ cellxgene/21-08-2025 │ CD8+ T-cells │ Naive CD8 T cells │ CD8 TCM │ 1001 │ 4180.012710000006 │ false │ TTTCCTCTCAAAGTAG_F02526 │ progenitor_t cd8_cd8 naive_t cd4 │ t cd4 │ cd8 naive │ t cd4 │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 10 │ 64 │ 22 │ 8 │ 7 │ 5 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 5 │ 2 │ e52795dec7b626b6276b867d55328d9f___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 0.6666666666666666 │ TRUE │ European │ 336 │
│ LAP92_CTCAAGACAGGCCTGT-1_duong___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ VZIjsND18z │ 9c8fa5a8d2ae37179b579a0217670512___LAP92_1_duong │ CD4-positive, alpha-beta T cell │ CL:0000624 │ 9c8fa5a8d2ae37179b579a0217670512 │ 10x 3' v3 │ EFO:0009922 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239___lung parenchyma___37-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 13505 │ respiratory system │ cellxgene/21-08-2025 │ CD4+ T-cells │ Th1/Th17 cells │ CD4 TCM │ 1635 │ 7540.086690000006 │ false │ LAP92_CTCAAGACAGGCCTGT-1_duong │ progenitor_t cd4_cd4 th1/th17 em_t cd4 │ t cd4 │ cd4 th1/th17 em │ cd4 th1/th17 em │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 2 │ 2 │ 2 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 11 │ 2 │ 505f851988e91eb226d9542ec5870881___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 1.0 │ FALSE │ African │ 14 │
│ TAGAGCTGTACCCAAT_F00409___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ %H2CL-Dl4P │ bfe624d44f7e5868cc22e11ad0f13866 │ CD4-positive, alpha-beta T cell │ CL:0000624 │ bfe624d44f7e5868cc22e11ad0f13866 │ 10x 5' v1 │ EFO:0011025 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 31-year-old human stage │ HsapDv:0000125 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD69 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD69___lung parenchyma___31-year-old human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 11315 │ respiratory system │ cellxgene/21-08-2025 │ CD4+ T-cells │ Th2 cells │ CD4 TCM │ 1289 │ 4389.498459999986 │ false │ TAGAGCTGTACCCAAT_F00409 │ cd4 tcm_t cd4_cd4 th2 em_t cd4 │ t cd4 │ t cd4 │ t cd4 │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 12 │ 8 │ 4 │ 3 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 2eddb46fd091cbaa989731833867bfce___1.h5ad │ a4942dd92de40cc23c6161df7e02ccc7___1.h5ad │ 1.0 │ FALSE │ African │ 77 │
│ TTGTTCAGTTCCTACC_SC84___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ lpLQAK-A9- │ 4f067f7e5f960bc72b0710684a521e84____SC84 │ CD4-positive, alpha-beta T cell │ CL:0000624 │ 4f067f7e5f960bc72b0710684a521e84 │ 10x 3' v3 │ EFO:0009922 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 52-year-old human stage │ HsapDv:0000146 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747NU_CZI01 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747NU_CZI01___lung parenchyma___52-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 18980 │ respiratory system │ cellxgene/21-08-2025 │ Tregs │ T regulatory cells │ CD4 TCM │ 1435 │ 5752.0132600000015 │ false │ TTGTTCAGTTCCTACC_SC84 │ cd14 mono_treg_treg_t cd4 │ t cd4 │ treg │ treg │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 5 │ 9 │ 2 │ 1 │ 2 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 14 │ 2 │ 5dcd68cc5017f513da840caaa6e9fc8f___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 0.5 │ TRUE │ European │ 52 │
