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_single_cell_experiment, get_pseudobulk, SAMPLE_DATABASE_URL
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(parquet_url = SAMPLE_DATABASE_URL)
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 │ age_days │ tissue_groups │ nFeature_expressed_in_sample │ nCount_RNA │ empty_droplet │ cell_type_unified_ensemble │ is_immune │ subsets_Mito_percent │ subsets_Ribo_percent │ high_mitochondrion │ high_ribosome │ 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 │ alive │ atlas_id │ cell_annotation_blueprint_singler │ cell_annotation_monaco_singler │ cell_annotation_azimuth_l2 │ ethnicity_flagging_score │ low_confidence_ethnicity │ .aggregated_cells │ imputed_ethnicity │
│ double │ 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 │ int32 │ varchar │ int32 │ double │ boolean │ varchar │ boolean │ int32 │ int32 │ boolean │ boolean │ varchar │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ varchar │ varchar │ boolean │ varchar │ varchar │ varchar │ varchar │ double │ varchar │ int32 │ varchar │
├─────────┼──────────────────────────────────────┼────────────────────┼──────────────────────────────────────────────────────┼─────────────────────────────────┼────────────────────────────┼──────────────────────────────────┼────────────────────────────────┼────────────────────────┼────────────┼────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┼──────────────────────────────────────┼──────────────────────────────────────┼───────────────────┼──────────────────────────────────────────┼────────────────────────────────────┼───────────────────────────┼──────────────────────────┼───────────────────────────────────────────────────────────────────────────────────┼───────────────┼──────────────────────────────────────────────────────────────────────────────┼───────────────┼───────────────┼──────────┼─────────────────┼─────────────────────┼──────────────┼───────────────────────────┼────────────────────┼──────────────┼───────────────────┼────────────┼──────────────────┼───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┼────────────────┼─────────────────────────┼──────────────────────────────────────────┼─────────┼──────────────────────┼─────────────────┼─────────┼─────────────────────────┼─────────────┼─────────────────────────────────────────────────────────────────────────────────────────┼───────────┼─────────────────────────────────────────────────────────────────────────────────────┼────────────────────────────┼──────────┼────────────────────┼──────────────────────────────┼────────────────────┼───────────────┼────────────────────────────┼───────────┼──────────────────────┼──────────────────────┼────────────────────┼───────────────┼───────────────────┼────────────┼────────────┼────────────┼─────────────┼─────────────┼─────────────┼──────────────┼──────────────┼──────────────┼───────────────┼───────────────┼───────────────┼───────────────┼────────────────┼────────────────┼────────────────┼──────────────┼────────────┼─────────────────────────┼───────────────────────────────────────────┼───────────────────────────────────────────┼─────────┼──────────────────────┼───────────────────────────────────┼────────────────────────────────┼────────────────────────────┼──────────────────────────┼──────────────────────────┼───────────────────┼───────────────────┤
│ 81.0 │ cda2c8cd-be1c-42e5-b2cd-162caa1c4ce7 │ *NUPW@J{c2 │ 034f0fb1b1dfabfd15d0a19431cd1f59 │ monocyte │ CL:0000576 │ 034f0fb1b1dfabfd15d0a19431cd1f59 │ 10x 5' v1 │ EFO:0011025 │ 255901 │ Publication: https://doi.org/10.1126/science.aay3224 Dataset Version: https://datasets.cellxgene.cziscience.com/c6e08ab6-ab3b-41dc-8058-8e6442e081ec.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/de13e3e2-23b6-40ed-a413-e9e12d7d3910 │ de13e3e2-23b6-40ed-a413-e9e12d7d3910 │ c6e08ab6-ab3b-41dc-8058-8e6442e081ec │ NULL │ 13th week post-fertilization human stage │ HsapDv:0000050 │ normal │ PATO:0000461 │ F38 │ │ https://cellxgene.cziscience.com/e/cda2c8cd-be1c-42e5-b2cd-162caa1c4ce7.cxg/ │ 32839 │ 2633195386.0 │ H5AD │ TRUE │ 2145.70318599771 │ Homo sapiens │ NCBITaxon:9606 │ 255901 │ 2022-07-26 │ raw.X │ 2024-06-11 │ NULL │ F38_TH_45P_5GEX___F38___thymus___13th week post-fertilization human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ unknown │ unknown │ male │ PATO:0000384 │ cell │ thymus │ UBERON:0002370 │ tissue │ Figure 1 - A cell atlas of human thymic development defines T cell repertoire formation │ false │ https://datasets.cellxgene.cziscience.com/c6e08ab6-ab3b-41dc-8058-8e6442e081ec.h5ad │ NULL │ 91 │ thymus │ 2853 │ 64343.977450000086 │ false │ cd14 mono │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 03319e4f54220f534de2c4e42e607126___1.h5ad │ f0946b9064dead3a6b2228fb70af8de1___1.h5ad │ true │ cellxgene/01-07-2024 │ Monocytes │ Classical monocytes │ CD4 TCM │ NULL │ NULL │ 9 │ unknown │
│ 82.0 │ cda2c8cd-be1c-42e5-b2cd-162caa1c4ce7 │ KIV>qGFIS? │ 034f0fb1b1dfabfd15d0a19431cd1f59 │ monocyte │ CL:0000576 │ 034f0fb1b1dfabfd15d0a19431cd1f59 │ 10x 5' v1 │ EFO:0011025 │ 255901 │ Publication: https://doi.org/10.1126/science.aay3224 Dataset Version: https://datasets.cellxgene.cziscience.com/c6e08ab6-ab3b-41dc-8058-8e6442e081ec.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/de13e3e2-23b6-40ed-a413-e9e12d7d3910 │ de13e3e2-23b6-40ed-a413-e9e12d7d3910 │ c6e08ab6-ab3b-41dc-8058-8e6442e081ec │ NULL │ 13th week post-fertilization human stage │ HsapDv:0000050 │ normal │ PATO:0000461 │ F38 │ │ https://cellxgene.cziscience.com/e/cda2c8cd-be1c-42e5-b2cd-162caa1c4ce7.cxg/ │ 32839 │ 2633195386.0 │ H5AD │ TRUE │ 2145.70318599771 │ Homo sapiens │ NCBITaxon:9606 │ 255901 │ 2022-07-26 │ raw.X │ 2024-06-11 │ NULL │ F38_TH_45P_5GEX___F38___thymus___13th week post-fertilization human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ unknown │ unknown │ male │ PATO:0000384 │ cell │ thymus │ UBERON:0002370 │ tissue │ Figure 1 - A cell atlas of human thymic development defines T cell repertoire formation │ false │ https://datasets.cellxgene.cziscience.com/c6e08ab6-ab3b-41dc-8058-8e6442e081ec.h5ad │ NULL │ 91 │ thymus │ 2374 │ 81901.13326999985 │ false │ cd14 mono │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 03319e4f54220f534de2c4e42e607126___1.h5ad │ f0946b9064dead3a6b2228fb70af8de1___1.h5ad │ true │ cellxgene/01-07-2024 │ Monocytes │ Classical monocytes │ CD4 TCM │ NULL │ NULL │ 9 │ unknown │
│ 83.0 │ cda2c8cd-be1c-42e5-b2cd-162caa1c4ce7 │ p5e=WoIq0d │ 034f0fb1b1dfabfd15d0a19431cd1f59 │ monocyte │ CL:0000576 │ 034f0fb1b1dfabfd15d0a19431cd1f59 │ 10x 5' v1 │ EFO:0011025 │ 255901 │ Publication: https://doi.org/10.1126/science.aay3224 Dataset Version: https://datasets.cellxgene.cziscience.com/c6e08ab6-ab3b-41dc-8058-8e6442e081ec.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/de13e3e2-23b6-40ed-a413-e9e12d7d3910 │ de13e3e2-23b6-40ed-a413-e9e12d7d3910 │ c6e08ab6-ab3b-41dc-8058-8e6442e081ec │ NULL │ 13th week post-fertilization human stage │ HsapDv:0000050 │ normal │ PATO:0000461 │ F38 │ │ https://cellxgene.cziscience.com/e/cda2c8cd-be1c-42e5-b2cd-162caa1c4ce7.cxg/ │ 32839 │ 2633195386.0 │ H5AD │ TRUE │ 2145.70318599771 │ Homo sapiens │ NCBITaxon:9606 │ 255901 │ 2022-07-26 │ raw.X │ 2024-06-11 │ NULL │ F38_TH_45P_5GEX___F38___thymus___13th week post-fertilization human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ unknown │ unknown │ male │ PATO:0000384 │ cell │ thymus │ UBERON:0002370 │ tissue │ Figure 1 - A cell atlas of human thymic development defines T cell repertoire formation │ false │ https://datasets.cellxgene.cziscience.com/c6e08ab6-ab3b-41dc-8058-8e6442e081ec.h5ad │ NULL │ 91 │ thymus │ 2064 │ 87096.28738000002 │ false │ cd14 mono │ true │ 0 │ 0 │ false │ false │ singlet │ 3 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 03319e4f54220f534de2c4e42e607126___1.h5ad │ f0946b9064dead3a6b2228fb70af8de1___1.h5ad │ true │ cellxgene/01-07-2024 │ Monocytes │ Classical monocytes │ CD4 TCM │ NULL │ NULL │ 9 │ unknown │
