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:
conn, table = get_metadata()
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 │ .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 │ int32 │
├──────────────────────────────────────────────────────────────────┼──────────────────────────────────────┼────────────────────┼──────────────────────────────────┼───────────┼────────────────────────────┼──────────────────────────────────┼───────────┼────────────────────────┼────────────┼─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┼──────────────────────────────────────┼──────────────────────────────────────┼───────────────────┼─────────────────────────┼────────────────────────────────────┼─────────┼──────────────────────────┼────────────┼───────────────┼──────────────────────────────────────────────────────────────────────────────┼───────────────┼────────────┼──────────┼─────────────────┼─────────────────────┼──────────────┼───────────────────────────┼────────────────────┼──────────────┼───────────────────┼────────────┼──────────────────┼──────────────────────────────────────────────────────────────────────────────────────┼────────────────┼─────────────────────────┼──────────────────────────────────────────┼─────────┼──────────────────────┼─────────────────┼────────────────┼─────────────────────────┼─────────────┼────────────────────────────────────────────────────────────────────────────────────────────────────────┼───────────┼─────────────────────────────────────────────────────────────────────────────────────┼────────────────────────────┼─────────┼─────────┼──────────┼─────────────────────────────────────┼──────────────────────┼───────────────────────────────────┼────────────────────────────────┼────────────────────────────┼──────────────────────────────┼────────────────────┼───────────────┼───────────────────────────┼────────────────────────────────────┼───────────────────┼──────────────────────┼────────────────────────────┼───────────┼──────────────────┼───────────────────────┼──────────────────────┼──────────────────────┼────────────────────┼───────────────┼─────────┼───────────────────┼────────────┼────────────┼────────────┼─────────────┼─────────────┼─────────────┼──────────────┼──────────────┼──────────────┼───────────────┼───────────────┼───────────────┼───────────────┼────────────────┼────────────────┼────────────────┼──────────────┼────────────┼─────────────────────────┼───────────────────────────────────────────┼───────────────────────────────────────────┼───────────────────┤
│ 10X383_6:CCTCATGGTACACGCC___0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ 0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ *|Vt;4ATOI │ e732d3bf987f8dedf9c6d5365865d353 │ leukocyte │ CL:0000738 │ e732d3bf987f8dedf9c6d5365865d353 │ 10x 3' v3 │ EFO:0009922 │ 13623 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.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 │ 6918480f-892a-42bf-a5cd-5e988f6e46b9 │ NULL │ 29-year-old human stage │ HsapDv:0000123 │ normal │ PATO:0000461 │ H19.30.002 │ │ https://cellxgene.cziscience.com/e/0ee5ae70-c3f5-473f-bd1c-287f4690ffc5.cxg/ │ 59236 │ 74734654.0 │ H5AD │ TRUE │ 2034.543125596418 │ Homo sapiens │ NCBITaxon:9606 │ 13623 │ 2022-12-08 │ X │ 2024-06-11 │ NULL │ H19.30.002___myelencephalon___29-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ nucleus │ myelencephalon │ UBERON:0005290 │ tissue │ Dissection: Myelencephalon (medulla oblongata) (Mo) - sensory relay nuclei in medulla oblongata - MoSR │ false │ https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.h5ad │ NULL │ NULL │ NULL │ 10585 │ brainstem and cerebellar structures │ cellxgene/21-08-2025 │ NK cells │ Natural killer cells │ CD4 TCM │ 640 │ 8.61724000001459 │ false │ 10X383_6:CCTCATGGTACACGCC │ cd4 tcm_nk_nk_immune │ immune │ nk │ immune │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 6 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 951aa2f741fc5b64acc1b7d72456d05c___1.h5ad │ 1d93977fde2e30c44b82205e48d88228___1.h5ad │ 14 │
│ 10X383_6:GATTTCTTCCAACCAA___0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ 0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ #z5ft!kwbn │ e732d3bf987f8dedf9c6d5365865d353 │ leukocyte │ CL:0000738 │ e732d3bf987f8dedf9c6d5365865d353 │ 10x 3' v3 │ EFO:0009922 │ 13623 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.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 │ 6918480f-892a-42bf-a5cd-5e988f6e46b9 │ NULL │ 29-year-old human stage │ HsapDv:0000123 │ normal │ PATO:0000461 │ H19.30.002 │ │ https://cellxgene.cziscience.com/e/0ee5ae70-c3f5-473f-bd1c-287f4690ffc5.cxg/ │ 59236 │ 74734654.0 │ H5AD │ TRUE │ 2034.543125596418 │ Homo sapiens │ NCBITaxon:9606 │ 13623 │ 2022-12-08 │ X │ 2024-06-11 │ NULL │ H19.30.002___myelencephalon___29-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ nucleus │ myelencephalon │ UBERON:0005290 │ tissue │ Dissection: Myelencephalon (medulla oblongata) (Mo) - sensory relay nuclei in medulla oblongata - MoSR │ false │ https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.h5ad │ NULL │ NULL │ NULL │ 10585 │ brainstem and cerebellar structures │ cellxgene/21-08-2025 │ NK cells │ Natural killer cells │ CD4 TCM │ 584 │ 7.653930000013588 │ false │ 10X383_6:GATTTCTTCCAACCAA │ cd4 tcm_nk_nk_immune │ immune │ nk │ immune │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 3 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 951aa2f741fc5b64acc1b7d72456d05c___1.h5ad │ 1d93977fde2e30c44b82205e48d88228___1.h5ad │ 14 │
│ 10X383_5:CTCCAACTCGCTCTAC___0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ 0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ kd(R>I7G#- │ e732d3bf987f8dedf9c6d5365865d353 │ leukocyte │ CL:0000738 │ e732d3bf987f8dedf9c6d5365865d353 │ 10x 3' v3 │ EFO:0009922 │ 13623 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.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 │ 6918480f-892a-42bf-a5cd-5e988f6e46b9 │ NULL │ 29-year-old human stage │ HsapDv:0000123 │ normal │ PATO:0000461 │ H19.30.002 │ │ https://cellxgene.cziscience.com/e/0ee5ae70-c3f5-473f-bd1c-287f4690ffc5.cxg/ │ 59236 │ 74734654.0 │ H5AD │ TRUE │ 2034.543125596418 │ Homo sapiens │ NCBITaxon:9606 │ 13623 │ 2022-12-08 │ X │ 2024-06-11 │ NULL │ H19.30.002___myelencephalon___29-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ nucleus │ myelencephalon │ UBERON:0005290 │ tissue │ Dissection: Myelencephalon (medulla oblongata) (Mo) - sensory relay nuclei in medulla oblongata - MoSR │ false │ https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.h5ad │ NULL │ NULL │ NULL │ 10585 │ brainstem and cerebellar structures │ cellxgene/21-08-2025 │ CD4+ Tcm │ Th17 cells │ CD4 TCM │ 776 │ 10.61494000001926 │ false │ 10X383_5:CTCCAACTCGCTCTAC │ cd4 tcm_cd4 tcm_cd4 th17 em_immune │ immune │ cd4 tcm │ immune │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 1 │ 3 │ 2 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 951aa2f741fc5b64acc1b7d72456d05c___1.h5ad │ 1d93977fde2e30c44b82205e48d88228___1.h5ad │ 14 │
│ 10X383_5:GATCATGCATGTGGTT___0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ 0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ mSylksfIn3 │ e732d3bf987f8dedf9c6d5365865d353 │ leukocyte │ CL:0000738 │ e732d3bf987f8dedf9c6d5365865d353 │ 10x 3' v3 │ EFO:0009922 │ 13623 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.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 │ 6918480f-892a-42bf-a5cd-5e988f6e46b9 │ NULL │ 29-year-old human stage │ HsapDv:0000123 │ normal │ PATO:0000461 │ H19.30.002 │ │ https://cellxgene.cziscience.com/e/0ee5ae70-c3f5-473f-bd1c-287f4690ffc5.cxg/ │ 59236 │ 74734654.0 │ H5AD │ TRUE │ 2034.543125596418 │ Homo sapiens │ NCBITaxon:9606 │ 13623 │ 2022-12-08 │ X │ 2024-06-11 │ NULL │ H19.30.002___myelencephalon___29-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ nucleus │ myelencephalon │ UBERON:0005290 │ tissue │ Dissection: Myelencephalon (medulla oblongata) (Mo) - sensory relay nuclei in medulla oblongata - MoSR │ false │ https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.h5ad │ NULL │ NULL │ NULL │ 10585 │ brainstem and cerebellar structures │ cellxgene/21-08-2025 │ CD8+ Tem │ MAIT cells │ CD4 TCM │ 627 │ 7.980630000013889 │ false │ 10X383_5:GATCATGCATGTGGTT │ cd4 tcm_cd8 tem_mait_immune │ immune │ t │ immune │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 1 │ 3 │ 2 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 951aa2f741fc5b64acc1b7d72456d05c___1.h5ad │ 1d93977fde2e30c44b82205e48d88228___1.h5ad │ 14 │
│ 10X218_3:CAATCGATCCGATGTA___0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ 0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ XEl?wkHAcg │ 979206e179f85043e0c653a7a8e5c2ac │ leukocyte │ CL:0000738 │ 979206e179f85043e0c653a7a8e5c2ac │ 10x 3' v3 │ EFO:0009922 │ 13623 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.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 │ 6918480f-892a-42bf-a5cd-5e988f6e46b9 │ NULL │ 50-year-old human stage │ HsapDv:0000144 │ normal │ PATO:0000461 │ H18.30.002 │ │ https://cellxgene.cziscience.com/e/0ee5ae70-c3f5-473f-bd1c-287f4690ffc5.cxg/ │ 59236 │ 74734654.0 │ H5AD │ TRUE │ 2034.543125596418 │ Homo sapiens │ NCBITaxon:9606 │ 13623 │ 2022-12-08 │ X │ 2024-06-11 │ NULL │ H18.30.002___myelencephalon___50-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ nucleus │ myelencephalon │ UBERON:0005290 │ tissue │ Dissection: Myelencephalon (medulla oblongata) (Mo) - sensory relay nuclei in medulla oblongata - MoSR │ false │ https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.h5ad │ NULL │ NULL │ NULL │ 18250 │ brainstem and cerebellar structures │ cellxgene/21-08-2025 │ CD8+ Tem │ MAIT cells │ CD4 TCM │ 1209 │ 6.5761000000534295 │ false │ 10X218_3:CAATCGATCCGATGTA │ cd4 tcm_cd8 tem_mait_immune │ immune │ t │ immune │ false │ 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 │ 1 │ 1 │ 951aa2f741fc5b64acc1b7d72456d05c___1.h5ad │ 1d93977fde2e30c44b82205e48d88228___1.h5ad │ 8 │
│ 10X383_5:CTTCCTTCATGGCCCA___0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ 0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ T_4$MfQ!Ss │ e732d3bf987f8dedf9c6d5365865d353 │ leukocyte │ CL:0000738 │ e732d3bf987f8dedf9c6d5365865d353 │ 10x 3' v3 │ EFO:0009922 │ 13623 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.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 │ 6918480f-892a-42bf-a5cd-5e988f6e46b9 │ NULL │ 29-year-old human stage │ HsapDv:0000123 │ normal │ PATO:0000461 │ H19.30.002 │ │ https://cellxgene.cziscience.com/e/0ee5ae70-c3f5-473f-bd1c-287f4690ffc5.cxg/ │ 59236 │ 74734654.0 │ H5AD │ TRUE │ 2034.543125596418 │ Homo sapiens │ NCBITaxon:9606 │ 13623 │ 2022-12-08 │ X │ 2024-06-11 │ NULL │ H19.30.002___myelencephalon___29-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ nucleus │ myelencephalon │ UBERON:0005290 │ tissue │ Dissection: Myelencephalon (medulla oblongata) (Mo) - sensory relay nuclei in medulla oblongata - MoSR │ false │ https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.h5ad │ NULL │ NULL │ NULL │ 10585 │ brainstem and cerebellar structures │ cellxgene/21-08-2025 │ CD8+ Tem │ Terminal effector CD8 T cells │ CD4 TCM │ 800 │ 10.928610000019034 │ false │ 10X383_5:CTTCCTTCATGGCCCA │ cd4 tcm_cd8 tem_cd8 tem_immune │ immune │ cd8 tem │ immune │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 4 │ 2 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 951aa2f741fc5b64acc1b7d72456d05c___1.h5ad │ 1d93977fde2e30c44b82205e48d88228___1.h5ad │ 14 │