│ AACCTGAAGTAGTGCG_SC84___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ ueyYhqXEVE │ 4f067f7e5f960bc72b0710684a521e84____SC84 │ CD4-positive, alpha-beta T cell │ CL:0000624 │ 4f067f7e5f960bc72b0710684a521e84 │ 10x 3' v3 │ EFO:0009922 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 52-year-old human stage │ HsapDv:0000146 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747NU_CZI01 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747NU_CZI01___lung parenchyma___52-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 18980 │ respiratory system │ cellxgene/21-08-2025 │ CD4+ T-cells │ Th1 cells │ CD4 TCM │ 1636 │ 4877.007010000003 │ false │ AACCTGAAGTAGTGCG_SC84 │ cd14 mono_t cd4_cd4 th1 em_t cd4 │ t cd4 │ cd4 th1 em │ cd4 th1 em │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 14 │ 2 │ f4a5aa07713be579a14fa5e545d4f609___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 0.5 │ TRUE │ European │ 7 │
│ CCACCTAGTGGCGAAT_F02526___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ KjrWyU@_4n │ d0a8856647d20b1fa1e83edb4bb9313e │ CD4-positive, alpha-beta T cell │ CL:0000624 │ d0a8856647d20b1fa1e83edb4bb9313e │ 10x 5' v1 │ EFO:0011025 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 55-year-old human stage │ HsapDv:0000149 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD92 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD92___lung parenchyma___55-year-old human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 20075 │ respiratory system │ cellxgene/21-08-2025 │ CD4+ Tem │ Terminal effector CD4 T cells │ CD4 TCM │ 890 │ 5321.9078300000065 │ false │ CCACCTAGTGGCGAAT_F02526 │ progenitor_cd4 tem_cd4 tem_t cd4 │ t cd4 │ cd4 tem │ t cd4 │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 137 │ 12 │ 20 │ 1 │ 1 │ 1 │ 2 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 5 │ 2 │ e52795dec7b626b6276b867d55328d9f___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 0.6666666666666666 │ TRUE │ European │ 336 │
│ LAP93_AACTTCTTCCTAGCGG-1_duong___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ ph?I|S#j$s │ 9c8fa5a8d2ae37179b579a0217670512___LAP93_1_duong │ CD4-positive, alpha-beta T cell │ CL:0000624 │ 9c8fa5a8d2ae37179b579a0217670512 │ 10x 3' v3 │ EFO:0009922 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239___lung parenchyma___37-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ NULL │ 13505 │ respiratory system │ cellxgene/21-08-2025 │ CD4+ T-cells │ Th2 cells │ CD4 TCM │ 1759 │ 7238.649989999993 │ false │ LAP93_AACTTCTTCCTAGCGG-1_duong │ progenitor_t cd4_cd4 th2 em_t cd4 │ t cd4 │ cd4 th2 em │ cd4 th2 em │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 12 │ 2 │ 2792e50ed8e63eba95be451710643292___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 1.0 │ FALSE │ African │ 3 │
├───────────────────────────────────────────────────────────────────────┴──────────────────────────────────────┴────────────────────┴──────────────────────────────────────────────────┴─────────────────────────────────┴────────────────────────────┴──────────────────────────────────┴───────────┴────────────────────────┴────────────┴────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┴──────────────────────────────────────┴──────────────────────────────────────┴───────────────────┴─────────────────────────┴────────────────────────────────────┴─────────┴──────────────────────────┴───────────────────────────────────────────────────────────────────────────────┴───────────────┴──────────────────────────────────────────────────────────────────────────────┴───────────────┴───────────────┴──────────┴─────────────────┴─────────────────────┴──────────────┴───────────────────────────┴────────────────────┴──────────────┴───────────────────┴────────────┴──────────────────┴──