│ 84.0 │ cda2c8cd-be1c-42e5-b2cd-162caa1c4ce7 │ I6>u{Gb-J_ │ 034f0fb1b1dfabfd15d0a19431cd1f59 │ monocyte │ CL:0000576 │ 034f0fb1b1dfabfd15d0a19431cd1f59 │ 10x 5' v1 │ EFO:0011025 │ 255901 │ Publication: https://doi.org/10.1126/science.aay3224 Dataset Version: https://datasets.cellxgene.cziscience.com/c6e08ab6-ab3b-41dc-8058-8e6442e081ec.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/de13e3e2-23b6-40ed-a413-e9e12d7d3910 │ de13e3e2-23b6-40ed-a413-e9e12d7d3910 │ c6e08ab6-ab3b-41dc-8058-8e6442e081ec │ NULL │ 13th week post-fertilization human stage │ HsapDv:0000050 │ normal │ PATO:0000461 │ F38 │ │ https://cellxgene.cziscience.com/e/cda2c8cd-be1c-42e5-b2cd-162caa1c4ce7.cxg/ │ 32839 │ 2633195386.0 │ H5AD │ TRUE │ 2145.70318599771 │ Homo sapiens │ NCBITaxon:9606 │ 255901 │ 2022-07-26 │ raw.X │ 2024-06-11 │ NULL │ F38_TH_45P_5GEX___F38___thymus___13th week post-fertilization human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ unknown │ unknown │ male │ PATO:0000384 │ cell │ thymus │ UBERON:0002370 │ tissue │ Figure 1 - A cell atlas of human thymic development defines T cell repertoire formation │ false │ https://datasets.cellxgene.cziscience.com/c6e08ab6-ab3b-41dc-8058-8e6442e081ec.h5ad │ NULL │ 91 │ thymus │ 2684 │ 74944.24382999937 │ false │ cd14 mono │ true │ 0 │ 0 │ false │ false │ singlet │ 2 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 03319e4f54220f534de2c4e42e607126___1.h5ad │ f0946b9064dead3a6b2228fb70af8de1___1.h5ad │ true │ cellxgene/01-07-2024 │ Monocytes │ Classical monocytes │ CD4 TCM │ NULL │ NULL │ 9 │ unknown │
│ 85.0 │ cda2c8cd-be1c-42e5-b2cd-162caa1c4ce7 │ lx`7Bo-&7n │ 034f0fb1b1dfabfd15d0a19431cd1f59 │ monocyte │ CL:0000576 │ 034f0fb1b1dfabfd15d0a19431cd1f59 │ 10x 5' v1 │ EFO:0011025 │ 255901 │ Publication: https://doi.org/10.1126/science.aay3224 Dataset Version: https://datasets.cellxgene.cziscience.com/c6e08ab6-ab3b-41dc-8058-8e6442e081ec.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/de13e3e2-23b6-40ed-a413-e9e12d7d3910 │ de13e3e2-23b6-40ed-a413-e9e12d7d3910 │ c6e08ab6-ab3b-41dc-8058-8e6442e081ec │ NULL │ 13th week post-fertilization human stage │ HsapDv:0000050 │ normal │ PATO:0000461 │ F38 │ │ https://cellxgene.cziscience.com/e/cda2c8cd-be1c-42e5-b2cd-162caa1c4ce7.cxg/ │ 32839 │ 2633195386.0 │ H5AD │ TRUE │ 2145.70318599771 │ Homo sapiens │ NCBITaxon:9606 │ 255901 │ 2022-07-26 │ raw.X │ 2024-06-11 │ NULL │ F38_TH_45P_5GEX___F38___thymus___13th week post-fertilization human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ unknown │ unknown │ male │ PATO:0000384 │ cell │ thymus │ UBERON:0002370 │ tissue │ Figure 1 - A cell atlas of human thymic development defines T cell repertoire formation │ false │ https://datasets.cellxgene.cziscience.com/c6e08ab6-ab3b-41dc-8058-8e6442e081ec.h5ad │ NULL │ 91 │ thymus │ 1361 │ 77091.73000000005 │ false │ cd14 mono │ true │ 0 │ 0 │ false │ false │ singlet │ 4 │ 2 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 03319e4f54220f534de2c4e42e607126___1.h5ad │ f0946b9064dead3a6b2228fb70af8de1___1.h5ad │ true │ cellxgene/01-07-2024 │ Monocytes │ Classical monocytes │ CD4 TCM │ NULL │ NULL │ 9 │ unknown │
│ 86.0 │ cda2c8cd-be1c-42e5-b2cd-162caa1c4ce7 │ 6mRCZW}rOM │ 034f0fb1b1dfabfd15d0a19431cd1f59 │ monocyte │ CL:0000576 │ 034f0fb1b1dfabfd15d0a19431cd1f59 │ 10x 5' v1 │ EFO:0011025 │ 255901 │ Publication: https://doi.org/10.1126/science.aay3224 Dataset Version: https://datasets.cellxgene.cziscience.com/c6e08ab6-ab3b-41dc-8058-8e6442e081ec.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/de13e3e2-23b6-40ed-a413-e9e12d7d3910 │ de13e3e2-23b6-40ed-a413-e9e12d7d3910 │ c6e08ab6-ab3b-41dc-8058-8e6442e081ec │ NULL │ 13th week post-fertilization human stage │ HsapDv:0000050 │ normal │ PATO:0000461 │ F38 │ │ https://cellxgene.cziscience.com/e/cda2c8cd-be1c-42e5-b2cd-162caa1c4ce7.cxg/ │ 32839 │ 2633195386.0 │ H5AD │ TRUE │ 2145.70318599771 │ Homo sapiens │ NCBITaxon:9606 │ 255901 │ 2022-07-26 │ raw.X │ 2024-06-11 │ NULL │ F38_TH_45P_5GEX___F38___thymus___13th week post-fertilization human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ unknown │ unknown │ male │ PATO:0000384 │ cell │ thymus │ UBERON:0002370 │ tissue │ Figure 1 - A cell atlas of human thymic development defines T cell repertoire formation │ false │ https://datasets.cellxgene.cziscience.com/c6e08ab6-ab3b-41dc-8058-8e6442e081ec.h5ad │ NULL │ 91 │ thymus │ 2123 │ 80974.27661999944 │ false │ cd14 mono │ true │ 0 │ 0 │ false │ false │ singlet │ 2 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 03319e4f54220f534de2c4e42e607126___1.h5ad │ f0946b9064dead3a6b2228fb70af8de1___1.h5ad │ true │ cellxgene/01-07-2024 │ Monocytes │ Classical monocytes │ CD4 TCM │ NULL │ NULL │ 9 │ unknown │
│ 87.0 │ cda2c8cd-be1c-42e5-b2cd-162caa1c4ce7 │ -NL-OH3!IA │ 034f0fb1b1dfabfd15d0a19431cd1f59 │ monocyte │ CL:0000576 │ 034f0fb1b1dfabfd15d0a19431cd1f59 │ 10x 5' v1 │ EFO:0011025 │ 255901 │ Publication: https://doi.org/10.1126/science.aay3224 Dataset Version: https://datasets.cellxgene.cziscience.com/c6e08ab6-ab3b-41dc-8058-8e6442e081ec.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/de13e3e2-23b6-40ed-a413-e9e12d7d3910 │ de13e3e2-23b6-40ed-a413-e9e12d7d3910 │ c6e08ab6-ab3b-41dc-8058-8e6442e081ec │ NULL │ 13th week post-fertilization human stage │ HsapDv:0000050 │ normal │ PATO:0000461 │ F38 │ │ https://cellxgene.cziscience.com/e/cda2c8cd-be1c-42e5-b2cd-162caa1c4ce7.cxg/ │ 32839 │ 2633195386.0 │ H5AD │ TRUE │ 2145.70318599771 │ Homo sapiens │ NCBITaxon:9606 │ 255901 │ 2022-07-26 │ raw.X │ 2024-06-11 │ NULL │ F38_TH_45P_5GEX___F38___thymus___13th week post-fertilization human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ unknown │ unknown │ male │ PATO:0000384 │ cell │ thymus │ UBERON:0002370 │ tissue │ Figure 1 - A cell atlas of human thymic development defines T cell repertoire formation │ false │ https://datasets.cellxgene.cziscience.com/c6e08ab6-ab3b-41dc-8058-8e6442e081ec.h5ad │ NULL │ 91 │ thymus │ 2033 │ 82355.15189000044 │ false │ cd14 mono │ true │ 0 │ 0 │ false │ false │ singlet │ 2 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 03319e4f54220f534de2c4e42e607126___1.h5ad │ f0946b9064dead3a6b2228fb70af8de1___1.h5ad │ true │ cellxgene/01-07-2024 │ Monocytes │ Classical monocytes │ CD4 TCM │ NULL │ NULL │ 9 │ unknown │
│ 88.0 │ cda2c8cd-be1c-42e5-b2cd-162caa1c4ce7 │ zHCZWNmUHu │ 034f0fb1b1dfabfd15d0a19431cd1f59 │ monocyte │ CL:0000576 │ 034f0fb1b1dfabfd15d0a19431cd1f59 │ 10x 5' v1 │ EFO:0011025 │ 255901 │ Publication: https://doi.org/10.1126/science.aay3224 Dataset Version: https://datasets.cellxgene.cziscience.com/c6e08ab6-ab3b-41dc-8058-8e6442e081ec.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/de13e3e2-23b6-40ed-a413-e9e12d7d3910 │ de13e3e2-23b6-40ed-a413-e9e12d7d3910 │ c6e08ab6-ab3b-41dc-8058-8e6442e081ec │ NULL │ 13th week post-fertilization human stage │ HsapDv:0000050 │ normal │ PATO:0000461 │ F38 │ │ https://cellxgene.cziscience.com/e/cda2c8cd-be1c-42e5-b2cd-162caa1c4ce7.cxg/ │ 32839 │ 2633195386.0 │ H5AD │ TRUE │ 2145.70318599771 │ Homo sapiens │ NCBITaxon:9606 │ 255901 │ 2022-07-26 │ raw.X │ 2024-06-11 │ NULL │ F38_TH_45P_5GEX___F38___thymus___13th week post-fertilization human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ unknown │ unknown │ male │ PATO:0000384 │ cell │ thymus │ UBERON:0002370 │ tissue │ Figure 1 - A cell atlas of human thymic development defines T cell repertoire formation │ false │ https://datasets.cellxgene.cziscience.com/c6e08ab6-ab3b-41dc-8058-8e6442e081ec.h5ad │ NULL │ 91 │ thymus │ 3705 │ 79029.37513999944 │ false │ cd14 mono │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 03319e4f54220f534de2c4e42e607126___1.h5ad │ f0946b9064dead3a6b2228fb70af8de1___1.h5ad │ true │ cellxgene/01-07-2024 │ Monocytes │ Classical monocytes │ CD4 TCM │ NULL │ NULL │ 9 │ unknown │
│ 89.0 │ cda2c8cd-be1c-42e5-b2cd-162caa1c4ce7 │ *_#lQ<oUnT │ 034f0fb1b1dfabfd15d0a19431cd1f59 │ monocyte │ CL:0000576 │ 034f0fb1b1dfabfd15d0a19431cd1f59 │ 10x 5' v1 │ EFO:0011025 │ 255901 │ Publication: https://doi.org/10.1126/science.aay3224 Dataset Version: https://datasets.cellxgene.cziscience.com/c6e08ab6-ab3b-41dc-8058-8e6442e081ec.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/de13e3e2-23b6-40ed-a413-e9e12d7d3910 │ de13e3e2-23b6-40ed-a413-e9e12d7d3910 │ c6e08ab6-ab3b-41dc-8058-8e6442e081ec │ NULL │ 13th week post-fertilization human stage │ HsapDv:0000050 │ normal │ PATO:0000461 │ F38 │ │ https://cellxgene.cziscience.com/e/cda2c8cd-be1c-42e5-b2cd-162caa1c4ce7.cxg/ │ 32839 │ 2633195386.0 │ H5AD │ TRUE │ 2145.70318599771 │ Homo sapiens │ NCBITaxon:9606 │ 255901 │ 2022-07-26 │ raw.X │ 2024-06-11 │ NULL │ F38_TH_45P_5GEX___F38___thymus___13th week post-fertilization human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ unknown │ unknown │ male │ PATO:0000384 │ cell │ thymus │ UBERON:0002370 │ tissue │ Figure 1 - A cell atlas of human thymic development defines T cell repertoire formation │ false │ https://datasets.cellxgene.cziscience.com/c6e08ab6-ab3b-41dc-8058-8e6442e081ec.h5ad │ NULL │ 91 │ thymus │ 2965 │ 78896.33439999982 │ false │ cd14 mono │ true │ 0 │ 0 │ false │ false │ singlet │ 2 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 03319e4f54220f534de2c4e42e607126___1.h5ad │ f0946b9064dead3a6b2228fb70af8de1___1.h5ad │ true │ cellxgene/01-07-2024 │ Monocytes │ Classical monocytes │ CD4 TCM │ NULL │ NULL │ 9 │ unknown │