│ 10X218_3:TATTGCTTCATCGCTC___0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ 0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ &yS%7ee<`? │ 979206e179f85043e0c653a7a8e5c2ac │ leukocyte │ CL:0000738 │ 979206e179f85043e0c653a7a8e5c2ac │ 10x 3' v3 │ EFO:0009922 │ 13623 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.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 │ 6918480f-892a-42bf-a5cd-5e988f6e46b9 │ NULL │ 50-year-old human stage │ HsapDv:0000144 │ normal │ PATO:0000461 │ H18.30.002 │ │ https://cellxgene.cziscience.com/e/0ee5ae70-c3f5-473f-bd1c-287f4690ffc5.cxg/ │ 59236 │ 74734654.0 │ H5AD │ TRUE │ 2034.543125596418 │ Homo sapiens │ NCBITaxon:9606 │ 13623 │ 2022-12-08 │ X │ 2024-06-11 │ NULL │ H18.30.002___myelencephalon___50-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ nucleus │ myelencephalon │ UBERON:0005290 │ tissue │ Dissection: Myelencephalon (medulla oblongata) (Mo) - sensory relay nuclei in medulla oblongata - MoSR │ false │ https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.h5ad │ NULL │ NULL │ NULL │ 18250 │ brainstem and cerebellar structures │ cellxgene/21-08-2025 │ CD8+ Tem │ MAIT cells │ CD4 TCM │ 1297 │ 7.5459900000537345 │ false │ 10X218_3:TATTGCTTCATCGCTC │ cd4 tcm_cd8 tem_mait_immune │ immune │ t │ immune │ false │ 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 │ 1 │ 1 │ 951aa2f741fc5b64acc1b7d72456d05c___1.h5ad │ 1d93977fde2e30c44b82205e48d88228___1.h5ad │ 8 │
│ 10X218_3:CCATAAGGTGTCGATT___0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ 0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ 0*ArkI0ju; │ 979206e179f85043e0c653a7a8e5c2ac │ leukocyte │ CL:0000738 │ 979206e179f85043e0c653a7a8e5c2ac │ 10x 3' v3 │ EFO:0009922 │ 13623 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.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 │ 6918480f-892a-42bf-a5cd-5e988f6e46b9 │ NULL │ 50-year-old human stage │ HsapDv:0000144 │ normal │ PATO:0000461 │ H18.30.002 │ │ https://cellxgene.cziscience.com/e/0ee5ae70-c3f5-473f-bd1c-287f4690ffc5.cxg/ │ 59236 │ 74734654.0 │ H5AD │ TRUE │ 2034.543125596418 │ Homo sapiens │ NCBITaxon:9606 │ 13623 │ 2022-12-08 │ X │ 2024-06-11 │ NULL │ H18.30.002___myelencephalon___50-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ nucleus │ myelencephalon │ UBERON:0005290 │ tissue │ Dissection: Myelencephalon (medulla oblongata) (Mo) - sensory relay nuclei in medulla oblongata - MoSR │ false │ https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.h5ad │ NULL │ NULL │ NULL │ 18250 │ brainstem and cerebellar structures │ cellxgene/21-08-2025 │ CD8+ Tem │ Effector memory CD8 T cells │ CD4 TCM │ 1005 │ 5.1562300000396135 │ false │ 10X218_3:CCATAAGGTGTCGATT │ cd4 tcm_cd8 tem_cd8 tem_immune │ immune │ cd8 tem │ immune │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 2 │ 2 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 951aa2f741fc5b64acc1b7d72456d05c___1.h5ad │ 1d93977fde2e30c44b82205e48d88228___1.h5ad │ 8 │
│ 10X218_3:ACTCTCGTCACCGCTT___0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ 0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ r<pyq>qS=W │ 979206e179f85043e0c653a7a8e5c2ac │ leukocyte │ CL:0000738 │ 979206e179f85043e0c653a7a8e5c2ac │ 10x 3' v3 │ EFO:0009922 │ 13623 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.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 │ 6918480f-892a-42bf-a5cd-5e988f6e46b9 │ NULL │ 50-year-old human stage │ HsapDv:0000144 │ normal │ PATO:0000461 │ H18.30.002 │ │ https://cellxgene.cziscience.com/e/0ee5ae70-c3f5-473f-bd1c-287f4690ffc5.cxg/ │ 59236 │ 74734654.0 │ H5AD │ TRUE │ 2034.543125596418 │ Homo sapiens │ NCBITaxon:9606 │ 13623 │ 2022-12-08 │ X │ 2024-06-11 │ NULL │ H18.30.002___myelencephalon___50-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ nucleus │ myelencephalon │ UBERON:0005290 │ tissue │ Dissection: Myelencephalon (medulla oblongata) (Mo) - sensory relay nuclei in medulla oblongata - MoSR │ false │ https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.h5ad │ NULL │ NULL │ NULL │ 18250 │ brainstem and cerebellar structures │ cellxgene/21-08-2025 │ CD8+ Tem │ Vd2 gd T cells │ CD4 TCM │ 986 │ 4.7659900000426205 │ false │ 10X218_3:ACTCTCGTCACCGCTT │ cd4 tcm_cd8 tem_tgd_immune │ immune │ t │ immune │ false │ 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 │ 1 │ 1 │ 951aa2f741fc5b64acc1b7d72456d05c___1.h5ad │ 1d93977fde2e30c44b82205e48d88228___1.h5ad │ 8 │
│ 10X383_6:CCCTTAGGTATTCTCT___0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ 0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ )tfjoT&}j{ │ e732d3bf987f8dedf9c6d5365865d353 │ leukocyte │ CL:0000738 │ e732d3bf987f8dedf9c6d5365865d353 │ 10x 3' v3 │ EFO:0009922 │ 13623 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.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 │ 6918480f-892a-42bf-a5cd-5e988f6e46b9 │ NULL │ 29-year-old human stage │ HsapDv:0000123 │ normal │ PATO:0000461 │ H19.30.002 │ │ https://cellxgene.cziscience.com/e/0ee5ae70-c3f5-473f-bd1c-287f4690ffc5.cxg/ │ 59236 │ 74734654.0 │ H5AD │ TRUE │ 2034.543125596418 │ Homo sapiens │ NCBITaxon:9606 │ 13623 │ 2022-12-08 │ X │ 2024-06-11 │ NULL │ H19.30.002___myelencephalon___29-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ nucleus │ myelencephalon │ UBERON:0005290 │ tissue │ Dissection: Myelencephalon (medulla oblongata) (Mo) - sensory relay nuclei in medulla oblongata - MoSR │ false │ https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.h5ad │ NULL │ NULL │ NULL │ 10585 │ brainstem and cerebellar structures │ cellxgene/21-08-2025 │ CD8+ Tem │ Vd2 gd T cells │ CD4 TCM │ 799 │ 10.85975000002054 │ false │ 10X383_6:CCCTTAGGTATTCTCT │ cd4 tcm_cd8 tem_tgd_immune │ immune │ t │ immune │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 4 │ 2 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 951aa2f741fc5b64acc1b7d72456d05c___1.h5ad │ 1d93977fde2e30c44b82205e48d88228___1.h5ad │ 14 │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ 10X379_2:GTGGAAGAGCGTATGG___0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ 0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ )03`X$FOAt │ 4a72334766418cf47e22ba0b9921df3f │ neuron │ CL:0000540 │ 4a72334766418cf47e22ba0b9921df3f │ 10x 3' v3 │ EFO:0009922 │ 13623 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.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 │ 6918480f-892a-42bf-a5cd-5e988f6e46b9 │ NULL │ 42-year-old human stage │ HsapDv:0000136 │ normal │ PATO:0000461 │ H19.30.001 │ │ https://cellxgene.cziscience.com/e/0ee5ae70-c3f5-473f-bd1c-287f4690ffc5.cxg/ │ 59236 │ 74734654.0 │ H5AD │ TRUE │ 2034.543125596418 │ Homo sapiens │ NCBITaxon:9606 │ 13623 │ 2022-12-08 │ X │ 2024-06-11 │ NULL │ H19.30.001___myelencephalon___42-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ nucleus │ myelencephalon │ UBERON:0005290 │ tissue │ Dissection: Myelencephalon (medulla oblongata) (Mo) - sensory relay nuclei in medulla oblongata - MoSR │ false │ https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.h5ad │ NULL │ NULL │ NULL │ 15330 │ brainstem and cerebellar structures │ cellxgene/21-08-2025 │ Neurons │ Myeloid dendritic cells │ Other │ 2223 │ 12.317679999937809 │ false │ 10X379_2:GTGGAAGAGCGTATGG │ NA_non immune_cdc_neuron │ neuron │ non immune │ neuron │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 63 │ 91 │ 25 │ 6 │ 3 │ 13 │ 3 │ 1 │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 88c644a9fe23d692cec09a1267c6f26f___1.h5ad │ 1d93977fde2e30c44b82205e48d88228___1.h5ad │ 2339 │
│ 10X379_2:GTTACAGTCACCTACC___0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ 0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ dH|m|2l~-i │ 4a72334766418cf47e22ba0b9921df3f │ neuron │ CL:0000540 │ 4a72334766418cf47e22ba0b9921df3f │ 10x 3' v3 │ EFO:0009922 │ 13623 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.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 │ 6918480f-892a-42bf-a5cd-5e988f6e46b9 │ NULL │ 42-year-old human stage │ HsapDv:0000136 │ normal │ PATO:0000461 │ H19.30.001 │ │ https://cellxgene.cziscience.com/e/0ee5ae70-c3f5-473f-bd1c-287f4690ffc5.cxg/ │ 59236 │ 74734654.0 │ H5AD │ TRUE │ 2034.543125596418 │ Homo sapiens │ NCBITaxon:9606 │ 13623 │ 2022-12-08 │ X │ 2024-06-11 │ NULL │ H19.30.001___myelencephalon___42-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ nucleus │ myelencephalon │ UBERON:0005290 │ tissue │ Dissection: Myelencephalon (medulla oblongata) (Mo) - sensory relay nuclei in medulla oblongata - MoSR │ false │ https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.h5ad │ NULL │ NULL │ NULL │ 15330 │ brainstem and cerebellar structures │ cellxgene/21-08-2025 │ Neurons │ Progenitor cells │ Other │ 2129 │ 15.406209999942575 │ false │ 10X379_2:GTTACAGTCACCTACC │ NA_non immune_progenitor_neuron │ neuron │ non immune │ neuron │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 31 │ 182 │ 7 │ 49 │ 5 │ 10 │ 3 │ 1 │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 88c644a9fe23d692cec09a1267c6f26f___1.h5ad │ 1d93977fde2e30c44b82205e48d88228___1.h5ad │ 2339 │
│ 10X218_3:GATTGGTCAGATACCT___0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ 0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ m9Zo<d5(*t │ 979206e179f85043e0c653a7a8e5c2ac │ neuron │ CL:0000540 │ 979206e179f85043e0c653a7a8e5c2ac │ 10x 3' v3 │ EFO:0009922 │ 13623 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.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 │ 6918480f-892a-42bf-a5cd-5e988f6e46b9 │ NULL │ 50-year-old human stage │ HsapDv:0000144 │ normal │ PATO:0000461 │ H18.30.002 │ │ https://cellxgene.cziscience.com/e/0ee5ae70-c3f5-473f-bd1c-287f4690ffc5.cxg/ │ 59236 │ 74734654.0 │ H5AD │ TRUE │ 2034.543125596418 │ Homo sapiens │ NCBITaxon:9606 │ 13623 │ 2022-12-08 │ X │ 2024-06-11 │ NULL │ H18.30.002___myelencephalon___50-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ nucleus │ myelencephalon │ UBERON:0005290 │ tissue │ Dissection: Myelencephalon (medulla oblongata) (Mo) - sensory relay nuclei in medulla oblongata - MoSR │ false │ https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.h5ad │ NULL │ NULL │ NULL │ 18250 │ brainstem and cerebellar structures │ cellxgene/21-08-2025 │ Neurons │ Myeloid dendritic cells │ HSPC │ 6792 │ 110.16515000051277 │ false │ 10X218_3:GATTGGTCAGATACCT │ cd4 tcm_non immune_cdc_neuron │ neuron │ non immune │ neuron │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 40 │ 73 │ 10 │ 32 │ 7 │ 6 │ 2 │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 88c644a9fe23d692cec09a1267c6f26f___1.h5ad │ 1d93977fde2e30c44b82205e48d88228___1.h5ad │ 1755 │