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┴────────────────┴─────────────────────────┴──────────────────────────────────────────┴─────────┴──────────────────────┴─────────────────┴─────────────────┴─────────────────────────┴─────────────┴─────────────────────────────────────────────────────────────────────────┴───────────┴─────────────────────────────────────────────────────────────────────────────────────┴────────────────────────────┴─────────┴─────────┴──────────┴────────────────────┴──────────────────────┴───────────────────────────────────┴────────────────────────────────┴────────────────────────────┴──────────────────────────────┴────────────────────┴───────────────┴────────────────────────────────┴──────────────────────────────────────────┴───────────────────┴──────────────────────┴────────────────────────────┴───────────┴──────────────────┴───────────────────────┴──────────────────────┴──────────────────────┴────────────────────┴───────────────┴─────────┴───────────────────┴────────────┴────────────┴────────────┴─────────────┴─────────────┴─────────────┴──────────────┴──────────────┴──────────────┴───────────────┴───────────────┴───────────────┴───────────────┴────────────────┴────────────────┴────────────────┴──────────────┴────────────┴─────────────────────────┴───────────────────────────────────────────┴───────────────────────────────────────────┴──────────────────────────┴──────────────────────────┴───────────────────┴──────────────────┤
│ 1780 rows (20 shown) 97 columns │
└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
Query raw counts
Once you have filtered your query accordingly, you can pass it into get_anndata() to obtain an AnnData object:
adata = get_anndata(query, assay ="counts")
adata
View of AnnData object with n_obs × n_vars = 1780 × 56239
obs: 'cell_id', 'dataset_id', 'observation_joinid', 'sample_id', 'cell_type', 'cell_type_ontology_term_id', 'sample_', 'assay', 'assay_ontology_term_id', 'cell_count', 'citation', 'collection_id', 'dataset_version_id', 'default_embedding', 'development_stage', 'development_stage_ontology_term_id', 'disease', 'disease_ontology_term_id', 'donor_id', 'experiment___', 'explorer_url', 'feature_count', 'filesize', 'filetype', 'is_primary_data', 'mean_genes_per_cell', 'organism', 'organism_ontology_term_id', 'primary_cell_count', 'published_at', 'raw_data_location', 'revised_at', 'run_from_cell_id', 'sample_heuristic', 'schema_version', 'self_reported_ethnicity', 'self_reported_ethnicity_ontology_term_id', 'sex', 'sex_ontology_term_id', 'suspension_type', 'tissue', 'tissue_ontology_term_id', 'tissue_type', 'title', 'tombstone', 'url', 'x_approximate_distribution', 'X_umap1', 'X_umap2', 'age_days', 'tissue_groups', 'atlas_id', 'cell_annotation_blueprint_singler', 'cell_annotation_monaco_singler', 'cell_annotation_azimuth_l2', 'nFeature_expressed_in_sample', 'nCount_RNA', 'empty_droplet', 'observation_originalid', 'ensemble_joinid', 'cell_type_unified', 'data_driven_ensemble', 'cell_type_unified_ensemble', 'is_immune', 'subsets_Mito_sum', 'subsets_Mito_detected', 'subsets_Mito_percent', 'subsets_Ribo_percent', 'high_mitochondrion', 'high_ribosome', 'alive', 'scDblFinder.class', 'metacell_2', 'metacell_4', 'metacell_8', 'metacell_16', 'metacell_32', 'metacell_64', 'metacell_128', 'metacell_256', 'metacell_512', 'metacell_1024', 'metacell_2048', 'metacell_4096', 'metacell_8192', 'metacell_16384', 'metacell_32768', 'metacell_65536', 'sample_chunk', 'cell_chunk', 'sample_pseudobulk_chunk', 'file_id_cellNexus_single_cell', 'file_id_cellNexus_pseudobulk', 'ethnicity_flagging_score', 'low_confidence_ethnicity', 'imputed_ethnicity', 'aggregated_cells'