│ 99.0 │ cda2c8cd-be1c-42e5-b2cd-162caa1c4ce7 │ IdHwp1GBZm │ 03ddfd577963ac4c5d33903f8bd3ef0e │ monocyte │ CL:0000576 │ 03ddfd577963ac4c5d33903f8bd3ef0e │ 10x 3' v2 │ EFO:0009899 │ 255901 │ Publication: https://doi.org/10.1126/science.aay3224 Dataset Version: https://datasets.cellxgene.cziscience.com/c6e08ab6-ab3b-41dc-8058-8e6442e081ec.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/de13e3e2-23b6-40ed-a413-e9e12d7d3910 │ de13e3e2-23b6-40ed-a413-e9e12d7d3910 │ c6e08ab6-ab3b-41dc-8058-8e6442e081ec │ NULL │ 12th week post-fertilization human stage │ HsapDv:0000049 │ normal │ PATO:0000461 │ F45 │ │ https://cellxgene.cziscience.com/e/cda2c8cd-be1c-42e5-b2cd-162caa1c4ce7.cxg/ │ 32839 │ 2633195386.0 │ H5AD │ TRUE │ 2145.70318599771 │ Homo sapiens │ NCBITaxon:9606 │ 255901 │ 2022-07-26 │ raw.X │ 2024-06-11 │ NULL │ F45_TH_45P___F45___thymus___12th week post-fertilization human stage___10x 3' v2______normal___TRUE │ 5.1.0 │ unknown │ unknown │ female │ PATO:0000383 │ cell │ thymus │ UBERON:0002370 │ tissue │ Figure 1 - A cell atlas of human thymic development defines T cell repertoire formation │ false │ https://datasets.cellxgene.cziscience.com/c6e08ab6-ab3b-41dc-8058-8e6442e081ec.h5ad │ NULL │ 84 │ thymus │ 1354 │ 62693.02996999965 │ false │ cd14 mono │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 03319e4f54220f534de2c4e42e607126___1.h5ad │ f0946b9064dead3a6b2228fb70af8de1___1.h5ad │ true │ cellxgene/01-07-2024 │ Monocytes │ Classical monocytes │ CD8 Naive │ NULL │ NULL │ 3 │ unknown │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ 206.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ tUlYc_F#LM │ 1a28ccedf9f2fdb340f63e18512c231f___BT1299_lambrechts │ CD4-positive, alpha-beta T cell │ CL:0000624 │ 1a28ccedf9f2fdb340f63e18512c231f │ 10x 3' transcription profiling │ EFO:0030003 │ 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 │ unknown │ unknown │ lung large cell carcinoma │ MONDO:0003050 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747lambrechts_5 │ │ 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_483747lambrechts_5___lung___unknown___10x 3' transcription profiling______lung large cell carcinoma___TRUE │ 5.1.0 │ unknown │ unknown │ unknown │ unknown │ NULL │ lung │ UBERON:0002048 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ respiratory system │ 320 │ 5181.85273 │ false │ cd4 tcm │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 2 │ 2 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 9 │ 2 │ 1af9e4710374605bb904949487c6108e___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ Tcm │ Vd2 gd T cells │ CD14 Mono │ NULL │ NULL │ 13 │ unknown │
│ 205.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ i0`KDD?<w8 │ 1a28ccedf9f2fdb340f63e18512c231f___BT1299_lambrechts │ CD4-positive, alpha-beta T cell │ CL:0000624 │ 1a28ccedf9f2fdb340f63e18512c231f │ 10x 3' transcription profiling │ EFO:0030003 │ 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 │ unknown │ unknown │ lung large cell carcinoma │ MONDO:0003050 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747lambrechts_5 │ │ 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_483747lambrechts_5___lung___unknown___10x 3' transcription profiling______lung large cell carcinoma___TRUE │ 5.1.0 │ unknown │ unknown │ unknown │ unknown │ NULL │ lung │ UBERON:0002048 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ respiratory system │ 475 │ 5344.387310000004 │ false │ cd4 tcm │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 2 │ 2 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 9 │ 2 │ 1af9e4710374605bb904949487c6108e___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ Tcm │ Natural killer cells │ CD14 Mono │ NULL │ NULL │ 13 │ unknown │
│ 210.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ Wq5^6LL`D{ │ 1a28ccedf9f2fdb340f63e18512c231f___BT1299_lambrechts │ CD4-positive, alpha-beta T cell │ CL:0000624 │ 1a28ccedf9f2fdb340f63e18512c231f │ 10x 3' transcription profiling │ EFO:0030003 │ 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 │ unknown │ unknown │ lung large cell carcinoma │ MONDO:0003050 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747lambrechts_5 │ │ 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_483747lambrechts_5___lung___unknown___10x 3' transcription profiling______lung large cell carcinoma___TRUE │ 5.1.0 │ unknown │ unknown │ unknown │ unknown │ NULL │ lung │ UBERON:0002048 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ respiratory system │ 388 │ 4059.6996 │ false │ cd4 tcm │ true │ 0 │ 0 │ false │ false │ singlet │ 2 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 9 │ 2 │ 1af9e4710374605bb904949487c6108e___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ Tcm │ Non-Vd2 gd T cells │ CD14 Mono │ NULL │ NULL │ 13 │ unknown │
│ 207.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ !Fywp4GA&o │ 1a28ccedf9f2fdb340f63e18512c231f___BT1299_lambrechts │ CD4-positive, alpha-beta T cell │ CL:0000624 │ 1a28ccedf9f2fdb340f63e18512c231f │ 10x 3' transcription profiling │ EFO:0030003 │ 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 │ unknown │ unknown │ lung large cell carcinoma │ MONDO:0003050 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747lambrechts_5 │ │ 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_483747lambrechts_5___lung___unknown___10x 3' transcription profiling______lung large cell carcinoma___TRUE │ 5.1.0 │ unknown │ unknown │ unknown │ unknown │ NULL │ lung │ UBERON:0002048 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ respiratory system │ 571 │ 5077.593970000004 │ false │ cd4 tcm │ true │ 0 │ 0 │ false │ false │ singlet │ 5 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 9 │ 2 │ 1af9e4710374605bb904949487c6108e___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ Tcm │ MAIT cells │ CD14 Mono │ NULL │ NULL │ 13 │ unknown │
│ 208.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ _UGCk+)yuF │ 1a28ccedf9f2fdb340f63e18512c231f___BT1299_lambrechts │ CD4-positive, alpha-beta T cell │ CL:0000624 │ 1a28ccedf9f2fdb340f63e18512c231f │ 10x 3' transcription profiling │ EFO:0030003 │ 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 │ unknown │ unknown │ lung large cell carcinoma │ MONDO:0003050 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747lambrechts_5 │ │ 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_483747lambrechts_5___lung___unknown___10x 3' transcription profiling______lung large cell carcinoma___TRUE │ 5.1.0 │ unknown │ unknown │ unknown │ unknown │ NULL │ lung │ UBERON:0002048 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ respiratory system │ 209 │ 4928.649439999999 │ false │ cd4 tcm │ true │ 0 │ 0 │ false │ false │ singlet │ 3 │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 9 │ 2 │ 1af9e4710374605bb904949487c6108e___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ Tcm │ Non-switched memory B cells │ CD14 Mono │ NULL │ NULL │ 13 │ unknown │
│ 215.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ GV13#H_%9C │ 301da3fe7726a2b6bd7b6ac75cd1098e │ CD4-positive, alpha-beta T cell │ CL:0000624 │ 301da3fe7726a2b6bd7b6ac75cd1098e │ Seq-Well │ EFO:0008919 │ 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_483747LuT_553 │ │ 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_483747LuT_553___lung___55-year-old human stage___Seq-Well______normal___TRUE │ 5.1.0 │ unknown │ unknown │ male │ PATO:0000384 │ NULL │ lung │ UBERON:0002048 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ 20075 │ respiratory system │ 265 │ 5787.7740799999965 │ false │ cd4 tcm │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 9 │ 2 │ 1af9e4710374605bb904949487c6108e___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ Tcm │ MAIT cells │ cDC2 │ NULL │ NULL │ 1 │ European │
│ 219.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ y;G=XI-tkT │ 356a5cda613b1b4b10d9ce7350d5d247 │ CD4-positive, alpha-beta T cell │ CL:0000624 │ 356a5cda613b1b4b10d9ce7350d5d247 │ 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 │ unknown │ unknown │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747SAMN15153958 │ │ 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_483747SAMN15153958___lung___unknown___10x 3' v3______normal___TRUE │ 5.1.0 │ unknown │ unknown │ unknown │ unknown │ NULL │ lung │ UBERON:0002048 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ respiratory system │ 1132 │ 3405.1476400000015 │ false │ cd4 tcm │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 9 │ 2 │ 1af9e4710374605bb904949487c6108e___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ Tcm │ MAIT cells │ CD16 Mono │ NULL │ NULL │ 2 │ unknown │