│ 10X379_2:TGTCCTGTCACTCTTA___0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ 0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ NB1(?B|lEq │ 4a72334766418cf47e22ba0b9921df3f │ neuron │ CL:0000540 │ 4a72334766418cf47e22ba0b9921df3f │ 10x 3' v3 │ EFO:0009922 │ 13623 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.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 │ 6918480f-892a-42bf-a5cd-5e988f6e46b9 │ NULL │ 42-year-old human stage │ HsapDv:0000136 │ normal │ PATO:0000461 │ H19.30.001 │ │ https://cellxgene.cziscience.com/e/0ee5ae70-c3f5-473f-bd1c-287f4690ffc5.cxg/ │ 59236 │ 74734654.0 │ H5AD │ TRUE │ 2034.543125596418 │ Homo sapiens │ NCBITaxon:9606 │ 13623 │ 2022-12-08 │ X │ 2024-06-11 │ NULL │ H19.30.001___myelencephalon___42-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ nucleus │ myelencephalon │ UBERON:0005290 │ tissue │ Dissection: Myelencephalon (medulla oblongata) (Mo) - sensory relay nuclei in medulla oblongata - MoSR │ false │ https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.h5ad │ NULL │ NULL │ NULL │ 15330 │ brainstem and cerebellar structures │ cellxgene/21-08-2025 │ Neurons │ Plasmacytoid dendritic cells │ Other │ 4474 │ 42.006319999873995 │ false │ 10X379_2:TGTCCTGTCACTCTTA │ NA_non immune_pdc_neuron │ neuron │ non immune │ neuron │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 326 │ 270 │ 71 │ 12 │ 10 │ 13 │ 3 │ 1 │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 88c644a9fe23d692cec09a1267c6f26f___1.h5ad │ 1d93977fde2e30c44b82205e48d88228___1.h5ad │ 2339 │
│ 10X218_3:GGAATGGTCGTTAGAC___0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ 0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ D^gy*x|QdF │ 979206e179f85043e0c653a7a8e5c2ac │ neuron │ CL:0000540 │ 979206e179f85043e0c653a7a8e5c2ac │ 10x 3' v3 │ EFO:0009922 │ 13623 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.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 │ 6918480f-892a-42bf-a5cd-5e988f6e46b9 │ NULL │ 50-year-old human stage │ HsapDv:0000144 │ normal │ PATO:0000461 │ H18.30.002 │ │ https://cellxgene.cziscience.com/e/0ee5ae70-c3f5-473f-bd1c-287f4690ffc5.cxg/ │ 59236 │ 74734654.0 │ H5AD │ TRUE │ 2034.543125596418 │ Homo sapiens │ NCBITaxon:9606 │ 13623 │ 2022-12-08 │ X │ 2024-06-11 │ NULL │ H18.30.002___myelencephalon___50-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ nucleus │ myelencephalon │ UBERON:0005290 │ tissue │ Dissection: Myelencephalon (medulla oblongata) (Mo) - sensory relay nuclei in medulla oblongata - MoSR │ false │ https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.h5ad │ NULL │ NULL │ NULL │ 18250 │ brainstem and cerebellar structures │ cellxgene/21-08-2025 │ Neurons │ Myeloid dendritic cells │ CD4 TCM │ 3323 │ 26.248140000177955 │ false │ 10X218_3:GGAATGGTCGTTAGAC │ cd4 tcm_non immune_cdc_neuron │ neuron │ non immune │ neuron │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 255 │ 220 │ 4 │ 17 │ 10 │ 4 │ 2 │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 88c644a9fe23d692cec09a1267c6f26f___1.h5ad │ 1d93977fde2e30c44b82205e48d88228___1.h5ad │ 1755 │
│ 10X218_3:AAATGGAAGCCTCAGC___0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ 0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ @$ibcAF*Ql │ 979206e179f85043e0c653a7a8e5c2ac │ neuron │ CL:0000540 │ 979206e179f85043e0c653a7a8e5c2ac │ 10x 3' v3 │ EFO:0009922 │ 13623 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.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 │ 6918480f-892a-42bf-a5cd-5e988f6e46b9 │ NULL │ 50-year-old human stage │ HsapDv:0000144 │ normal │ PATO:0000461 │ H18.30.002 │ │ https://cellxgene.cziscience.com/e/0ee5ae70-c3f5-473f-bd1c-287f4690ffc5.cxg/ │ 59236 │ 74734654.0 │ H5AD │ TRUE │ 2034.543125596418 │ Homo sapiens │ NCBITaxon:9606 │ 13623 │ 2022-12-08 │ X │ 2024-06-11 │ NULL │ H18.30.002___myelencephalon___50-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ nucleus │ myelencephalon │ UBERON:0005290 │ tissue │ Dissection: Myelencephalon (medulla oblongata) (Mo) - sensory relay nuclei in medulla oblongata - MoSR │ false │ https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.h5ad │ NULL │ NULL │ NULL │ 18250 │ brainstem and cerebellar structures │ cellxgene/21-08-2025 │ Neurons │ Plasmacytoid dendritic cells │ HSPC │ 6194 │ 77.93321000041624 │ false │ 10X218_3:AAATGGAAGCCTCAGC │ cd4 tcm_non immune_pdc_neuron │ neuron │ non immune │ neuron │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 246 │ 383 │ 218 │ 57 │ 5 │ 4 │ 2 │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 88c644a9fe23d692cec09a1267c6f26f___1.h5ad │ 1d93977fde2e30c44b82205e48d88228___1.h5ad │ 1755 │
│ 10X379_1:ACAACCATCAAATGAG___0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ 0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ (-Z-tJIoL) │ 4a72334766418cf47e22ba0b9921df3f │ neuron │ CL:0000540 │ 4a72334766418cf47e22ba0b9921df3f │ 10x 3' v3 │ EFO:0009922 │ 13623 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.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 │ 6918480f-892a-42bf-a5cd-5e988f6e46b9 │ NULL │ 42-year-old human stage │ HsapDv:0000136 │ normal │ PATO:0000461 │ H19.30.001 │ │ https://cellxgene.cziscience.com/e/0ee5ae70-c3f5-473f-bd1c-287f4690ffc5.cxg/ │ 59236 │ 74734654.0 │ H5AD │ TRUE │ 2034.543125596418 │ Homo sapiens │ NCBITaxon:9606 │ 13623 │ 2022-12-08 │ X │ 2024-06-11 │ NULL │ H19.30.001___myelencephalon___42-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ nucleus │ myelencephalon │ UBERON:0005290 │ tissue │ Dissection: Myelencephalon (medulla oblongata) (Mo) - sensory relay nuclei in medulla oblongata - MoSR │ false │ https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.h5ad │ NULL │ NULL │ NULL │ 15330 │ brainstem and cerebellar structures │ cellxgene/21-08-2025 │ Neurons │ Natural killer cells │ Other │ 3343 │ 30.31796999990638 │ false │ 10X379_1:ACAACCATCAAATGAG │ NA_non immune_nk_neuron │ neuron │ non immune │ neuron │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ doublet │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 88c644a9fe23d692cec09a1267c6f26f___1.h5ad │ 1d93977fde2e30c44b82205e48d88228___1.h5ad │ 2339 │
│ 10X379_2:TGGAGGACAAGCTCTA___0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ 0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ ueXEPC1Yky │ 4a72334766418cf47e22ba0b9921df3f │ neuron │ CL:0000540 │ 4a72334766418cf47e22ba0b9921df3f │ 10x 3' v3 │ EFO:0009922 │ 13623 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.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 │ 6918480f-892a-42bf-a5cd-5e988f6e46b9 │ NULL │ 42-year-old human stage │ HsapDv:0000136 │ normal │ PATO:0000461 │ H19.30.001 │ │ https://cellxgene.cziscience.com/e/0ee5ae70-c3f5-473f-bd1c-287f4690ffc5.cxg/ │ 59236 │ 74734654.0 │ H5AD │ TRUE │ 2034.543125596418 │ Homo sapiens │ NCBITaxon:9606 │ 13623 │ 2022-12-08 │ X │ 2024-06-11 │ NULL │ H19.30.001___myelencephalon___42-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ nucleus │ myelencephalon │ UBERON:0005290 │ tissue │ Dissection: Myelencephalon (medulla oblongata) (Mo) - sensory relay nuclei in medulla oblongata - MoSR │ false │ https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.h5ad │ NULL │ NULL │ NULL │ 15330 │ brainstem and cerebellar structures │ cellxgene/21-08-2025 │ Neurons │ Myeloid dendritic cells │ Other │ 2992 │ 21.58553999991568 │ false │ 10X379_2:TGGAGGACAAGCTCTA │ NA_non immune_cdc_neuron │ neuron │ non immune │ neuron │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 98 │ 113 │ 160 │ 68 │ 3 │ 13 │ 3 │ 1 │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 88c644a9fe23d692cec09a1267c6f26f___1.h5ad │ 1d93977fde2e30c44b82205e48d88228___1.h5ad │ 2339 │
│ 10X379_2:TAATTCCCAAAGGATT___0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ 0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ V1j&`F4rVM │ 4a72334766418cf47e22ba0b9921df3f │ neuron │ CL:0000540 │ 4a72334766418cf47e22ba0b9921df3f │ 10x 3' v3 │ EFO:0009922 │ 13623 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.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 │ 6918480f-892a-42bf-a5cd-5e988f6e46b9 │ NULL │ 42-year-old human stage │ HsapDv:0000136 │ normal │ PATO:0000461 │ H19.30.001 │ │ https://cellxgene.cziscience.com/e/0ee5ae70-c3f5-473f-bd1c-287f4690ffc5.cxg/ │ 59236 │ 74734654.0 │ H5AD │ TRUE │ 2034.543125596418 │ Homo sapiens │ NCBITaxon:9606 │ 13623 │ 2022-12-08 │ X │ 2024-06-11 │ NULL │ H19.30.001___myelencephalon___42-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ nucleus │ myelencephalon │ UBERON:0005290 │ tissue │ Dissection: Myelencephalon (medulla oblongata) (Mo) - sensory relay nuclei in medulla oblongata - MoSR │ false │ https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.h5ad │ NULL │ NULL │ NULL │ 15330 │ brainstem and cerebellar structures │ cellxgene/21-08-2025 │ Neurons │ Progenitor cells │ Other │ 2448 │ 15.06425999993121 │ false │ 10X379_2:TAATTCCCAAAGGATT │ NA_non immune_progenitor_neuron │ neuron │ non immune │ neuron │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 423 │ 241 │ 249 │ 68 │ 3 │ 13 │ 3 │ 1 │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 88c644a9fe23d692cec09a1267c6f26f___1.h5ad │ 1d93977fde2e30c44b82205e48d88228___1.h5ad │ 2339 │
│ 10X379_2:TAAGCACCATTCTGTT___0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ 0ee5ae70-c3f5-473f-bd1c-287f4690ffc5 │ {e6_Uc@2F* │ 4a72334766418cf47e22ba0b9921df3f │ neuron │ CL:0000540 │ 4a72334766418cf47e22ba0b9921df3f │ 10x 3' v3 │ EFO:0009922 │ 13623 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.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 │ 6918480f-892a-42bf-a5cd-5e988f6e46b9 │ NULL │ 42-year-old human stage │ HsapDv:0000136 │ normal │ PATO:0000461 │ H19.30.001 │ │ https://cellxgene.cziscience.com/e/0ee5ae70-c3f5-473f-bd1c-287f4690ffc5.cxg/ │ 59236 │ 74734654.0 │ H5AD │ TRUE │ 2034.543125596418 │ Homo sapiens │ NCBITaxon:9606 │ 13623 │ 2022-12-08 │ X │ 2024-06-11 │ NULL │ H19.30.001___myelencephalon___42-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ nucleus │ myelencephalon │ UBERON:0005290 │ tissue │ Dissection: Myelencephalon (medulla oblongata) (Mo) - sensory relay nuclei in medulla oblongata - MoSR │ false │ https://datasets.cellxgene.cziscience.com/6918480f-892a-42bf-a5cd-5e988f6e46b9.h5ad │ NULL │ NULL │ NULL │ 15330 │ brainstem and cerebellar structures │ cellxgene/21-08-2025 │ Neurons │ Myeloid dendritic cells │ Other │ 4086 │ 33.4330399998812 │ false │ 10X379_2:TAAGCACCATTCTGTT │ NA_non immune_cdc_neuron │ neuron │ non immune │ neuron │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ doublet │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 88c644a9fe23d692cec09a1267c6f26f___1.h5ad │ 1d93977fde2e30c44b82205e48d88228___1.h5ad │ 2339 │