Query counts scaled per million
You can query counts scaled per million. This is helpful if just few genes are of interest:
adata = get_anndata(query, assay = 'cpm')
adata
View of AnnData object with n_obs × n_vars = 1780 × 56239
obs: 'cell_id', 'dataset_id', 'observation_joinid', 'sample_id', 'cell_type', 'cell_type_ontology_term_id', 'sample_', 'assay', 'assay_ontology_term_id', 'cell_count', 'citation', 'collection_id', 'dataset_version_id', 'default_embedding', 'development_stage', 'development_stage_ontology_term_id', 'disease', 'disease_ontology_term_id', 'donor_id', 'experiment___', 'explorer_url', 'feature_count', 'filesize', 'filetype', 'is_primary_data', 'mean_genes_per_cell', 'organism', 'organism_ontology_term_id', 'primary_cell_count', 'published_at', 'raw_data_location', 'revised_at', 'run_from_cell_id', 'sample_heuristic', 'schema_version', 'self_reported_ethnicity', 'self_reported_ethnicity_ontology_term_id', 'sex', 'sex_ontology_term_id', 'suspension_type', 'tissue', 'tissue_ontology_term_id', 'tissue_type', 'title', 'tombstone', 'url', 'x_approximate_distribution', 'X_umap1', 'X_umap2', 'age_days', 'tissue_groups', 'atlas_id', 'cell_annotation_blueprint_singler', 'cell_annotation_monaco_singler', 'cell_annotation_azimuth_l2', 'nFeature_expressed_in_sample', 'nCount_RNA', 'empty_droplet', 'observation_originalid', 'ensemble_joinid', 'cell_type_unified', 'data_driven_ensemble', 'cell_type_unified_ensemble', 'is_immune', 'subsets_Mito_sum', 'subsets_Mito_detected', 'subsets_Mito_percent', 'subsets_Ribo_percent', 'high_mitochondrion', 'high_ribosome', 'alive', 'scDblFinder.class', 'metacell_2', 'metacell_4', 'metacell_8', 'metacell_16', 'metacell_32', 'metacell_64', 'metacell_128', 'metacell_256', 'metacell_512', 'metacell_1024', 'metacell_2048', 'metacell_4096', 'metacell_8192', 'metacell_16384', 'metacell_32768', 'metacell_65536', 'sample_chunk', 'cell_chunk', 'sample_pseudobulk_chunk', 'file_id_cellNexus_single_cell', 'file_id_cellNexus_pseudobulk', 'ethnicity_flagging_score', 'low_confidence_ethnicity', 'imputed_ethnicity', 'aggregated_cells'
Query pseudobulk
cellNexusPy metadata allows to work with pseudobulk data:
get_anndata(query, aggregation = "pseudobulk")
View of AnnData object with n_obs × n_vars = 68 × 56239
obs: 'dataset_id', 'sample_id', 'sample_', 'assay', 'assay_ontology_term_id', 'cell_count', 'citation', 'collection_id', 'dataset_version_id', 'default_embedding', 'development_stage', 'development_stage_ontology_term_id', 'disease', 'disease_ontology_term_id', 'donor_id', 'experiment___', 'explorer_url', 'feature_count', 'filesize', 'filetype', 'is_primary_data', 'mean_genes_per_cell', 'organism', 'organism_ontology_term_id', 'primary_cell_count', 'published_at', 'raw_data_location', 'revised_at', 'run_from_cell_id', 'sample_heuristic', 'schema_version', 'self_reported_ethnicity', 'self_reported_ethnicity_ontology_term_id', 'sex', 'sex_ontology_term_id', 'suspension_type', 'tissue', 'tissue_ontology_term_id', 'tissue_type', 'title', 'tombstone', 'url', 'x_approximate_distribution', 'X_umap1', 'X_umap2', 'age_days', 'tissue_groups', 'atlas_id', 'cell_type_unified_ensemble', 'sample_chunk', 'cell_chunk', 'sample_pseudobulk_chunk', 'file_id_cellNexus_pseudobulk', 'ethnicity_flagging_score', 'low_confidence_ethnicity', 'imputed_ethnicity', 'aggregated_cells'
Query metacell
cellNexusPy metadata provides a series of metacell affrefation levels, starting with 2, 4, 8, and so on.