│ 3.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ >KT|OFc=35 │ 356a5cda613b1b4b10d9ce7350d5d247 │ CD4-positive, alpha-beta T cell │ CL:0000624 │ 356a5cda613b1b4b10d9ce7350d5d247 │ 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 │ unknown │ unknown │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747SAMN15153958 │ │ 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_483747SAMN15153958___lung___unknown___10x 3' v3______normal___TRUE │ 5.1.0 │ unknown │ unknown │ unknown │ unknown │ NULL │ lung │ UBERON:0002048 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ respiratory system │ 864 │ 4556.799749999999 │ false │ cd4 tcm │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 9 │ 2 │ 1af9e4710374605bb904949487c6108e___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ Tcm │ MAIT cells │ CD16 Mono │ NULL │ NULL │ 2 │ unknown │
│ 216.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ fwSFnQYiqr │ dcc8bb25c068048c13168de10ce4fed0 │ CD4-positive, alpha-beta T cell │ CL:0000624 │ dcc8bb25c068048c13168de10ce4fed0 │ 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 │ unknown │ unknown │ interstitial lung disease │ MONDO:0015925 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747SSc-ILD_01 │ │ 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_483747SSc-ILD_01___lung___unknown___10x 3' v2______interstitial lung disease___TRUE │ 5.1.0 │ unknown │ unknown │ unknown │ unknown │ NULL │ lung │ UBERON:0002048 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ respiratory system │ 702 │ 4304.67398 │ false │ cd4 tcm │ true │ 0 │ 0 │ false │ false │ singlet │ 2 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 9 │ 2 │ 1af9e4710374605bb904949487c6108e___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ Tcm │ MAIT cells │ CD14 Mono │ NULL │ NULL │ 3 │ unknown │
│ 218.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ x=vgeTx#*D │ dcc8bb25c068048c13168de10ce4fed0 │ CD4-positive, alpha-beta T cell │ CL:0000624 │ dcc8bb25c068048c13168de10ce4fed0 │ 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 │ unknown │ unknown │ interstitial lung disease │ MONDO:0015925 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747SSc-ILD_01 │ │ 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_483747SSc-ILD_01___lung___unknown___10x 3' v2______interstitial lung disease___TRUE │ 5.1.0 │ unknown │ unknown │ unknown │ unknown │ NULL │ lung │ UBERON:0002048 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ NULL │ respiratory system │ 581 │ 3489.4483700000014 │ false │ cd4 tcm │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 9 │ 2 │ 1af9e4710374605bb904949487c6108e___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ Tcm │ MAIT cells │ CD14 Mono │ NULL │ NULL │ 3 │ unknown │
└─────────┴──────────────────────────────────────┴────────────────────┴──────────────────────────────────────────────────────┴─────────────────────────────────┴────────────────────────────┴──────────────────────────────────┴────────────────────────────────┴────────────────────────┴────────────┴────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┴──────────────────────────────────────┴──────────────────────────────────────┴───────────────────┴──────────────────────────────────────────┴────────────────────────────────────┴───────────────────────────┴──────────────────────────┴───────────────────────────────────────────────────────────────────────────────────┴───────────────┴──────────────────────────────────────────────────────────────────────────────┴───────────────┴───────────────┴──────────┴─────────────────┴─────────────────────┴──────────────┴───────────────────────────┴────────────────────┴──────────────┴───────────────────┴────────────┴──────────────────┴───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┴────────────────┴─────────────────────────┴──────────────────────────────────────────┴─────────┴──────────────────────┴─────────────────┴─────────┴─────────────────────────┴─────────────┴─────────────────────────────────────────────────────────────────────────────────────────┴───────────┴─────────────────────────────────────────────────────────────────────────────────────┴────────────────────────────┴──────────┴────────────────────┴──────────────────────────────┴────────────────────┴───────────────┴────────────────────────────┴───────────┴──────────────────────┴──────────────────────┴────────────────────┴───────────────┴───────────────────┴────────────┴────────────┴────────────┴─────────────┴─────────────┴─────────────┴──────────────┴──────────────┴──────────────┴───────────────┴───────────────┴───────────────┴───────────────┴────────────────┴────────────────┴────────────────┴──────────────┴────────────┴─────────────────────────┴───────────────────────────────────────────┴───────────────────────────────────────────┴─────────┴──────────────────────┴───────────────────────────────────┴────────────────────────────────┴────────────────────────────┴──────────────────────────┴──────────────────────────┴───────────────────┴───────────────────┘
? rows (>9999 rows, 20 shown) 89 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 │
├────────────────────────────────┼────────────────────────────┼───────┤
│ lung │ cd4 fh em │ 416 │
│ kidney │ nk │ 185 │
│ body of stomach │ nk │ 47 │
│ large intestine │ cd14 mono │ 16 │
│ renal medulla │ cd14 mono │ 45 │
│ submucosal esophageal gland │ cd14 mono │ 3 │
│ nose │ t │ 1 │
│ right colon │ cd14 mono │ 60 │
│ lung │ cd4 tcm │ 992 │
│ sigmoid colon │ cd14 mono │ 31 │
│ · │ · │ · │
│ · │ · │ · │
│ · │ · │ · │
│ lung │ cd4 th1/th17 em │ 1852 │
│ body of stomach │ cd14 mono │ 119 │
│ dorsolateral prefrontal cortex │ cd14 mono │ 2 │
│ skin of cheek │ cd14 mono │ 7 │
│ submucosal esophageal gland │ nk │ 6 │
│ left temporal lobe │ nk │ 5 │
│ parietal lobe │ nk │ 1 │
│ respiratory airway │ epithelial │ 415 │
│ temporoparietal junction │ nk │ 1 │
│ lung parenchyma │ t cd4 │ 679 │
└────────────────────────────────┴────────────────────────────┴───────┘
143 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 │ age_days │ tissue_groups │ nFeature_expressed_in_sample │ nCount_RNA │ empty_droplet │ cell_type_unified_ensemble │ is_immune │ subsets_Mito_percent │ subsets_Ribo_percent │ high_mitochondrion │ high_ribosome │ 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 │ alive │ atlas_id │ cell_annotation_blueprint_singler │ cell_annotation_monaco_singler │ cell_annotation_azimuth_l2 │ ethnicity_flagging_score │ low_confidence_ethnicity │ .aggregated_cells │ imputed_ethnicity │
│ double │ 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 │ int32 │ varchar │ int32 │ double │ boolean │ varchar │ boolean │ int32 │ int32 │ boolean │ boolean │ varchar │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ varchar │ varchar │ boolean │ varchar │ varchar │ varchar │ varchar │ double │ varchar │ int32 │ varchar │
├─────────┼──────────────────────────────────────┼────────────────────┼──────────────────────────────────────────────────┼─────────────────────────────────┼────────────────────────────┼──────────────────────────────────┼───────────┼────────────────────────┼────────────┼────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┼──────────────────────────────────────┼──────────────────────────────────────┼───────────────────┼─────────────────────────┼────────────────────────────────────┼─────────┼──────────────────────────┼───────────────────────────────────────────────────────────────────────────────┼───────────────┼──────────────────────────────────────────────────────────────────────────────┼───────────────┼───────────────┼──────────┼─────────────────┼─────────────────────┼──────────────┼───────────────────────────┼────────────────────┼──────────────┼───────────────────┼────────────┼──────────────────┼──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┼────────────────┼─────────────────────────┼──────────────────────────────────────────┼─────────┼──────────────────────┼─────────────────┼────────────────────┼─────────────────────────┼─────────────┼─────────────────────────────────────────────────────────────────────────┼───────────┼─────────────────────────────────────────────────────────────────────────────────────┼────────────────────────────┼──────────┼────────────────────┼──────────────────────────────┼────────────────────┼───────────────┼────────────────────────────┼───────────┼──────────────────────┼──────────────────────┼────────────────────┼───────────────┼───────────────────┼────────────┼────────────┼────────────┼─────────────┼─────────────┼─────────────┼──────────────┼──────────────┼──────────────┼───────────────┼───────────────┼───────────────┼───────────────┼────────────────┼────────────────┼────────────────┼──────────────┼────────────┼─────────────────────────┼───────────────────────────────────────────┼───────────────────────────────────────────┼─────────┼──────────────────────┼───────────────────────────────────┼────────────────────────────────┼────────────────────────────┼──────────────────────────┼──────────────────────────┼───────────────────┼───────────────────┤