├──────────────────────────────────────────────────────────────────┴──────────────────────────────────────┴────────────────────┴──────────────────────────────────┴───────────┴────────────────────────────┴──────────────────────────────────┴───────────┴────────────────────────┴────────────┴─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┴──────────────────────────────────────┴──────────────────────────────────────┴───────────────────┴─────────────────────────┴────────────────────────────────────┴─────────┴──────────────────────────┴────────────┴───────────────┴──────────────────────────────────────────────────────────────────────────────┴───────────────┴────────────┴──────────┴─────────────────┴─────────────────────┴──────────────┴───────────────────────────┴────────────────────┴──────────────┴───────────────────┴────────────┴──────────────────┴──────────────────────────────────────────────────────────────────────────────────────┴────────────────┴─────────────────────────┴──────────────────────────────────────────┴─────────┴──────────────────────┴─────────────────┴────────────────┴─────────────────────────┴─────────────┴────────────────────────────────────────────────────────────────────────────────────────────────────────┴───────────┴─────────────────────────────────────────────────────────────────────────────────────┴────────────────────────────┴─────────┴─────────┴──────────┴─────────────────────────────────────┴──────────────────────┴───────────────────────────────────┴────────────────────────────────┴────────────────────────────┴──────────────────────────────┴────────────────────┴───────────────┴───────────────────────────┴────────────────────────────────────┴───────────────────┴──────────────────────┴────────────────────────────┴───────────┴──────────────────┴───────────────────────┴──────────────────────┴──────────────────────┴────────────────────┴───────────────┴─────────┴───────────────────┴────────────┴────────────┴────────────┴─────────────┴─────────────┴─────────────┴──────────────┴──────────────┴──────────────┴───────────────┴───────────────┴───────────────┴───────────────┴────────────────┴────────────────┴────────────────┴──────────────┴────────────┴─────────────────────────┴───────────────────────────────────────────┴───────────────────────────────────────────┴───────────────────┤
│ ? rows (>9999 rows, 20 shown) 94 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 │
├───────────────────────┼────────────────────────────┼───────┤
│ ileum │ t cd4 │ 7156 │
│ ileum │ cd4 th1 em │ 1400 │
│ ileum │ cd8 tem │ 7276 │
│ lung │ treg │ 58929 │
│ lung │ cd4 tem │ 2670 │
│ lung │ plasma │ 69854 │
│ lung │ cd8 naive │ 1859 │
│ mesenteric lymph node │ cd8 naive │ 2366 │
│ mesenteric lymph node │ treg │ 7103 │
│ mesenteric lymph node │ cd4 tem │ 338 │
│ · │ · │ · │
│ · │ · │ · │
│ · │ · │ · │
│ inguinal lymph node │ cd4 tcm │ 55 │
│ nasopharynx │ granulocyte │ 1 │
│ eye │ secretory │ 1 │
│ muscle tissue │ cytotoxic │ 28 │
│ muscle tissue │ cd8 tcm │ 20 │
│ endocrine pancreas │ b naive │ 3 │
│ aorta │ b │ 9 │
│ parietal lobe │ pericyte │ 10 │
│ sublingual gland │ cd4 fh em │ 1 │
│ gastrocnemius │ cd8 tcm │ 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 │ .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 │ int32 │
├──────────────────────────────────────────────────────────────┼──────────────────────────────────────┼────────────────────┼──────────────────────────────────┼──────────────────────────────────────────────────────┼────────────────────────────┼──────────────────────────────────┼───────────┼────────────────────────┼────────────┼────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┼──────────────────────────────────────┼──────────────────────────────────────┼────────────────────┼─────────────────────────────┼────────────────────────────────────┼─────────┼──────────────────────────┼──────────┼───────────────┼──────────────────────────────────────────────────────────────────────────────┼───────────────┼──────────────┼──────────┼─────────────────┼─────────────────────┼──────────────┼───────────────────────────┼────────────────────┼──────────────┼───────────────────┼────────────┼──────────────────┼───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┼────────────────┼─────────────────────────┼──────────────────────────────────────────┼─────────┼──────────────────────┼─────────────────┼───────────────────────┼─────────────────────────┼─────────────┼───────────────────────────────────────────────────────┼───────────┼─────────────────────────────────────────────────────────────────────────────────────┼────────────────────────────┼─────────┼─────────┼──────────┼───────────────────────────────────┼──────────────────────┼───────────────────────────────────┼────────────────────────────────┼────────────────────────────┼──────────────────────────────┼────────────────────┼───────────────┼────────────────────────┼─────────────────────────────────────┼───────────────────┼──────────────────────┼────────────────────────────┼───────────┼──────────────────┼───────────────────────┼──────────────────────┼──────────────────────┼────────────────────┼───────────────┼─────────┼───────────────────┼────────────┼────────────┼────────────┼─────────────┼─────────────┼─────────────┼──────────────┼──────────────┼──────────────┼───────────────┼───────────────┼───────────────┼───────────────┼────────────────┼────────────────┼────────────────┼──────────────┼────────────┼─────────────────────────┼───────────────────────────────────────────┼───────────────────────────────────────────┼───────────────────┤
│ C43_ACGCAGCTCGCCTGTT___0c9a8cfb-6649-4d52-b418-6d8e56bd7afe │ 0c9a8cfb-6649-4d52-b418-6d8e56bd7afe │ )Z_yvnB=j) │ eec28f1c966b73c7c657c805e671bce4 │ intrahepatic cholangiocyte │ CL:0002538 │ eec28f1c966b73c7c657c805e671bce4 │ 10x 3' v2 │ EFO:0009899 │ 1011 │ Publication: https://doi.org/10.1016/j.jhep.2023.12.023 Dataset Version: https://datasets.cellxgene.cziscience.com/f2321e56-12c9-4ffa-a808-7394d976b172.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/0c8a364b-97b5-4cc8-a593-23c38c6f0ac5 │ 0c8a364b-97b5-4cc8-a593-23c38c6f0ac5 │ f2321e56-12c9-4ffa-a808-7394d976b172 │ X_umap │ human early adulthood stage │ HsapDv:0000088 │ normal │ PATO:0000461 │ C43 │ │ https://cellxgene.cziscience.com/e/0c9a8cfb-6649-4d52-b418-6d8e56bd7afe.cxg/ │ 33363 │ 14455693.0 │ H5AD │ TRUE │ 1754.5272007912959 │ Homo sapiens │ NCBITaxon:9606 │ 832 │ 2024-02-22 │ raw.X │ 2024-06-11 │ NULL │ 10862faa-ac07-4849-9620-bf4de343f86c___C43___8f30670c-3e90-4e44-93b9-732168ddc3be___3690858c-9978-4934-ad08-eb1a9ade9a02___caudate lobe of liver___human early adulthood stage___10x 3' v2______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ cell │ caudate lobe of liver │ UBERON:0001117 │ tissue │ Cholangiocytes from human healthy donor liver samples │ false │ https://datasets.cellxgene.cziscience.com/f2321e56-12c9-4ffa-a808-7394d976b172.h5ad │ NULL │ NULL │ NULL │ 9125 │ gastrointestinal accessory organs │ cellxgene/21-08-2025 │ Epithelial cells │ Intermediate monocytes │ Other │ 1394 │ 979.256140000002 │ false │ C43_ACGCAGCTCGCCTGTT │ NA_non immune_cd14 mono_epithelial │ epithelial │ non immune │ epithelial │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 8 │ 5 │ 4 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ d17f42a873f974929d62bee855c6a5aa___1.h5ad │ 0df21779296514b3e9c20b7f4e7fd84e___1.h5ad │ 31 │
│ C43_AGTAGTCAGCTAACAA___0c9a8cfb-6649-4d52-b418-6d8e56bd7afe │ 0c9a8cfb-6649-4d52-b418-6d8e56bd7afe │ k;pY$Pq7#- │ eec28f1c966b73c7c657c805e671bce4 │ intrahepatic cholangiocyte │ CL:0002538 │ eec28f1c966b73c7c657c805e671bce4 │ 10x 3' v2 │ EFO:0009899 │ 1011 │ Publication: https://doi.org/10.1016/j.jhep.2023.12.023 Dataset Version: https://datasets.cellxgene.cziscience.com/f2321e56-12c9-4ffa-a808-7394d976b172.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/0c8a364b-97b5-4cc8-a593-23c38c6f0ac5 │ 0c8a364b-97b5-4cc8-a593-23c38c6f0ac5 │ f2321e56-12c9-4ffa-a808-7394d976b172 │ X_umap │ human early adulthood stage │ HsapDv:0000088 │ normal │ PATO:0000461 │ C43 │ │ https://cellxgene.cziscience.com/e/0c9a8cfb-6649-4d52-b418-6d8e56bd7afe.cxg/ │ 33363 │ 14455693.0 │ H5AD │ TRUE │ 1754.5272007912959 │ Homo sapiens │ NCBITaxon:9606 │ 832 │ 2024-02-22 │ raw.X │ 2024-06-11 │ NULL │ 10862faa-ac07-4849-9620-bf4de343f86c___C43___8f30670c-3e90-4e44-93b9-732168ddc3be___3690858c-9978-4934-ad08-eb1a9ade9a02___caudate lobe of liver___human early adulthood stage___10x 3' v2______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ cell │ caudate lobe of liver │ UBERON:0001117 │ tissue │ Cholangiocytes from human healthy donor liver samples │ false │ https://datasets.cellxgene.cziscience.com/f2321e56-12c9-4ffa-a808-7394d976b172.h5ad │ NULL │ NULL │ NULL │ 9125 │ gastrointestinal accessory organs │ cellxgene/21-08-2025 │ Epithelial cells │ Classical monocytes │ Other │ 1001 │ 957.5471500000111 │ false │ C43_AGTAGTCAGCTAACAA │ NA_non immune_cd14 mono_epithelial │ epithelial │ non immune │ epithelial │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 5 │ 7 │ 2 │ 2 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ d17f42a873f974929d62bee855c6a5aa___1.h5ad │ 0df21779296514b3e9c20b7f4e7fd84e___1.h5ad │ 31 │
│ C43_ATAAGAGGTACCATCA___0c9a8cfb-6649-4d52-b418-6d8e56bd7afe │ 0c9a8cfb-6649-4d52-b418-6d8e56bd7afe │ %V9A!v11>i │ eec28f1c966b73c7c657c805e671bce4 │ intrahepatic cholangiocyte │ CL:0002538 │ eec28f1c966b73c7c657c805e671bce4 │ 10x 3' v2 │ EFO:0009899 │ 1011 │ Publication: https://doi.org/10.1016/j.jhep.2023.12.023 Dataset Version: https://datasets.cellxgene.cziscience.com/f2321e56-12c9-4ffa-a808-7394d976b172.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/0c8a364b-97b5-4cc8-a593-23c38c6f0ac5 │ 0c8a364b-97b5-4cc8-a593-23c38c6f0ac5 │ f2321e56-12c9-4ffa-a808-7394d976b172 │ X_umap │ human early adulthood stage │ HsapDv:0000088 │ normal │ PATO:0000461 │ C43 │ │ https://cellxgene.cziscience.com/e/0c9a8cfb-6649-4d52-b418-6d8e56bd7afe.cxg/ │ 33363 │ 14455693.0 │ H5AD │ TRUE │ 1754.5272007912959 │ Homo sapiens │ NCBITaxon:9606 │ 832 │ 2024-02-22 │ raw.X │ 2024-06-11 │ NULL │ 10862faa-ac07-4849-9620-bf4de343f86c___C43___8f30670c-3e90-4e44-93b9-732168ddc3be___3690858c-9978-4934-ad08-eb1a9ade9a02___caudate lobe of liver___human early adulthood stage___10x 3' v2______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ cell │ caudate lobe of liver │ UBERON:0001117 │ tissue │ Cholangiocytes from human healthy donor liver samples │ false │ https://datasets.cellxgene.cziscience.com/f2321e56-12c9-4ffa-a808-7394d976b172.h5ad │ NULL │ NULL │ NULL │ 9125 │ gastrointestinal accessory organs │ cellxgene/21-08-2025 │ Epithelial cells │ Classical monocytes │ Other │ 2857 │ 989.9988899999803 │ false │ C43_ATAAGAGGTACCATCA │ NA_non immune_cd14 mono_epithelial │ epithelial │ non immune │ epithelial │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 5 │ 7 │ 2 │ 2 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ d17f42a873f974929d62bee855c6a5aa___1.h5ad │ 0df21779296514b3e9c20b7f4e7fd84e___1.h5ad │ 31 │