For example, metacel_2 represents group of cells that can be split into two distinct metacells:
get_anndata(query, aggregation = "metacell_2")
View of AnnData object with n_obs × n_vars = 543 × 56239
obs: 'dataset_id', 'sample_id', 'assay', 'assay_ontology_term_id', 'development_stage', 'development_stage_ontology_term_id', 'disease', 'disease_ontology_term_id', 'donor_id', 'experiment___', 'explorer_url', 'feature_count', 'is_primary_data', 'organism', 'organism_ontology_term_id', 'published_at', 'raw_data_location', 'revised_at', 'sample_heuristic', 'schema_version', 'self_reported_ethnicity', 'self_reported_ethnicity_ontology_term_id', 'sex', 'sex_ontology_term_id', 'tissue', 'tissue_ontology_term_id', 'tissue_type', 'title', 'tombstone', 'url', 'age_days', 'tissue_groups', 'atlas_id', 'sample_chunk', 'file_id_cellNexus_single_cell', 'file_id_cellNexus_metacell'
Extract only a subset of genes
We can query a subset of genes. Notice how the result only has nvars = 1:
get_anndata(query, assay = "cpm", features = ['ENSG00000134644'])
View of AnnData object with n_obs × n_vars = 1055 × 1
obs: 'cell_id', 'dataset_id', 'observation_joinid', 'sample_id', 'cell_type', 'cell_type_ontology_term_id', 'sample_', 'assay', 'assay_ontology_term_id', 'cell_count', 'citation', 'collection_id', 'dataset_version_id', 'default_embedding', 'development_stage', 'development_stage_ontology_term_id', 'disease', 'disease_ontology_term_id', 'donor_id', 'experiment___', 'explorer_url', 'feature_count', 'filesize', 'filetype', 'is_primary_data', 'mean_genes_per_cell', 'organism', 'organism_ontology_term_id', 'primary_cell_count', 'published_at', 'raw_data_location', 'revised_at', 'run_from_cell_id', 'sample_heuristic', 'schema_version', 'self_reported_ethnicity', 'self_reported_ethnicity_ontology_term_id', 'sex', 'sex_ontology_term_id', 'suspension_type', 'tissue', 'tissue_ontology_term_id', 'tissue_type', 'title', 'tombstone', 'url', 'x_approximate_distribution', 'X_umap1', 'X_umap2', 'age_days', 'tissue_groups', 'atlas_id', 'cell_annotation_blueprint_singler', 'cell_annotation_monaco_singler', 'cell_annotation_azimuth_l2', 'nFeature_expressed_in_sample', 'nCount_RNA', 'empty_droplet', 'observation_originalid', 'ensemble_joinid', 'cell_type_unified', 'data_driven_ensemble', 'cell_type_unified_ensemble', 'is_immune', 'subsets_Mito_sum', 'subsets_Mito_detected', 'subsets_Mito_percent', 'subsets_Ribo_percent', 'high_mitochondrion', 'high_ribosome', 'alive', 'scDblFinder.class', 'metacell_2', 'metacell_4', 'metacell_8', 'metacell_16', 'metacell_32', 'metacell_64', 'metacell_128', 'metacell_256', 'metacell_512', 'metacell_1024', 'metacell_2048', 'metacell_4096', 'metacell_8192', 'metacell_16384', 'metacell_32768', 'metacell_65536', 'sample_chunk', 'cell_chunk', 'sample_pseudobulk_chunk', 'file_id_cellNexus_single_cell', 'file_id_cellNexus_pseudobulk', 'ethnicity_flagging_score', 'low_confidence_ethnicity', 'imputed_ethnicity', 'aggregated_cells'
Visualizing gene expression
Taking advantage of the AnnData object, we can use scanpy library to visualize gene expression gfor a groups of interest:
query = table.filter("""
cell_type_unified_ensemble = 'cd14 mono'
""")
adata = get_anndata(query, assay = 'cpm')
from matplotlib.pyplot import rc_context
import scanpy as sc
with rc_context({"figure.figsize": (15, 5)}):
sc.pl.violin(adata, ["ENSG00000085265"], groupby="disease",rotation=90)
Furthermore, it is possible to use matplotlib to generate customized plots:
import matplotlib.pyplot as plt
gene = "ENSG00000085265"
group = "tissue"