│ 71.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ lyppDZKU;5 │ 9c8fa5a8d2ae37179b579a0217670512___LAP92_1_duong │ CD4-positive, alpha-beta T cell │ CL:0000624 │ 9c8fa5a8d2ae37179b579a0217670512 │ 10x 3' v3 │ EFO:0009922 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239___lung parenchyma___37-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ 13505 │ respiratory system │ 1447 │ 7592.489229999996 │ false │ cd4 th2 em │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 11 │ 2 │ 08c5020f2fdc8fb97897827e8258ba97___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ T-cells │ Th2 cells │ HSPC │ 1.0 │ FALSE │ 4 │ African │
│ 70.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ )i-{f4(#c3 │ 9c8fa5a8d2ae37179b579a0217670512___LAP92_1_duong │ CD4-positive, alpha-beta T cell │ CL:0000624 │ 9c8fa5a8d2ae37179b579a0217670512 │ 10x 3' v3 │ EFO:0009922 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239___lung parenchyma___37-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ 13505 │ respiratory system │ 1295 │ 7536.390920000011 │ false │ cd4 th2 em │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 11 │ 2 │ 08c5020f2fdc8fb97897827e8258ba97___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ T-cells │ Th2 cells │ HSPC │ 1.0 │ FALSE │ 4 │ African │
│ 69.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ WMYiKuYI2T │ 9c8fa5a8d2ae37179b579a0217670512___LAP92_1_duong │ CD4-positive, alpha-beta T cell │ CL:0000624 │ 9c8fa5a8d2ae37179b579a0217670512 │ 10x 3' v3 │ EFO:0009922 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239___lung parenchyma___37-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ 13505 │ respiratory system │ 1292 │ 7401.793599999996 │ false │ cd4 th2 em │ true │ 0 │ 0 │ false │ false │ singlet │ 2 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 11 │ 2 │ 08c5020f2fdc8fb97897827e8258ba97___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ T-cells │ Th2 cells │ HSPC │ 1.0 │ FALSE │ 4 │ African │
│ 68.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ C@Lbno3>(F │ 9c8fa5a8d2ae37179b579a0217670512___LAP92_1_duong │ CD4-positive, alpha-beta T cell │ CL:0000624 │ 9c8fa5a8d2ae37179b579a0217670512 │ 10x 3' v3 │ EFO:0009922 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239___lung parenchyma___37-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ 13505 │ respiratory system │ 1681 │ 7363.542430000009 │ false │ cd4 th2 em │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 11 │ 2 │ 08c5020f2fdc8fb97897827e8258ba97___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ T-cells │ Th2 cells │ HSPC │ 1.0 │ FALSE │ 4 │ African │
│ 65.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9XEB6y1sct │ b3d27bbec53d4fa905dddf174f974842___LAP40_duong │ CD4-positive, alpha-beta T cell │ CL:0000624 │ b3d27bbec53d4fa905dddf174f974842 │ 10x 3' v3 │ EFO:0009922 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239___respiratory airway___37-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ respiratory airway │ UBERON:0001005 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ 13505 │ respiratory system │ 1582 │ 7456.821029999988 │ false │ cd4 th2 em │ true │ 0 │ 0 │ false │ false │ singlet │ 2 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 11 │ 2 │ 08c5020f2fdc8fb97897827e8258ba97___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ T-cells │ Th2 cells │ NK │ 1.0 │ FALSE │ 3 │ African │
│ 66.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ I?*wqob@mY │ b3d27bbec53d4fa905dddf174f974842___LAP40_duong │ CD4-positive, alpha-beta T cell │ CL:0000624 │ b3d27bbec53d4fa905dddf174f974842 │ 10x 3' v3 │ EFO:0009922 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239___respiratory airway___37-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ respiratory airway │ UBERON:0001005 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ 13505 │ respiratory system │ 1275 │ 7554.083540000002 │ false │ cd4 th2 em │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 11 │ 2 │ 08c5020f2fdc8fb97897827e8258ba97___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ T-cells │ Th2 cells │ NK │ 1.0 │ FALSE │ 3 │ African │
│ 67.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ >$0D4u5I-^ │ b3d27bbec53d4fa905dddf174f974842___LAP40_duong │ CD4-positive, alpha-beta T cell │ CL:0000624 │ b3d27bbec53d4fa905dddf174f974842 │ 10x 3' v3 │ EFO:0009922 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239___respiratory airway___37-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ respiratory airway │ UBERON:0001005 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ 13505 │ respiratory system │ 1359 │ 7509.474099999986 │ false │ cd4 th2 em │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 11 │ 2 │ 08c5020f2fdc8fb97897827e8258ba97___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ T-cells │ Th2 cells │ NK │ 1.0 │ FALSE │ 3 │ African │
│ 63.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ iFA<ESpL;5 │ 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 │ 10585 │ respiratory system │ 744 │ 4801.754430000002 │ false │ cd4 th2 em │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 11 │ 2 │ 08c5020f2fdc8fb97897827e8258ba97___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CLP │ Th2 cells │ Platelet │ 0.0 │ TRUE │ 1 │ European │
│ 27.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ O#X!v37H)7 │ a2459ad4272363e6eb775e8e99607c3e │ CD4-positive, alpha-beta T cell │ CL:0000624 │ a2459ad4272363e6eb775e8e99607c3e │ 10x 5' v1 │ EFO:0011025 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 53-year-old human stage │ HsapDv:0000147 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD85 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD85___lung parenchyma___53-year-old human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ 19345 │ respiratory system │ 484 │ 5006.575919999997 │ false │ cd4 th1 em │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 0a68d60a27c6fbdb297102abcb16a0d0___1.h5ad │ a4942dd92de40cc23c6161df7e02ccc7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ Tem │ Th1 cells │ Platelet │ 1.0 │ FALSE │ 3 │ African │
│ 76.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ t2otTQDn7G │ a2459ad4272363e6eb775e8e99607c3e │ CD4-positive, alpha-beta T cell │ CL:0000624 │ a2459ad4272363e6eb775e8e99607c3e │ 10x 5' v1 │ EFO:0011025 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 53-year-old human stage │ HsapDv:0000147 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD85 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD85___lung parenchyma___53-year-old human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ 19345 │ respiratory system │ 1117 │ 4958.486779999996 │ false │ cd4 th1 em │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 0a68d60a27c6fbdb297102abcb16a0d0___1.h5ad │ a4942dd92de40cc23c6161df7e02ccc7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ T-cells │ Th1 cells │ Platelet │ 1.0 │ FALSE │ 3 │ African │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ 323.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ N((-F5PKgZ │ 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 │ 8030 │ respiratory system │ 861 │ 4261.94886 │ false │ cd4 th1/th17 em │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 7 │ 2 │ fa2f8f101864a1cd13d53a7c2f8de8a2___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ Tem │ Th1/Th17 cells │ CD16 Mono │ 0.5 │ TRUE │ 7 │ South Asian │
│ 349.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ EfxV<G8_^7 │ 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 │ 8030 │ respiratory system │ 855 │ 3581.263549999998 │ false │ cd4 th1/th17 em │ true │ 0 │ 0 │ false │ false │ singlet │ 2 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 7 │ 2 │ fa2f8f101864a1cd13d53a7c2f8de8a2___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ Tem │ Th1/Th17 cells │ CD16 Mono │ 0.5 │ TRUE │ 7 │ South Asian │
│ 319.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ {b_Pkz8;(X │ 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 │ 8030 │ respiratory system │ 811 │ 4101.3349499999995 │ false │ cd4 th1/th17 em │ true │ 0 │ 0 │ false │ false │ singlet │ 4 │ 2 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 7 │ 2 │ fa2f8f101864a1cd13d53a7c2f8de8a2___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ Tem │ Th1/Th17 cells │ CD16 Mono │ 0.5 │ TRUE │ 7 │ South Asian │