│ C43_ATGTGTGGTCTCTTAT___0c9a8cfb-6649-4d52-b418-6d8e56bd7afe │ 0c9a8cfb-6649-4d52-b418-6d8e56bd7afe │ X1snBZk(Y| │ eec28f1c966b73c7c657c805e671bce4 │ intrahepatic cholangiocyte │ CL:0002538 │ eec28f1c966b73c7c657c805e671bce4 │ 10x 3' v2 │ EFO:0009899 │ 1011 │ Publication: https://doi.org/10.1016/j.jhep.2023.12.023 Dataset Version: https://datasets.cellxgene.cziscience.com/f2321e56-12c9-4ffa-a808-7394d976b172.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/0c8a364b-97b5-4cc8-a593-23c38c6f0ac5 │ 0c8a364b-97b5-4cc8-a593-23c38c6f0ac5 │ f2321e56-12c9-4ffa-a808-7394d976b172 │ X_umap │ human early adulthood stage │ HsapDv:0000088 │ normal │ PATO:0000461 │ C43 │ │ https://cellxgene.cziscience.com/e/0c9a8cfb-6649-4d52-b418-6d8e56bd7afe.cxg/ │ 33363 │ 14455693.0 │ H5AD │ TRUE │ 1754.5272007912959 │ Homo sapiens │ NCBITaxon:9606 │ 832 │ 2024-02-22 │ raw.X │ 2024-06-11 │ NULL │ 10862faa-ac07-4849-9620-bf4de343f86c___C43___8f30670c-3e90-4e44-93b9-732168ddc3be___3690858c-9978-4934-ad08-eb1a9ade9a02___caudate lobe of liver___human early adulthood stage___10x 3' v2______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ cell │ caudate lobe of liver │ UBERON:0001117 │ tissue │ Cholangiocytes from human healthy donor liver samples │ false │ https://datasets.cellxgene.cziscience.com/f2321e56-12c9-4ffa-a808-7394d976b172.h5ad │ NULL │ NULL │ NULL │ 9125 │ gastrointestinal accessory organs │ cellxgene/21-08-2025 │ Epithelial cells │ Myeloid dendritic cells │ Other │ 1589 │ 1038.0219499999992 │ false │ C43_ATGTGTGGTCTCTTAT │ NA_non immune_cdc_epithelial │ epithelial │ non immune │ epithelial │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 4 │ 3 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ d17f42a873f974929d62bee855c6a5aa___1.h5ad │ 0df21779296514b3e9c20b7f4e7fd84e___1.h5ad │ 31 │
│ C43_CATGCCTGTGTAAGTA___0c9a8cfb-6649-4d52-b418-6d8e56bd7afe │ 0c9a8cfb-6649-4d52-b418-6d8e56bd7afe │ #et@P4b#v> │ eec28f1c966b73c7c657c805e671bce4 │ intrahepatic cholangiocyte │ CL:0002538 │ eec28f1c966b73c7c657c805e671bce4 │ 10x 3' v2 │ EFO:0009899 │ 1011 │ Publication: https://doi.org/10.1016/j.jhep.2023.12.023 Dataset Version: https://datasets.cellxgene.cziscience.com/f2321e56-12c9-4ffa-a808-7394d976b172.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/0c8a364b-97b5-4cc8-a593-23c38c6f0ac5 │ 0c8a364b-97b5-4cc8-a593-23c38c6f0ac5 │ f2321e56-12c9-4ffa-a808-7394d976b172 │ X_umap │ human early adulthood stage │ HsapDv:0000088 │ normal │ PATO:0000461 │ C43 │ │ https://cellxgene.cziscience.com/e/0c9a8cfb-6649-4d52-b418-6d8e56bd7afe.cxg/ │ 33363 │ 14455693.0 │ H5AD │ TRUE │ 1754.5272007912959 │ Homo sapiens │ NCBITaxon:9606 │ 832 │ 2024-02-22 │ raw.X │ 2024-06-11 │ NULL │ 10862faa-ac07-4849-9620-bf4de343f86c___C43___8f30670c-3e90-4e44-93b9-732168ddc3be___3690858c-9978-4934-ad08-eb1a9ade9a02___caudate lobe of liver___human early adulthood stage___10x 3' v2______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ cell │ caudate lobe of liver │ UBERON:0001117 │ tissue │ Cholangiocytes from human healthy donor liver samples │ false │ https://datasets.cellxgene.cziscience.com/f2321e56-12c9-4ffa-a808-7394d976b172.h5ad │ NULL │ NULL │ NULL │ 9125 │ gastrointestinal accessory organs │ cellxgene/21-08-2025 │ Epithelial cells │ Myeloid dendritic cells │ Other │ 1177 │ 1125.3869500000073 │ false │ C43_CATGCCTGTGTAAGTA │ NA_non immune_cdc_epithelial │ epithelial │ non immune │ epithelial │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 3 │ 6 │ 3 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ d17f42a873f974929d62bee855c6a5aa___1.h5ad │ 0df21779296514b3e9c20b7f4e7fd84e___1.h5ad │ 31 │
│ C43_CGAACATTCTGCAAGT___0c9a8cfb-6649-4d52-b418-6d8e56bd7afe │ 0c9a8cfb-6649-4d52-b418-6d8e56bd7afe │ P;&A<wL?4D │ eec28f1c966b73c7c657c805e671bce4 │ intrahepatic cholangiocyte │ CL:0002538 │ eec28f1c966b73c7c657c805e671bce4 │ 10x 3' v2 │ EFO:0009899 │ 1011 │ Publication: https://doi.org/10.1016/j.jhep.2023.12.023 Dataset Version: https://datasets.cellxgene.cziscience.com/f2321e56-12c9-4ffa-a808-7394d976b172.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/0c8a364b-97b5-4cc8-a593-23c38c6f0ac5 │ 0c8a364b-97b5-4cc8-a593-23c38c6f0ac5 │ f2321e56-12c9-4ffa-a808-7394d976b172 │ X_umap │ human early adulthood stage │ HsapDv:0000088 │ normal │ PATO:0000461 │ C43 │ │ https://cellxgene.cziscience.com/e/0c9a8cfb-6649-4d52-b418-6d8e56bd7afe.cxg/ │ 33363 │ 14455693.0 │ H5AD │ TRUE │ 1754.5272007912959 │ Homo sapiens │ NCBITaxon:9606 │ 832 │ 2024-02-22 │ raw.X │ 2024-06-11 │ NULL │ 10862faa-ac07-4849-9620-bf4de343f86c___C43___8f30670c-3e90-4e44-93b9-732168ddc3be___3690858c-9978-4934-ad08-eb1a9ade9a02___caudate lobe of liver___human early adulthood stage___10x 3' v2______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ cell │ caudate lobe of liver │ UBERON:0001117 │ tissue │ Cholangiocytes from human healthy donor liver samples │ false │ https://datasets.cellxgene.cziscience.com/f2321e56-12c9-4ffa-a808-7394d976b172.h5ad │ NULL │ NULL │ NULL │ 9125 │ gastrointestinal accessory organs │ cellxgene/21-08-2025 │ Epithelial cells │ Progenitor cells │ Other │ 777 │ 931.4838199999913 │ false │ C43_CGAACATTCTGCAAGT │ NA_non immune_progenitor_epithelial │ epithelial │ non immune │ epithelial │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 10 │ 2 │ 3 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ d17f42a873f974929d62bee855c6a5aa___1.h5ad │ 0df21779296514b3e9c20b7f4e7fd84e___1.h5ad │ 31 │
│ C43_CGGCTAGAGAGCCCAA___0c9a8cfb-6649-4d52-b418-6d8e56bd7afe │ 0c9a8cfb-6649-4d52-b418-6d8e56bd7afe │ rL#zms)=aG │ eec28f1c966b73c7c657c805e671bce4 │ intrahepatic cholangiocyte │ CL:0002538 │ eec28f1c966b73c7c657c805e671bce4 │ 10x 3' v2 │ EFO:0009899 │ 1011 │ Publication: https://doi.org/10.1016/j.jhep.2023.12.023 Dataset Version: https://datasets.cellxgene.cziscience.com/f2321e56-12c9-4ffa-a808-7394d976b172.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/0c8a364b-97b5-4cc8-a593-23c38c6f0ac5 │ 0c8a364b-97b5-4cc8-a593-23c38c6f0ac5 │ f2321e56-12c9-4ffa-a808-7394d976b172 │ X_umap │ human early adulthood stage │ HsapDv:0000088 │ normal │ PATO:0000461 │ C43 │ │ https://cellxgene.cziscience.com/e/0c9a8cfb-6649-4d52-b418-6d8e56bd7afe.cxg/ │ 33363 │ 14455693.0 │ H5AD │ TRUE │ 1754.5272007912959 │ Homo sapiens │ NCBITaxon:9606 │ 832 │ 2024-02-22 │ raw.X │ 2024-06-11 │ NULL │ 10862faa-ac07-4849-9620-bf4de343f86c___C43___8f30670c-3e90-4e44-93b9-732168ddc3be___3690858c-9978-4934-ad08-eb1a9ade9a02___caudate lobe of liver___human early adulthood stage___10x 3' v2______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ cell │ caudate lobe of liver │ UBERON:0001117 │ tissue │ Cholangiocytes from human healthy donor liver samples │ false │ https://datasets.cellxgene.cziscience.com/f2321e56-12c9-4ffa-a808-7394d976b172.h5ad │ NULL │ NULL │ NULL │ 9125 │ gastrointestinal accessory organs │ cellxgene/21-08-2025 │ Epithelial cells │ Classical monocytes │ Other │ 1604 │ 975.2703299999739 │ false │ C43_CGGCTAGAGAGCCCAA │ NA_non immune_cd14 mono_epithelial │ epithelial │ non immune │ epithelial │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 7 │ 3 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ d17f42a873f974929d62bee855c6a5aa___1.h5ad │ 0df21779296514b3e9c20b7f4e7fd84e___1.h5ad │ 31 │
│ C43_CGTTCTGTCATCTGTT___0c9a8cfb-6649-4d52-b418-6d8e56bd7afe │ 0c9a8cfb-6649-4d52-b418-6d8e56bd7afe │ WX>j5$YdH` │ eec28f1c966b73c7c657c805e671bce4 │ intrahepatic cholangiocyte │ CL:0002538 │ eec28f1c966b73c7c657c805e671bce4 │ 10x 3' v2 │ EFO:0009899 │ 1011 │ Publication: https://doi.org/10.1016/j.jhep.2023.12.023 Dataset Version: https://datasets.cellxgene.cziscience.com/f2321e56-12c9-4ffa-a808-7394d976b172.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/0c8a364b-97b5-4cc8-a593-23c38c6f0ac5 │ 0c8a364b-97b5-4cc8-a593-23c38c6f0ac5 │ f2321e56-12c9-4ffa-a808-7394d976b172 │ X_umap │ human early adulthood stage │ HsapDv:0000088 │ normal │ PATO:0000461 │ C43 │ │ https://cellxgene.cziscience.com/e/0c9a8cfb-6649-4d52-b418-6d8e56bd7afe.cxg/ │ 33363 │ 14455693.0 │ H5AD │ TRUE │ 1754.5272007912959 │ Homo sapiens │ NCBITaxon:9606 │ 832 │ 2024-02-22 │ raw.X │ 2024-06-11 │ NULL │ 10862faa-ac07-4849-9620-bf4de343f86c___C43___8f30670c-3e90-4e44-93b9-732168ddc3be___3690858c-9978-4934-ad08-eb1a9ade9a02___caudate lobe of liver___human early adulthood stage___10x 3' v2______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ cell │ caudate lobe of liver │ UBERON:0001117 │ tissue │ Cholangiocytes from human healthy donor liver samples │ false │ https://datasets.cellxgene.cziscience.com/f2321e56-12c9-4ffa-a808-7394d976b172.h5ad │ NULL │ NULL │ NULL │ 9125 │ gastrointestinal accessory organs │ cellxgene/21-08-2025 │ Epithelial cells │ Classical monocytes │ Other │ 1822 │ 981.3387100000137 │ false │ C43_CGTTCTGTCATCTGTT │ NA_non immune_cd14 mono_epithelial │ epithelial │ non immune │ epithelial │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 5 │ 7 │ 2 │ 2 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ d17f42a873f974929d62bee855c6a5aa___1.h5ad │ 0df21779296514b3e9c20b7f4e7fd84e___1.h5ad │ 31 │
│ C43_CTCTAATCAATGGAAT___0c9a8cfb-6649-4d52-b418-6d8e56bd7afe │ 0c9a8cfb-6649-4d52-b418-6d8e56bd7afe │ 6UkYuD&iPQ │ eec28f1c966b73c7c657c805e671bce4 │ unknown │ unknown │ eec28f1c966b73c7c657c805e671bce4 │ 10x 3' v2 │ EFO:0009899 │ 1011 │ Publication: https://doi.org/10.1016/j.jhep.2023.12.023 Dataset Version: https://datasets.cellxgene.cziscience.com/f2321e56-12c9-4ffa-a808-7394d976b172.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/0c8a364b-97b5-4cc8-a593-23c38c6f0ac5 │ 0c8a364b-97b5-4cc8-a593-23c38c6f0ac5 │ f2321e56-12c9-4ffa-a808-7394d976b172 │ X_umap │ human early adulthood stage │ HsapDv:0000088 │ normal │ PATO:0000461 │ C43 │ │ https://cellxgene.cziscience.com/e/0c9a8cfb-6649-4d52-b418-6d8e56bd7afe.cxg/ │ 33363 │ 14455693.0 │ H5AD │ TRUE │ 1754.5272007912959 │ Homo sapiens │ NCBITaxon:9606 │ 832 │ 2024-02-22 │ raw.X │ 2024-06-11 │ NULL │ 10862faa-ac07-4849-9620-bf4de343f86c___C43___8f30670c-3e90-4e44-93b9-732168ddc3be___3690858c-9978-4934-ad08-eb1a9ade9a02___caudate lobe of liver___human early adulthood stage___10x 3' v2______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ cell │ caudate lobe of liver │ UBERON:0001117 │ tissue │ Cholangiocytes from human healthy donor liver samples │ false │ https://datasets.cellxgene.cziscience.com/f2321e56-12c9-4ffa-a808-7394d976b172.h5ad │ NULL │ NULL │ NULL │ 9125 │ gastrointestinal accessory organs │ cellxgene/21-08-2025 │ Epithelial cells │ Myeloid dendritic cells │ Other │ 570 │ 744.3326699999958 │ false │ C43_CTCTAATCAATGGAAT │ NA_non immune_cdc_other │ other │ non immune │ other │ false │ 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 │ e97f74681427120200898f4b4f9603d8___1.h5ad │ 0df21779296514b3e9c20b7f4e7fd84e___1.h5ad │ 3 │