# Compute mean expression per condition
mean_expr = adata.to_df()[gene].groupby(adata.obs[group]).mean()
# Plot
colors = plt.cm.tab20.colors[:len(mean_expr)]
plt.figure(figsize=(15,5))
plt.bar(mean_expr.index, mean_expr.values,color=colors)
plt.ylabel(f"Mean expression of {gene}")
plt.xticks(rotation=90)
plt.title(f"{gene} expression per {group}")
plt.show()
/tmp/ipykernel_452882/4092819108.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
mean_expr = adata.to_df()[gene].groupby(adata.obs[group]).mean()
Saving as H5AD
It is possible to save AnnData objects using the function write_h5ad:
adata.obs.index.name = None
adata.obs["run_from_cell_id"] = adata.obs["run_from_cell_id"].fillna("NA").astype(str)
adata.obs["suspension_type"] = adata.obs["suspension_type"].fillna("NA").astype(str)
adata.obs["x_approximate_distribution"] = adata.obs["x_approximate_distribution"].fillna("NA").astype(str)
adata.write_h5ad("myH5ADfile.h5ad")
Finishing Up
When you are finished, you should close the connection:
conn.close()
Cell metadata
Dataset-specific columns (definitions available at cellxgene.cziscience.com)
cell_count, collection_id, filetype, is_primary_data, mean_genes_per_cell, published_at, revised_at, schema_version, tombstone, x_normalization, explorer_url, dataset_id, dataset_version_id
Sample-specific columns (definitions available at cellxgene.cziscience.com)
sample_id, sample_, age_days, assay, assay_ontology_term_id, development_stage, development_stage_ontology_term_id, self_reported_ethnicity, self_reported_ethnicity_ontology_term_id, experiment___, organism, organism_ontology_term_id, sample_placeholder, sex, sex_ontology_term_id, tissue, tissue_type, tissue_ontology_term_id, tissue_groups, disease, disease_ontology_term_id, is_primary_data, donor_id, is_immune
Cell-specific columns (definitions available at cellxgene.cziscience.com)
cell_id, cell_type, cell_type_ontology_term_id, cell_annotation_azimuth_l2, cell_annotation_blueprint_singler, observation_joinid, empty_droplet, alive, scDblFinder.class
Through harmonisation and curation we introduced custom column, not present in the original CELLxGENE metadata
age_days: donors' age in dayscell_type_unified_ensemble: the consensus call identity (for immune cells) using the original and three novel annotations using Seurat Azimuth and SingleRcell_annotation_azimuth_l2: Azimuth cell annotationcell_annotation_blueprint_singler: SingleR cell annotation using Blueprint referencecell_annotation_blueprint_monaco: SingleR cell annotation using Monaco referencesample_heuristic: sample subdivision for internal usefile_id_cellNexus_single_cell: file subdivision for internal usefile_id_cellNexus_pseudobulk: file subdivision for internal usesample_id: sample IDnCount_RNA: total number of RNA detected in a cell per samplenFeature_expressed_in_sample: total number of genes expressed in a cell per sample
RNA abundance
The counts assay includes RNA abundance in the positive real scale (not transformed with non-linear functions, e.g. log sqrt). Originally CELLxGENE include a mix of scales and transformations specified in the x_normalization column.
The cpm assay includes counts per million.
Other representations
The rank assay is the representation of each cell’s gene expression profile where genes are ranked by expression intensity.
The pseudobulk assay includes aggregated RNA abundance for sample and cell type combination.
The metacell (e.g metacell_2, metacell_4, etc) assays represent hierarchical partitions of cells into metacell groups.
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