│ 162.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ !!o2-M%o|s │ 9c8fa5a8d2ae37179b579a0217670512___LAP87_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 │ 13505 │ respiratory system │ 1509 │ 7379.126129999996 │ false │ cd4 th2 em │ true │ 0 │ 0 │ false │ false │ singlet │ 2 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 6 │ 2 │ fdf7ee00e9cfc1c8be52d0a5576a039b___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ T-cells │ Th2 cells │ CD14 Mono │ 1.0 │ FALSE │ 5 │ African │
│ 164.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ jVn#NanpI< │ 9c8fa5a8d2ae37179b579a0217670512___LAP87_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 │ 13505 │ respiratory system │ 1706 │ 7423.541559999985 │ false │ cd4 th2 em │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 6 │ 2 │ fdf7ee00e9cfc1c8be52d0a5576a039b___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ T-cells │ Th2 cells │ CD14 Mono │ 1.0 │ FALSE │ 5 │ African │
│ 163.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ meM?=LSl** │ 9c8fa5a8d2ae37179b579a0217670512___LAP87_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 │ 13505 │ respiratory system │ 1677 │ 7274.495030000003 │ false │ cd4 th2 em │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 6 │ 2 │ fdf7ee00e9cfc1c8be52d0a5576a039b___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ T-cells │ Th2 cells │ CD14 Mono │ 1.0 │ FALSE │ 5 │ African │
│ 165.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 7pLV-+i*6t │ 9c8fa5a8d2ae37179b579a0217670512___LAP87_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 │ 13505 │ respiratory system │ 1513 │ 7422.314680000018 │ false │ cd4 th2 em │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 6 │ 2 │ fdf7ee00e9cfc1c8be52d0a5576a039b___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ T-cells │ Th2 cells │ CD14 Mono │ 1.0 │ FALSE │ 5 │ African │
│ 166.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ Q9*E~=<w;{ │ 9c8fa5a8d2ae37179b579a0217670512___LAP87_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 │ 13505 │ respiratory system │ 1468 │ 7281.6563299999925 │ false │ cd4 th2 em │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 6 │ 2 │ fdf7ee00e9cfc1c8be52d0a5576a039b___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ T-cells │ Th2 cells │ CD14 Mono │ 1.0 │ FALSE │ 5 │ African │
│ 167.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ gb-VQ4DV{n │ b3d27bbec53d4fa905dddf174f974842___LAP88_1_duong │ CD4-positive, alpha-beta T cell │ CL:0000624 │ b3d27bbec53d4fa905dddf174f974842 │ 10x 3' v3 │ EFO:0009922 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239___respiratory airway___37-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ respiratory airway │ UBERON:0001005 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ 13505 │ respiratory system │ 1474 │ 7300.172359999997 │ false │ cd4 th2 em │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 6 │ 2 │ fdf7ee00e9cfc1c8be52d0a5576a039b___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ T-cells │ Th2 cells │ HSPC │ 1.0 │ FALSE │ 2 │ African │
│ 168.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ B4V=(%GA}V │ b3d27bbec53d4fa905dddf174f974842___LAP88_1_duong │ CD4-positive, alpha-beta T cell │ CL:0000624 │ b3d27bbec53d4fa905dddf174f974842 │ 10x 3' v3 │ EFO:0009922 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239___respiratory airway___37-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ respiratory airway │ UBERON:0001005 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ 13505 │ respiratory system │ 1316 │ 7461.791110000003 │ false │ cd4 th2 em │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 6 │ 2 │ fdf7ee00e9cfc1c8be52d0a5576a039b___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ T-cells │ Th2 cells │ HSPC │ 1.0 │ FALSE │ 2 │ African │
└─────────┴──────────────────────────────────────┴────────────────────┴──────────────────────────────────────────────────┴─────────────────────────────────┴────────────────────────────┴──────────────────────────────────┴───────────┴────────────────────────┴────────────┴────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┴──────────────────────────────────────┴──────────────────────────────────────┴───────────────────┴─────────────────────────┴────────────────────────────────────┴─────────┴──────────────────────────┴───────────────────────────────────────────────────────────────────────────────┴───────────────┴──────────────────────────────────────────────────────────────────────────────┴───────────────┴───────────────┴──────────┴─────────────────┴─────────────────────┴──────────────┴───────────────────────────┴────────────────────┴──────────────┴───────────────────┴────────────┴──────────────────┴──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┴────────────────┴─────────────────────────┴──────────────────────────────────────────┴─────────┴──────────────────────┴─────────────────┴────────────────────┴─────────────────────────┴─────────────┴─────────────────────────────────────────────────────────────────────────┴───────────┴─────────────────────────────────────────────────────────────────────────────────────┴────────────────────────────┴──────────┴────────────────────┴──────────────────────────────┴────────────────────┴───────────────┴────────────────────────────┴───────────┴──────────────────────┴──────────────────────┴────────────────────┴───────────────┴───────────────────┴────────────┴────────────┴────────────┴─────────────┴─────────────┴─────────────┴──────────────┴──────────────┴──────────────┴───────────────┴───────────────┴───────────────┴───────────────┴────────────────┴────────────────┴────────────────┴──────────────┴────────────┴─────────────────────────┴───────────────────────────────────────────┴───────────────────────────────────────────┴─────────┴──────────────────────┴───────────────────────────────────┴────────────────────────────────┴────────────────────────────┴──────────────────────────┴──────────────────────────┴───────────────────┴───────────────────┘
1207 rows (20 shown) 89 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
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│ 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 │ age_days │ tissue_groups │ nFeature_expressed_in_sample │ nCount_RNA │ empty_droplet │ cell_type_unified_ensemble │ is_immune │ subsets_Mito_percent │ subsets_Ribo_percent │ high_mitochondrion │ high_ribosome │ 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 │ alive │ atlas_id │ cell_annotation_blueprint_singler │ cell_annotation_monaco_singler │ cell_annotation_azimuth_l2 │ ethnicity_flagging_score │ low_confidence_ethnicity │ .aggregated_cells │ imputed_ethnicity │
│ double │ 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 │ int32 │ varchar │ int32 │ double │ boolean │ varchar │ boolean │ int32 │ int32 │ boolean │ boolean │ varchar │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ int32 │ varchar │ varchar │ boolean │ varchar │ varchar │ varchar │ varchar │ double │ varchar │ int32 │ varchar │
├─────────┼──────────────────────────────────────┼────────────────────┼──────────────────────────────────────────────────┼─────────────────────────────────┼────────────────────────────┼──────────────────────────────────┼───────────┼────────────────────────┼────────────┼────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┼──────────────────────────────────────┼──────────────────────────────────────┼───────────────────┼─────────────────────────┼────────────────────────────────────┼─────────┼──────────────────────────┼───────────────────────────────────────────────────────────────────────────────┼───────────────┼──────────────────────────────────────────────────────────────────────────────┼───────────────┼───────────────┼──────────┼─────────────────┼─────────────────────┼──────────────┼───────────────────────────┼────────────────────┼──────────────┼───────────────────┼────────────┼──────────────────┼──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┼────────────────┼─────────────────────────┼──────────────────────────────────────────┼─────────┼──────────────────────┼─────────────────┼─────────────────┼─────────────────────────┼─────────────┼─────────────────────────────────────────────────────────────────────────┼───────────┼─────────────────────────────────────────────────────────────────────────────────────┼────────────────────────────┼──────────┼────────────────────┼──────────────────────────────┼────────────────────┼───────────────┼────────────────────────────┼───────────┼──────────────────────┼──────────────────────┼────────────────────┼───────────────┼───────────────────┼────────────┼────────────┼────────────┼─────────────┼─────────────┼─────────────┼──────────────┼──────────────┼──────────────┼───────────────┼───────────────┼───────────────┼───────────────┼────────────────┼────────────────┼────────────────┼──────────────┼────────────┼─────────────────────────┼───────────────────────────────────────────┼───────────────────────────────────────────┼─────────┼──────────────────────┼───────────────────────────────────┼────────────────────────────────┼────────────────────────────┼──────────────────────────┼──────────────────────────┼───────────────────┼───────────────────┤