│ C43_CTTGGCTGTCTCCATC___0c9a8cfb-6649-4d52-b418-6d8e56bd7afe │ 0c9a8cfb-6649-4d52-b418-6d8e56bd7afe │ NMUF(PmIYV │ eec28f1c966b73c7c657c805e671bce4 │ intrahepatic cholangiocyte │ CL:0002538 │ eec28f1c966b73c7c657c805e671bce4 │ 10x 3' v2 │ EFO:0009899 │ 1011 │ Publication: https://doi.org/10.1016/j.jhep.2023.12.023 Dataset Version: https://datasets.cellxgene.cziscience.com/f2321e56-12c9-4ffa-a808-7394d976b172.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/0c8a364b-97b5-4cc8-a593-23c38c6f0ac5 │ 0c8a364b-97b5-4cc8-a593-23c38c6f0ac5 │ f2321e56-12c9-4ffa-a808-7394d976b172 │ X_umap │ human early adulthood stage │ HsapDv:0000088 │ normal │ PATO:0000461 │ C43 │ │ https://cellxgene.cziscience.com/e/0c9a8cfb-6649-4d52-b418-6d8e56bd7afe.cxg/ │ 33363 │ 14455693.0 │ H5AD │ TRUE │ 1754.5272007912959 │ Homo sapiens │ NCBITaxon:9606 │ 832 │ 2024-02-22 │ raw.X │ 2024-06-11 │ NULL │ 10862faa-ac07-4849-9620-bf4de343f86c___C43___8f30670c-3e90-4e44-93b9-732168ddc3be___3690858c-9978-4934-ad08-eb1a9ade9a02___caudate lobe of liver___human early adulthood stage___10x 3' v2______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ cell │ caudate lobe of liver │ UBERON:0001117 │ tissue │ Cholangiocytes from human healthy donor liver samples │ false │ https://datasets.cellxgene.cziscience.com/f2321e56-12c9-4ffa-a808-7394d976b172.h5ad │ NULL │ NULL │ NULL │ 9125 │ gastrointestinal accessory organs │ cellxgene/21-08-2025 │ Epithelial cells │ Classical monocytes │ Other │ 1642 │ 1084.9649800000163 │ false │ C43_CTTGGCTGTCTCCATC │ NA_non immune_cd14 mono_epithelial │ epithelial │ non immune │ epithelial │ false │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 3 │ 6 │ 3 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ d17f42a873f974929d62bee855c6a5aa___1.h5ad │ 0df21779296514b3e9c20b7f4e7fd84e___1.h5ad │ 31 │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ S5_CTTCTCTCAAAGCAAT-1___2a498ace-872a-4935-984b-1afa70fd9886 │ 2a498ace-872a-4935-984b-1afa70fd9886 │ ^RucxJsDI( │ 81b69f84384c7d264599231a2e40a272 │ naive B cell │ CL:0000788 │ 81b69f84384c7d264599231a2e40a272 │ 10x 5' v1 │ EFO:0011025 │ 422220 │ Publication: https://doi.org/10.1038/s41586-021-04345-x Dataset Version: https://datasets.cellxgene.cziscience.com/d911082e-b5e2-40e6-8f08-fb53c7894622.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/03f821b4-87be-4ff4-b65a-b5fc00061da7 │ 03f821b4-87be-4ff4-b65a-b5fc00061da7 │ d911082e-b5e2-40e6-8f08-fb53c7894622 │ X_umap_wnn_derived │ 2-5 year-old child stage │ HsapDv:0000084 │ normal │ PATO:0000461 │ NP16 │ │ https://cellxgene.cziscience.com/e/2a498ace-872a-4935-984b-1afa70fd9886.cxg/ │ 33105 │ 4462693785.0 │ H5AD │ TRUE │ 1338.366685614135 │ Homo sapiens │ NCBITaxon:9606 │ 339597 │ 2022-03-24 │ raw.X │ 2024-06-11 │ NULL │ NP16___blood___2-5 year-old child stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ cell │ blood │ UBERON:0000178 │ tissue │ PBMC │ false │ https://datasets.cellxgene.cziscience.com/d911082e-b5e2-40e6-8f08-fb53c7894622.h5ad │ NULL │ NULL │ NULL │ 1277 │ blood │ cellxgene/21-08-2025 │ naive B-cells │ Naive B cells │ B intermediate │ 1027 │ 6.42038000013963 │ false │ S5_CTTCTCTCAAAGCAAT-1 │ cd8 tem_b naive_b naive_b naive │ b naive │ b naive │ b naive │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 105 │ 32 │ 24 │ 22 │ 11 │ 2 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ c0ba78ab3b5093133f3d54c5cb495a72___1.h5ad │ 4b121a55084eac4b9bf654fee90066a5___1.h5ad │ 363 │
│ S5_CTTCTCTTCGAATGCT-1___2a498ace-872a-4935-984b-1afa70fd9886 │ 2a498ace-872a-4935-984b-1afa70fd9886 │ J@F&BSv>0P │ 81b69f84384c7d264599231a2e40a272 │ naive thymus-derived CD4-positive, alpha-beta T cell │ CL:0000895 │ 81b69f84384c7d264599231a2e40a272 │ 10x 5' v1 │ EFO:0011025 │ 422220 │ Publication: https://doi.org/10.1038/s41586-021-04345-x Dataset Version: https://datasets.cellxgene.cziscience.com/d911082e-b5e2-40e6-8f08-fb53c7894622.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/03f821b4-87be-4ff4-b65a-b5fc00061da7 │ 03f821b4-87be-4ff4-b65a-b5fc00061da7 │ d911082e-b5e2-40e6-8f08-fb53c7894622 │ X_umap_wnn_derived │ 2-5 year-old child stage │ HsapDv:0000084 │ normal │ PATO:0000461 │ NP16 │ │ https://cellxgene.cziscience.com/e/2a498ace-872a-4935-984b-1afa70fd9886.cxg/ │ 33105 │ 4462693785.0 │ H5AD │ TRUE │ 1338.366685614135 │ Homo sapiens │ NCBITaxon:9606 │ 339597 │ 2022-03-24 │ raw.X │ 2024-06-11 │ NULL │ NP16___blood___2-5 year-old child stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ cell │ blood │ UBERON:0000178 │ tissue │ PBMC │ false │ https://datasets.cellxgene.cziscience.com/d911082e-b5e2-40e6-8f08-fb53c7894622.h5ad │ NULL │ NULL │ NULL │ 1277 │ blood │ cellxgene/21-08-2025 │ CD4+ T-cells │ Naive CD4 T cells │ CD4 TCM │ 994 │ 5.811920000132886 │ false │ S5_CTTCTCTTCGAATGCT-1 │ cd8 tem_t cd4_cd4 naive_cd4 naive │ cd4 naive │ cd4 naive │ cd4 naive │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 113 │ 53 │ 3 │ 11 │ 1 │ 4 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 5e72d4cf8e568eea4b4031de3be85a91___1.h5ad │ 4b121a55084eac4b9bf654fee90066a5___1.h5ad │ 305 │
│ S5_CTTGGCTGTCCAGTTA-1___2a498ace-872a-4935-984b-1afa70fd9886 │ 2a498ace-872a-4935-984b-1afa70fd9886 │ <r5l-gOQ|M │ 81b69f84384c7d264599231a2e40a272 │ naive thymus-derived CD8-positive, alpha-beta T cell │ CL:0000900 │ 81b69f84384c7d264599231a2e40a272 │ 10x 5' v1 │ EFO:0011025 │ 422220 │ Publication: https://doi.org/10.1038/s41586-021-04345-x Dataset Version: https://datasets.cellxgene.cziscience.com/d911082e-b5e2-40e6-8f08-fb53c7894622.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/03f821b4-87be-4ff4-b65a-b5fc00061da7 │ 03f821b4-87be-4ff4-b65a-b5fc00061da7 │ d911082e-b5e2-40e6-8f08-fb53c7894622 │ X_umap_wnn_derived │ 2-5 year-old child stage │ HsapDv:0000084 │ normal │ PATO:0000461 │ NP16 │ │ https://cellxgene.cziscience.com/e/2a498ace-872a-4935-984b-1afa70fd9886.cxg/ │ 33105 │ 4462693785.0 │ H5AD │ TRUE │ 1338.366685614135 │ Homo sapiens │ NCBITaxon:9606 │ 339597 │ 2022-03-24 │ raw.X │ 2024-06-11 │ NULL │ NP16___blood___2-5 year-old child stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ cell │ blood │ UBERON:0000178 │ tissue │ PBMC │ false │ https://datasets.cellxgene.cziscience.com/d911082e-b5e2-40e6-8f08-fb53c7894622.h5ad │ NULL │ NULL │ NULL │ 1277 │ blood │ cellxgene/21-08-2025 │ CD8+ T-cells │ Naive CD8 T cells │ CD8 TCM │ 1142 │ 6.609180000156812 │ false │ S5_CTTGGCTGTCCAGTTA-1 │ cd8 tem_t cd8_cd8 naive_cd8 naive │ cd8 naive │ t cd8 │ cd8 naive │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 54 │ 42 │ 9 │ 2 │ 2 │ 2 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 571d2cd10b39f7675241dcea4e9aa7eb___1.h5ad │ 4b121a55084eac4b9bf654fee90066a5___1.h5ad │ 171 │
│ S5_CTTGGCTTCATGTGGT-1___2a498ace-872a-4935-984b-1afa70fd9886 │ 2a498ace-872a-4935-984b-1afa70fd9886 │ mc>h+gLTJw │ 81b69f84384c7d264599231a2e40a272 │ naive thymus-derived CD8-positive, alpha-beta T cell │ CL:0000900 │ 81b69f84384c7d264599231a2e40a272 │ 10x 5' v1 │ EFO:0011025 │ 422220 │ Publication: https://doi.org/10.1038/s41586-021-04345-x Dataset Version: https://datasets.cellxgene.cziscience.com/d911082e-b5e2-40e6-8f08-fb53c7894622.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/03f821b4-87be-4ff4-b65a-b5fc00061da7 │ 03f821b4-87be-4ff4-b65a-b5fc00061da7 │ d911082e-b5e2-40e6-8f08-fb53c7894622 │ X_umap_wnn_derived │ 2-5 year-old child stage │ HsapDv:0000084 │ normal │ PATO:0000461 │ NP16 │ │ https://cellxgene.cziscience.com/e/2a498ace-872a-4935-984b-1afa70fd9886.cxg/ │ 33105 │ 4462693785.0 │ H5AD │ TRUE │ 1338.366685614135 │ Homo sapiens │ NCBITaxon:9606 │ 339597 │ 2022-03-24 │ raw.X │ 2024-06-11 │ NULL │ NP16___blood___2-5 year-old child stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ cell │ blood │ UBERON:0000178 │ tissue │ PBMC │ false │ https://datasets.cellxgene.cziscience.com/d911082e-b5e2-40e6-8f08-fb53c7894622.h5ad │ NULL │ NULL │ NULL │ 1277 │ blood │ cellxgene/21-08-2025 │ CD8+ T-cells │ Naive CD8 T cells │ CD8 TCM │ 1460 │ 9.213590000204022 │ false │ S5_CTTGGCTTCATGTGGT-1 │ cd8 tem_t cd8_cd8 naive_cd8 naive │ cd8 naive │ t cd8 │ cd8 naive │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 2 │ 3 │ 13 │ 6 │ 1 │ 3 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 571d2cd10b39f7675241dcea4e9aa7eb___1.h5ad │ 4b121a55084eac4b9bf654fee90066a5___1.h5ad │ 171 │
│ S5_GAAACTCAGATCCCAT-1___2a498ace-872a-4935-984b-1afa70fd9886 │ 2a498ace-872a-4935-984b-1afa70fd9886 │ vu{b~TQlY< │ 81b69f84384c7d264599231a2e40a272 │ natural killer cell │ CL:0000623 │ 81b69f84384c7d264599231a2e40a272 │ 10x 5' v1 │ EFO:0011025 │ 422220 │ Publication: https://doi.org/10.1038/s41586-021-04345-x Dataset Version: https://datasets.cellxgene.cziscience.com/d911082e-b5e2-40e6-8f08-fb53c7894622.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/03f821b4-87be-4ff4-b65a-b5fc00061da7 │ 03f821b4-87be-4ff4-b65a-b5fc00061da7 │ d911082e-b5e2-40e6-8f08-fb53c7894622 │ X_umap_wnn_derived │ 2-5 year-old child stage │ HsapDv:0000084 │ normal │ PATO:0000461 │ NP16 │ │ https://cellxgene.cziscience.com/e/2a498ace-872a-4935-984b-1afa70fd9886.cxg/ │ 33105 │ 4462693785.0 │ H5AD │ TRUE │ 1338.366685614135 │ Homo sapiens │ NCBITaxon:9606 │ 339597 │ 2022-03-24 │ raw.X │ 2024-06-11 │ NULL │ NP16___blood___2-5 year-old child stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ cell │ blood │ UBERON:0000178 │ tissue │ PBMC │ false │ https://datasets.cellxgene.cziscience.com/d911082e-b5e2-40e6-8f08-fb53c7894622.h5ad │ NULL │ NULL │ NULL │ 1277 │ blood │ cellxgene/21-08-2025 │ NK cells │ Natural killer cells │ CD8 TEM │ 812 │ 4.384870000127194 │ false │ S5_GAAACTCAGATCCCAT-1 │ cd8 tem_nk_nk_nk │ nk │ nk │ nk │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 21 │ 41 │ 3 │ 3 │ 2 │ 2 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 2124207fd28fbd0ef086d136a45ca5ce___1.h5ad │ 4b121a55084eac4b9bf654fee90066a5___1.h5ad │ 333 │
│ S5_GAAACTCAGATCTGAA-1___2a498ace-872a-4935-984b-1afa70fd9886 │ 2a498ace-872a-4935-984b-1afa70fd9886 │ g_ly`Bn<^Q │ 81b69f84384c7d264599231a2e40a272 │ naive B cell │ CL:0000788 │ 81b69f84384c7d264599231a2e40a272 │ 10x 5' v1 │ EFO:0011025 │ 422220 │ Publication: https://doi.org/10.1038/s41586-021-04345-x Dataset Version: https://datasets.cellxgene.cziscience.com/d911082e-b5e2-40e6-8f08-fb53c7894622.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/03f821b4-87be-4ff4-b65a-b5fc00061da7 │ 03f821b4-87be-4ff4-b65a-b5fc00061da7 │ d911082e-b5e2-40e6-8f08-fb53c7894622 │ X_umap_wnn_derived │ 2-5 year-old child stage │ HsapDv:0000084 │ normal │ PATO:0000461 │ NP16 │ │ https://cellxgene.cziscience.com/e/2a498ace-872a-4935-984b-1afa70fd9886.cxg/ │ 33105 │ 4462693785.0 │ H5AD │ TRUE │ 1338.366685614135 │ Homo sapiens │ NCBITaxon:9606 │ 339597 │ 2022-03-24 │ raw.X │ 2024-06-11 │ NULL │ NP16___blood___2-5 year-old child stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ cell │ blood │ UBERON:0000178 │ tissue │ PBMC │ false │ https://datasets.cellxgene.cziscience.com/d911082e-b5e2-40e6-8f08-fb53c7894622.h5ad │ NULL │ NULL │ NULL │ 1277 │ blood │ cellxgene/21-08-2025 │ naive B-cells │ Naive B cells │ B naive │ 1064 │ 6.557580000136113 │ false │ S5_GAAACTCAGATCTGAA-1 │ cd8 tem_b naive_b naive_b naive │ b naive │ b naive │ b naive │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 50 │ 29 │ 20 │ 20 │ 2 │ 5 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ c0ba78ab3b5093133f3d54c5cb495a72___1.h5ad │ 4b121a55084eac4b9bf654fee90066a5___1.h5ad │ 363 │
│ S5_GAAACTCAGTTGTAGA-1___2a498ace-872a-4935-984b-1afa70fd9886 │ 2a498ace-872a-4935-984b-1afa70fd9886 │ WTupSE|>cu │ 81b69f84384c7d264599231a2e40a272 │ CD8-positive, alpha-beta cytotoxic T cell │ CL:0000794 │ 81b69f84384c7d264599231a2e40a272 │ 10x 5' v1 │ EFO:0011025 │ 422220 │ Publication: https://doi.org/10.1038/s41586-021-04345-x Dataset Version: https://datasets.cellxgene.cziscience.com/d911082e-b5e2-40e6-8f08-fb53c7894622.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/03f821b4-87be-4ff4-b65a-b5fc00061da7 │ 03f821b4-87be-4ff4-b65a-b5fc00061da7 │ d911082e-b5e2-40e6-8f08-fb53c7894622 │ X_umap_wnn_derived │ 2-5 year-old child stage │ HsapDv:0000084 │ normal │ PATO:0000461 │ NP16 │ │ https://cellxgene.cziscience.com/e/2a498ace-872a-4935-984b-1afa70fd9886.cxg/ │ 33105 │ 4462693785.0 │ H5AD │ TRUE │ 1338.366685614135 │ Homo sapiens │ NCBITaxon:9606 │ 339597 │ 2022-03-24 │ raw.X │ 2024-06-11 │ NULL │ NP16___blood___2-5 year-old child stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ cell │ blood │ UBERON:0000178 │ tissue │ PBMC │ false │ https://datasets.cellxgene.cziscience.com/d911082e-b5e2-40e6-8f08-fb53c7894622.h5ad │ NULL │ NULL │ NULL │ 1277 │ blood │ cellxgene/21-08-2025 │ CD8+ Tem │ Terminal effector CD8 T cells │ CD8 TEM │ 1035 │ 6.0701800001324955 │ false │ S5_GAAACTCAGTTGTAGA-1 │ cd8 tem_cd8 tem_cd8 tem_t cd8 │ t cd8 │ cd8 tem │ cd8 tem │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 20 │ 21 │ 9 │ 6 │ 2 │ 2 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 616b47a14643559c6dd2dae8cbcda684___1.h5ad │ 4b121a55084eac4b9bf654fee90066a5___1.h5ad │ 156 │
│ S5_GAAATGAAGTATCTCG-1___2a498ace-872a-4935-984b-1afa70fd9886 │ 2a498ace-872a-4935-984b-1afa70fd9886 │ XoI;91F}Yi │ 81b69f84384c7d264599231a2e40a272 │ central memory CD8-positive, alpha-beta T cell │ CL:0000907 │ 81b69f84384c7d264599231a2e40a272 │ 10x 5' v1 │ EFO:0011025 │ 422220 │ Publication: https://doi.org/10.1038/s41586-021-04345-x Dataset Version: https://datasets.cellxgene.cziscience.com/d911082e-b5e2-40e6-8f08-fb53c7894622.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/03f821b4-87be-4ff4-b65a-b5fc00061da7 │ 03f821b4-87be-4ff4-b65a-b5fc00061da7 │ d911082e-b5e2-40e6-8f08-fb53c7894622 │ X_umap_wnn_derived │ 2-5 year-old child stage │ HsapDv:0000084 │ normal │ PATO:0000461 │ NP16 │ │ https://cellxgene.cziscience.com/e/2a498ace-872a-4935-984b-1afa70fd9886.cxg/ │ 33105 │ 4462693785.0 │ H5AD │ TRUE │ 1338.366685614135 │ Homo sapiens │ NCBITaxon:9606 │ 339597 │ 2022-03-24 │ raw.X │ 2024-06-11 │ NULL │ NP16___blood___2-5 year-old child stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ cell │ blood │ UBERON:0000178 │ tissue │ PBMC │ false │ https://datasets.cellxgene.cziscience.com/d911082e-b5e2-40e6-8f08-fb53c7894622.h5ad │ NULL │ NULL │ NULL │ 1277 │ blood │ cellxgene/21-08-2025 │ CD4+ Tcm │ Non-Vd2 gd T cells │ CD4 TCM │ 638 │ 3.0184300000955773 │ false │ S5_GAAATGAAGTATCTCG-1 │ cd8 tem_cd4 tcm_tgd_cd8 tcm │ cd8 tcm │ t │ cd8 tcm │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 20 │ 3 │ 7 │ 3 │ 2 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 12698df8945e953c679439e9d47d02fe___1.h5ad │ 4b121a55084eac4b9bf654fee90066a5___1.h5ad │ 69 │
│ S5_GAACATCTCGTTACGA-1___2a498ace-872a-4935-984b-1afa70fd9886 │ 2a498ace-872a-4935-984b-1afa70fd9886 │ *{^Mv-@BE3 │ 81b69f84384c7d264599231a2e40a272 │ CD8-positive, alpha-beta cytotoxic T cell │ CL:0000794 │ 81b69f84384c7d264599231a2e40a272 │ 10x 5' v1 │ EFO:0011025 │ 422220 │ Publication: https://doi.org/10.1038/s41586-021-04345-x Dataset Version: https://datasets.cellxgene.cziscience.com/d911082e-b5e2-40e6-8f08-fb53c7894622.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/03f821b4-87be-4ff4-b65a-b5fc00061da7 │ 03f821b4-87be-4ff4-b65a-b5fc00061da7 │ d911082e-b5e2-40e6-8f08-fb53c7894622 │ X_umap_wnn_derived │ 2-5 year-old child stage │ HsapDv:0000084 │ normal │ PATO:0000461 │ NP16 │ │ https://cellxgene.cziscience.com/e/2a498ace-872a-4935-984b-1afa70fd9886.cxg/ │ 33105 │ 4462693785.0 │ H5AD │ TRUE │ 1338.366685614135 │ Homo sapiens │ NCBITaxon:9606 │ 339597 │ 2022-03-24 │ raw.X │ 2024-06-11 │ NULL │ NP16___blood___2-5 year-old child stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ cell │ blood │ UBERON:0000178 │ tissue │ PBMC │ false │ https://datasets.cellxgene.cziscience.com/d911082e-b5e2-40e6-8f08-fb53c7894622.h5ad │ NULL │ NULL │ NULL │ 1277 │ blood │ cellxgene/21-08-2025 │ NK cells │ Natural killer cells │ CD8 TEM │ 641 │ 3.2545700001146542 │ false │ S5_GAACATCTCGTTACGA-1 │ cd8 tem_nk_nk_t cd8 │ t cd8 │ nk │ cd8 tem │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 23 │ 33 │ 12 │ 5 │ 3 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 616b47a14643559c6dd2dae8cbcda684___1.h5ad │ 4b121a55084eac4b9bf654fee90066a5___1.h5ad │ 156 │
│ S5_GAACCTAAGGGCATGT-1___2a498ace-872a-4935-984b-1afa70fd9886 │ 2a498ace-872a-4935-984b-1afa70fd9886 │ s-IEWB~k!* │ 81b69f84384c7d264599231a2e40a272 │ mucosal invariant T cell │ CL:0000940 │ 81b69f84384c7d264599231a2e40a272 │ 10x 5' v1 │ EFO:0011025 │ 422220 │ Publication: https://doi.org/10.1038/s41586-021-04345-x Dataset Version: https://datasets.cellxgene.cziscience.com/d911082e-b5e2-40e6-8f08-fb53c7894622.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/03f821b4-87be-4ff4-b65a-b5fc00061da7 │ 03f821b4-87be-4ff4-b65a-b5fc00061da7 │ d911082e-b5e2-40e6-8f08-fb53c7894622 │ X_umap_wnn_derived │ 2-5 year-old child stage │ HsapDv:0000084 │ normal │ PATO:0000461 │ NP16 │ │ https://cellxgene.cziscience.com/e/2a498ace-872a-4935-984b-1afa70fd9886.cxg/ │ 33105 │ 4462693785.0 │ H5AD │ TRUE │ 1338.366685614135 │ Homo sapiens │ NCBITaxon:9606 │ 339597 │ 2022-03-24 │ raw.X │ 2024-06-11 │ NULL │ NP16___blood___2-5 year-old child stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ cell │ blood │ UBERON:0000178 │ tissue │ PBMC │ false │ https://datasets.cellxgene.cziscience.com/d911082e-b5e2-40e6-8f08-fb53c7894622.h5ad │ NULL │ NULL │ NULL │ 1277 │ blood │ cellxgene/21-08-2025 │ CD8+ Tem │ MAIT cells │ CD4 TEM │ 1047 │ 5.896910000125899 │ false │ S5_GAACCTAAGGGCATGT-1 │ cd8 tem_cd8 tem_mait_mait │ mait │ cd8 tem │ mait │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 5 │ 3 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 33f695cbacd6fe33cd4fb9b97f88f1f0___1.h5ad │ 4b121a55084eac4b9bf654fee90066a5___1.h5ad │ 19 │
├──────────────────────────────────────────────────────────────┴──────────────────────────────────────┴────────────────────┴──────────────────────────────────┴──────────────────────────────────────────────────────┴────────────────────────────┴──────────────────────────────────┴───────────┴────────────────────────┴────────────┴────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┴──────────────────────────────────────┴──────────────────────────────────────┴────────────────────┴─────────────────────────────┴────────────────────────────────────┴─────────┴──────────────────────────┴──────────┴───────────────┴──────────────────────────────────────────────────────────────────────────────┴───────────────┴──────────────┴──────────┴─────────────────┴─────────────────────┴──────────────┴───────────────────────────┴────────────────────┴──────────────┴───────────────────┴────────────┴──────────────────┴───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┴────────────────┴─────────────────────────┴──────────────────────────────────────────┴─────────┴──────────────────────┴─────────────────┴───────────────────────┴─────────────────────────┴─────────────┴───────────────────────────────────────────────────────┴───────────┴─────────────────────────────────────────────────────────────────────────────────────┴────────────────────────────┴─────────┴─────────┴──────────┴───────────────────────────────────┴──────────────────────┴───────────────────────────────────┴────────────────────────────────┴────────────────────────────┴──────────────────────────────┴────────────────────┴───────────────┴────────────────────────┴─────────────────────────────────────┴───────────────────┴──────────────────────┴────────────────────────────┴───────────┴──────────────────┴───────────────────────┴──────────────────────┴──────────────────────┴────────────────────┴───────────────┴─────────┴───────────────────┴────────────┴────────────┴────────────┴─────────────┴─────────────┴─────────────┴──────────────┴──────────────┴──────────────┴───────────────┴───────────────┴───────────────┴───────────────┴────────────────┴────────────────┴────────────────┴──────────────┴────────────┴─────────────────────────┴───────────────────────────────────────────┴───────────────────────────────────────────┴───────────────────┤
│ ? rows (>9999 rows, 20 shown) 94 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 │ .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 │ int32 │