│ 71.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ lyppDZKU;5 │ 9c8fa5a8d2ae37179b579a0217670512___LAP92_1_duong │ CD4-positive, alpha-beta T cell │ CL:0000624 │ 9c8fa5a8d2ae37179b579a0217670512 │ 10x 3' v3 │ EFO:0009922 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239___lung parenchyma___37-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ 13505 │ respiratory system │ 1447 │ 7592.489229999996 │ false │ cd4 th2 em │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 11 │ 2 │ 08c5020f2fdc8fb97897827e8258ba97___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ T-cells │ Th2 cells │ HSPC │ 1.0 │ FALSE │ 4 │ African │
│ 70.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ )i-{f4(#c3 │ 9c8fa5a8d2ae37179b579a0217670512___LAP92_1_duong │ CD4-positive, alpha-beta T cell │ CL:0000624 │ 9c8fa5a8d2ae37179b579a0217670512 │ 10x 3' v3 │ EFO:0009922 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239___lung parenchyma___37-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ 13505 │ respiratory system │ 1295 │ 7536.390920000011 │ false │ cd4 th2 em │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 11 │ 2 │ 08c5020f2fdc8fb97897827e8258ba97___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ T-cells │ Th2 cells │ HSPC │ 1.0 │ FALSE │ 4 │ African │
│ 69.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ WMYiKuYI2T │ 9c8fa5a8d2ae37179b579a0217670512___LAP92_1_duong │ CD4-positive, alpha-beta T cell │ CL:0000624 │ 9c8fa5a8d2ae37179b579a0217670512 │ 10x 3' v3 │ EFO:0009922 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239___lung parenchyma___37-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ 13505 │ respiratory system │ 1292 │ 7401.793599999996 │ false │ cd4 th2 em │ true │ 0 │ 0 │ false │ false │ singlet │ 2 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 11 │ 2 │ 08c5020f2fdc8fb97897827e8258ba97___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ T-cells │ Th2 cells │ HSPC │ 1.0 │ FALSE │ 4 │ African │
│ 68.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ C@Lbno3>(F │ 9c8fa5a8d2ae37179b579a0217670512___LAP92_1_duong │ CD4-positive, alpha-beta T cell │ CL:0000624 │ 9c8fa5a8d2ae37179b579a0217670512 │ 10x 3' v3 │ EFO:0009922 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239___lung parenchyma___37-year-old human stage___10x 3' v3______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ 13505 │ respiratory system │ 1681 │ 7363.542430000009 │ false │ cd4 th2 em │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 11 │ 2 │ 08c5020f2fdc8fb97897827e8258ba97___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ T-cells │ Th2 cells │ HSPC │ 1.0 │ FALSE │ 4 │ African │
│ 63.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ iFA<ESpL;5 │ 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 │ 10585 │ respiratory system │ 744 │ 4801.754430000002 │ false │ cd4 th2 em │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 11 │ 2 │ 08c5020f2fdc8fb97897827e8258ba97___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CLP │ Th2 cells │ Platelet │ 0.0 │ TRUE │ 1 │ European │
│ 27.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ O#X!v37H)7 │ a2459ad4272363e6eb775e8e99607c3e │ CD4-positive, alpha-beta T cell │ CL:0000624 │ a2459ad4272363e6eb775e8e99607c3e │ 10x 5' v1 │ EFO:0011025 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 53-year-old human stage │ HsapDv:0000147 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD85 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD85___lung parenchyma___53-year-old human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ 19345 │ respiratory system │ 484 │ 5006.575919999997 │ false │ cd4 th1 em │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 0a68d60a27c6fbdb297102abcb16a0d0___1.h5ad │ a4942dd92de40cc23c6161df7e02ccc7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ Tem │ Th1 cells │ Platelet │ 1.0 │ FALSE │ 3 │ African │
│ 76.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ t2otTQDn7G │ a2459ad4272363e6eb775e8e99607c3e │ CD4-positive, alpha-beta T cell │ CL:0000624 │ a2459ad4272363e6eb775e8e99607c3e │ 10x 5' v1 │ EFO:0011025 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 53-year-old human stage │ HsapDv:0000147 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD85 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD85___lung parenchyma___53-year-old human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ 19345 │ respiratory system │ 1117 │ 4958.486779999996 │ false │ cd4 th1 em │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 0a68d60a27c6fbdb297102abcb16a0d0___1.h5ad │ a4942dd92de40cc23c6161df7e02ccc7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ T-cells │ Th1 cells │ Platelet │ 1.0 │ FALSE │ 3 │ African │
│ 74.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ p`w9}^BGKH │ a2459ad4272363e6eb775e8e99607c3e │ CD4-positive, alpha-beta T cell │ CL:0000624 │ a2459ad4272363e6eb775e8e99607c3e │ 10x 5' v1 │ EFO:0011025 │ 2282447 │ Publication: https://doi.org/10.1038/s41591-023-02327-2 Dataset Version: https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 │ 6f6d381a-7701-4781-935c-db10d30de293 │ 8d84ba15-d367-4dce-979c-85da70b868a2 │ X_umap │ 53-year-old human stage │ HsapDv:0000147 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD85 │ │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 56239 │ 21851725645.0 │ H5AD │ TRUE │ 1760.6743113859818 │ Homo sapiens │ NCBITaxon:9606 │ 1959503 │ 2023-05-08 │ raw.X │ 2024-06-11 │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747VUHD85___lung parenchyma___53-year-old human stage___10x 5' v1______normal___TRUE │ 5.1.0 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ NULL │ lung parenchyma │ UBERON:0008946 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │ NULL │ 19345 │ respiratory system │ 828 │ 4157.985309999996 │ false │ cd4 th1 em │ true │ 0 │ 0 │ false │ false │ singlet │ 2 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 0a68d60a27c6fbdb297102abcb16a0d0___1.h5ad │ a4942dd92de40cc23c6161df7e02ccc7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ Tem │ Th1 cells │ Platelet │ 1.0 │ FALSE │ 3 │ African │
│ 82.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ aysU)HNYee │ 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 │ 11315 │ respiratory system │ 951 │ 6964.003780000031 │ false │ cd4 th1 em │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 0a68d60a27c6fbdb297102abcb16a0d0___1.h5ad │ a4942dd92de40cc23c6161df7e02ccc7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ Tem │ Th1 cells │ CD4 TCM │ 1.0 │ FALSE │ 2 │ African │
│ 73.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ qLF+N=4vwo │ 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 │ 11315 │ respiratory system │ 1054 │ 5223.278269999988 │ false │ cd4 th1 em │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 1 │ 1 │ 0a68d60a27c6fbdb297102abcb16a0d0___1.h5ad │ a4942dd92de40cc23c6161df7e02ccc7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ Tem │ Th1 cells │ CD4 TCM │ 1.0 │ FALSE │ 2 │ African │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ 267.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ lm}<WwG1QO │ 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 │ 8030 │ respiratory system │ 1382 │ 4851.792489999989 │ false │ cd4 th1/th17 em │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 7 │ 2 │ fa2f8f101864a1cd13d53a7c2f8de8a2___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ Tem │ Th1/Th17 cells │ CD16 Mono │ 0.5 │ TRUE │ 7 │ South Asian │
│ 315.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ _MFp`y$*fg │ 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 │ 8030 │ respiratory system │ 912 │ 5017.615849999996 │ false │ cd4 th1/th17 em │ true │ 0 │ 0 │ false │ false │ singlet │ 3 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 7 │ 2 │ fa2f8f101864a1cd13d53a7c2f8de8a2___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ Tem │ Th1/Th17 cells │ CD16 Mono │ 0.5 │ TRUE │ 7 │ South Asian │