├───────────────────────────────────────────────────────────────────────┼──────────────────────────────────────┼────────────────────┼──────────────────────────────────────────────────┼─────────────────────────────────┼────────────────────────────┼──────────────────────────────────┼───────────┼────────────────────────┼────────────┼────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┼──────────────────────────────────────┼──────────────────────────────────────┼───────────────────┼─────────────────────────┼────────────────────────────────────┼─────────┼──────────────────────────┼───────────────────────────────────────────────────────────────────────────────┼───────────────┼──────────────────────────────────────────────────────────────────────────────┼───────────────┼───────────────┼──────────┼─────────────────┼─────────────────────┼──────────────┼───────────────────────────┼────────────────────┼──────────────┼───────────────────┼────────────┼──────────────────┼──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┼────────────────┼─────────────────────────┼──────────────────────────────────────────┼─────────┼──────────────────────┼─────────────────┼─────────────────┼─────────────────────────┼─────────────┼─────────────────────────────────────────────────────────────────────────┼───────────┼─────────────────────────────────────────────────────────────────────────────────────┼────────────────────────────┼─────────┼─────────┼──────────┼────────────────────┼──────────────────────┼───────────────────────────────────┼────────────────────────────────┼────────────────────────────┼──────────────────────────────┼────────────────────┼───────────────┼────────────────────────────────┼──────────────────────────────────────────┼───────────────────┼──────────────────────┼────────────────────────────┼───────────┼──────────────────┼───────────────────────┼──────────────────────┼──────────────────────┼────────────────────┼───────────────┼─────────┼───────────────────┼────────────┼────────────┼────────────┼─────────────┼─────────────┼─────────────┼──────────────┼──────────────┼──────────────┼───────────────┼───────────────┼───────────────┼───────────────┼────────────────┼────────────────┼────────────────┼──────────────┼────────────┼─────────────────────────┼───────────────────────────────────────────┼───────────────────────────────────────────┼───────────────────┤
│ TGATTTCCAAGTCTAC_F02526___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 90oI-yXcRx │ 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 │ 847 │ 5050.436800000003 │ false │ TGATTTCCAAGTCTAC_F02526 │ progenitor_cd4 tem_cd8 tem_t cd4 │ t cd4 │ Unknown │ t cd4 │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 53 │ 73 │ 2 │ 3 │ 1 │ 1 │ 2 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 5 │ 2 │ e52795dec7b626b6276b867d55328d9f___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 336 │
│ AATCCAGGTCGCCATG_F02607___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ &FlQ;>*Jz8 │ 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 │ CD8+ Tcm │ Th1/Th17 cells │ CD4 TCM │ 545 │ 4411.847710000002 │ false │ AATCCAGGTCGCCATG_F02607 │ NA_cd8 tcm_cd4 th1/th17 em_t cd4 │ t cd4 │ Unknown │ 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 │ 14 │
│ TTGCGTCCATTTGCTT_SC24___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 0|3KB-UGFe │ 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 │ CD8+ T-cells │ T regulatory cells │ CD4 Naive │ 676 │ 3007.781379999998 │ false │ TTGCGTCCATTTGCTT_SC24 │ cd16 mono_t cd8_treg_t cd4 │ t cd4 │ t cd8 │ treg │ 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 │ 7 │ 2 │ 5d1ae361addc7eb8086448bd99ab7645___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 9 │
│ AGTACTGTCGACGAGA_SC84___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ SSDGes?+OK │ 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 │ CD8+ Tem │ MAIT cells │ CD4 TCM │ 1057 │ 4987.588660000004 │ false │ AGTACTGTCGACGAGA_SC84 │ cd14 mono_cd8 tem_mait_t cd4 │ t cd4 │ t │ t cd4 │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 30 │ 11 │ 13 │ 3 │ 2 │ 2 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 14 │ 2 │ 68aa23f4bbaaa7ff1068447055a7cec8___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 133 │
│ GACCAATAGGCACGAT_SC84___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ eONLJWTLLR │ 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 │ CD8+ Tem │ MAIT cells │ CD4 TCM │ 1389 │ 5914.264189999999 │ false │ GACCAATAGGCACGAT_SC84 │ cd14 mono_cd8 tem_mait_t cd4 │ t cd4 │ t │ t cd4 │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 21 │ 5 │ 10 │ 2 │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 14 │ 2 │ 68aa23f4bbaaa7ff1068447055a7cec8___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 133 │
│ TCGCGAGTCGCCAGCA_F02526___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ )I$YYi{b{o │ 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 │ T regulatory cells │ CD4 TCM │ 851 │ 5977.074549999996 │ false │ TCGCGAGTCGCCAGCA_F02526 │ progenitor_treg_treg_t cd4 │ t cd4 │ treg │ treg │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 24 │ 6 │ 2 │ 2 │ 2 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 5 │ 2 │ d4ba9668518d10ebe1c6cba1d585a094___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 58 │
│ TCTATACTCCCAGGAC_SC84___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ NrC|=8#pLD │ 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 │ Th1/Th17 cells │ CD4 TCM │ 1798 │ 5344.79440000001 │ false │ TCTATACTCCCAGGAC_SC84 │ cd14 mono_treg_cd4 th1/th17 em_t cd4 │ t cd4 │ t cd4 │ t cd4 │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 15 │ 3 │ 3 │ 1 │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 14 │ 2 │ 68aa23f4bbaaa7ff1068447055a7cec8___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 133 │
│ TCTTTCCAGATCCGAG_F02526___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ dFYC#hWA4x │ 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 │ 811 │ 5698.885979999994 │ false │ TCTTTCCAGATCCGAG_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 │ 52 │ 7 │ 16 │ 5 │ 3 │ 2 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 5 │ 2 │ 05caaf5f714b928ffe4f831211f30cf9___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 186 │
│ TCAGATGCATTGTGCA_F02526___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ $6y$c<f_c6 │ 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 │ Th1/Th17 cells │ CD4 TCM │ 852 │ 5477.241500000003 │ false │ TCAGATGCATTGTGCA_F02526 │ progenitor_cd8 tem_cd4 th1/th17 em_t cd4 │ t cd4 │ progenitor │ cd4 th1/th17 em │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 7 │ 38 │ 14 │ 2 │ 4 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 5 │ 2 │ 05caaf5f714b928ffe4f831211f30cf9___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 186 │
│ CCCTCAAGTGCCCACA_SC84___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ d;2T>uVCvn │ 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 │ CD8+ Tem │ Th1 cells │ CD4 TCM │ 971 │ 5412.887929999998 │ false │ CCCTCAAGTGCCCACA_SC84 │ cd14 mono_cd8 tem_cd4 th1 em_t cd4 │ t cd4 │ Unknown │ cd4 th1 em │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 3 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 14 │ 2 │ f4a5aa07713be579a14fa5e545d4f609___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 7 │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ TATCAGGAGCGGATCA_F00409___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ q#wGT@9n7j │ 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 │ CD8+ Tcm │ Central memory CD8 T cells │ CD8 TCM │ 985 │ 6692.504020000012 │ false │ TATCAGGAGCGGATCA_F00409 │ cd4 tcm_cd8 tcm_cd8 tcm_t cd4 │ t cd4 │ cd8 tcm │ cd4 tcm │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 8 │ 33 │ 11 │ 1 │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 19655d55c556c100dab6e30aeb54211f___1.h5ad │ a4942dd92de40cc23c6161df7e02ccc7___1.h5ad │ 175 │
│ CAAGAAAAGTTAGCGG_SC24___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ Cn7|IP&N)g │ 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+ Tcm │ Th2 cells │ CD4 TCM │ 909 │ 4180.536620000002 │ false │ CAAGAAAAGTTAGCGG_SC24 │ cd16 mono_cd4 tcm_cd4 th2 em_t cd4 │ t cd4 │ t cd4 │ t cd4 │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 8 │ 4 │ 2 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 7 │ 2 │ 8e1c12bf9a1d3ad7e805ac1a66fff5da___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 43 │
│ LAP93_ATCCATTAGCTAGTTC-1_duong___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ %*zmF_MzJA │ 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 │ Th1/Th17 cells │ CD4 TCM │ 1703 │ 7302.236790000001 │ false │ LAP93_ATCCATTAGCTAGTTC-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 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 12 │ 2 │ cc23d56c6845c89e89155ca508b28911___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 7 │
│ GCAAACTCAGACAAAT_F00409___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ b`7l~=D*^8 │ 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 │ CD8+ Tem │ Effector memory CD8 T cells │ CD8 TCM │ 1105 │ 6854.095270000003 │ false │ GCAAACTCAGACAAAT_F00409 │ cd4 tcm_cd8 tem_cd8 tem_t cd4 │ t cd4 │ cd8 tem │ cd4 tcm │ true │ 0 │ 0 │ 0 │ 0 │ false │ false │ true │ singlet │ 53 │ 22 │ 5 │ 4 │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 19655d55c556c100dab6e30aeb54211f___1.h5ad │ a4942dd92de40cc23c6161df7e02ccc7___1.h5ad │ 175 │
│ GTTCATTTCCACTGGG_F00409___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ zWua-8g03( │ 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 │ 1076 │ 7233.438800000024 │ false │ GTTCATTTCCACTGGG_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 │ 4 │ 7 │ 4 │ 3 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 3cef5b6aa0f5772485bb710f71e69456___1.h5ad │ a4942dd92de40cc23c6161df7e02ccc7___1.h5ad │ 47 │
│ AGTGTCAAGTACGACG_F02526___9f222629-9e39-47d0-b83f-e08d610c7479 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ u@Dh%PbRD~ │ 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 TEM │ 782 │ 5367.526519999999 │ false │ AGTGTCAAGTACGACG_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 │ 17 │ 34 │ 14 │ 2 │ 4 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 5 │ 2 │ 05caaf5f714b928ffe4f831211f30cf9___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 186 │
│ 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 │ 52 │
│ 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 │ 3 │
│ 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 │ 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 │ 336 │
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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', '.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
Query pseudobulk
cellNexusPy metadata allows to work with pseudobulk data:
get_anndata(query, aggregation = "pseudobulk")
View of AnnData object with n_obs × n_vars = 98 × 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', '.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 = 914 × 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 = 1780 × 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', '.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:
from matplotlib.pyplot import rc_context
import scanpy as sc
with rc_context({"figure.figsize": (4.5, 3)}):
sc.pl.violin(adata, ["ENSG00000085265"], groupby="sex")
Furthermore, it is possible to use matplotlib to generate customized plots:
import matplotlib.pyplot as plt
gene = "ENSG00000085265"
group = "sex"
# Compute mean expression per condition
mean_expr = adata.to_df()[gene].groupby(adata.obs[group]).mean()
# Plot
plt.figure(figsize=(6,4))
plt.bar(mean_expr.index, mean_expr.values, color=['red','blue'])
plt.ylabel(f"Mean expression of {gene}")
plt.title(f"{gene} expression per {group}")
plt.show()
/tmp/ipykernel_1965400/1821015775.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()
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