│ 323.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ N((-F5PKgZ │ 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 │ 8030 │ respiratory system │ 861 │ 4261.94886 │ false │ cd4 th1/th17 em │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 7 │ 2 │ fa2f8f101864a1cd13d53a7c2f8de8a2___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ Tem │ Th1/Th17 cells │ CD16 Mono │ 0.5 │ TRUE │ 7 │ South Asian │
│ 349.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ EfxV<G8_^7 │ 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 │ 8030 │ respiratory system │ 855 │ 3581.263549999998 │ false │ cd4 th1/th17 em │ true │ 0 │ 0 │ false │ false │ singlet │ 2 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 7 │ 2 │ fa2f8f101864a1cd13d53a7c2f8de8a2___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ Tem │ Th1/Th17 cells │ CD16 Mono │ 0.5 │ TRUE │ 7 │ South Asian │
│ 319.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ {b_Pkz8;(X │ 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 │ 8030 │ respiratory system │ 811 │ 4101.3349499999995 │ false │ cd4 th1/th17 em │ true │ 0 │ 0 │ false │ false │ singlet │ 4 │ 2 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 7 │ 2 │ fa2f8f101864a1cd13d53a7c2f8de8a2___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ Tem │ Th1/Th17 cells │ CD16 Mono │ 0.5 │ TRUE │ 7 │ South Asian │
│ 162.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ !!o2-M%o|s │ 9c8fa5a8d2ae37179b579a0217670512___LAP87_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 │ 13505 │ respiratory system │ 1509 │ 7379.126129999996 │ false │ cd4 th2 em │ true │ 0 │ 0 │ false │ false │ singlet │ 2 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 6 │ 2 │ fdf7ee00e9cfc1c8be52d0a5576a039b___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ T-cells │ Th2 cells │ CD14 Mono │ 1.0 │ FALSE │ 5 │ African │
│ 164.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ jVn#NanpI< │ 9c8fa5a8d2ae37179b579a0217670512___LAP87_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 │ 13505 │ respiratory system │ 1706 │ 7423.541559999985 │ false │ cd4 th2 em │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 6 │ 2 │ fdf7ee00e9cfc1c8be52d0a5576a039b___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ T-cells │ Th2 cells │ CD14 Mono │ 1.0 │ FALSE │ 5 │ African │
│ 163.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ meM?=LSl** │ 9c8fa5a8d2ae37179b579a0217670512___LAP87_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 │ 13505 │ respiratory system │ 1677 │ 7274.495030000003 │ false │ cd4 th2 em │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 6 │ 2 │ fdf7ee00e9cfc1c8be52d0a5576a039b___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ T-cells │ Th2 cells │ CD14 Mono │ 1.0 │ FALSE │ 5 │ African │
│ 165.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 7pLV-+i*6t │ 9c8fa5a8d2ae37179b579a0217670512___LAP87_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 │ 13505 │ respiratory system │ 1513 │ 7422.314680000018 │ false │ cd4 th2 em │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 6 │ 2 │ fdf7ee00e9cfc1c8be52d0a5576a039b___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ T-cells │ Th2 cells │ CD14 Mono │ 1.0 │ FALSE │ 5 │ African │
│ 166.0 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ Q9*E~=<w;{ │ 9c8fa5a8d2ae37179b579a0217670512___LAP87_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 │ 13505 │ respiratory system │ 1468 │ 7281.6563299999925 │ false │ cd4 th2 em │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ NULL │ 1 │ 6 │ 2 │ fdf7ee00e9cfc1c8be52d0a5576a039b___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ true │ cellxgene/01-07-2024 │ CD4+ T-cells │ Th2 cells │ CD14 Mono │ 1.0 │ FALSE │ 5 │ African │
└─────────┴──────────────────────────────────────┴────────────────────┴──────────────────────────────────────────────────┴─────────────────────────────────┴────────────────────────────┴──────────────────────────────────┴───────────┴────────────────────────┴────────────┴────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┴──────────────────────────────────────┴──────────────────────────────────────┴───────────────────┴─────────────────────────┴────────────────────────────────────┴─────────┴──────────────────────────┴───────────────────────────────────────────────────────────────────────────────┴───────────────┴──────────────────────────────────────────────────────────────────────────────┴───────────────┴───────────────┴──────────┴─────────────────┴─────────────────────┴──────────────┴───────────────────────────┴────────────────────┴──────────────┴───────────────────┴────────────┴──────────────────┴──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┴────────────────┴─────────────────────────┴──────────────────────────────────────────┴─────────┴──────────────────────┴─────────────────┴─────────────────┴─────────────────────────┴─────────────┴─────────────────────────────────────────────────────────────────────────┴───────────┴─────────────────────────────────────────────────────────────────────────────────────┴────────────────────────────┴──────────┴────────────────────┴──────────────────────────────┴────────────────────┴───────────────┴────────────────────────────┴───────────┴──────────────────────┴──────────────────────┴────────────────────┴───────────────┴───────────────────┴────────────┴────────────┴────────────┴─────────────┴─────────────┴─────────────┴──────────────┴──────────────┴──────────────┴───────────────┴───────────────┴───────────────┴───────────────┴────────────────┴────────────────┴────────────────┴──────────────┴────────────┴─────────────────────────┴───────────────────────────────────────────┴───────────────────────────────────────────┴─────────┴──────────────────────┴───────────────────────────────────┴────────────────────────────────┴────────────────────────────┴──────────────────────────┴──────────────────────────┴───────────────────┴───────────────────┘
1056 rows (20 shown) 89 columns
Query raw counts
Once you have filtered your query accordingly, you can pass it into get_anndata() to obtain an AnnData object:
adata = get_single_cell_experiment(query.limit(6), assays ="counts")
adata
View of AnnData object with n_obs × n_vars = 6 × 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', 'age_days', 'tissue_groups', 'nFeature_expressed_in_sample', 'nCount_RNA', 'empty_droplet', 'cell_type_unified_ensemble', 'is_immune', 'subsets_Mito_percent', 'subsets_Ribo_percent', 'high_mitochondrion', 'high_ribosome', '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', 'alive', 'atlas_id', 'cell_annotation_blueprint_singler', 'cell_annotation_monaco_singler', 'cell_annotation_azimuth_l2', 'ethnicity_flagging_score', 'low_confidence_ethnicity', '.aggregated_cells', 'imputed_ethnicity'
Query counts scaled per million
You can query counts scaled per million. This is helpful if just few genes are of interest:
adata = get_single_cell_experiment(query.limit(6), assays = 'cpm')
adata
View of AnnData object with n_obs × n_vars = 6 × 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', 'age_days', 'tissue_groups', 'nFeature_expressed_in_sample', 'nCount_RNA', 'empty_droplet', 'cell_type_unified_ensemble', 'is_immune', 'subsets_Mito_percent', 'subsets_Ribo_percent', 'high_mitochondrion', 'high_ribosome', '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', 'alive', 'atlas_id', 'cell_annotation_blueprint_singler', 'cell_annotation_monaco_singler', 'cell_annotation_azimuth_l2', 'ethnicity_flagging_score', 'low_confidence_ethnicity', '.aggregated_cells', 'imputed_ethnicity'
Query pseudobulk
cellNexusPy metadata allows to work with pseudobulk data:
get_pseudobulk(query.limit(6))
View of AnnData object with n_obs × n_vars = 3 × 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', 'age_days', 'tissue_groups', 'cell_type_unified_ensemble', 'sample_chunk', 'cell_chunk', 'sample_pseudobulk_chunk', 'file_id_cellNexus_pseudobulk', 'atlas_id', 'ethnicity_flagging_score', 'low_confidence_ethnicity', '.aggregated_cells', 'imputed_ethnicity'
Extract only a subset of genes
We can query a subset of genes. Notice how the result only has nvars = 1:
get_single_cell_experiment(query.limit(6), assays = "cpm", features = ['ENSG00000134644'])
View of AnnData object with n_obs × n_vars = 6 × 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', 'age_days', 'tissue_groups', 'nFeature_expressed_in_sample', 'nCount_RNA', 'empty_droplet', 'cell_type_unified_ensemble', 'is_immune', 'subsets_Mito_percent', 'subsets_Ribo_percent', 'high_mitochondrion', 'high_ribosome', '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', 'alive', 'atlas_id', 'cell_annotation_blueprint_singler', 'cell_annotation_monaco_singler', 'cell_annotation_azimuth_l2', 'ethnicity_flagging_score', 'low_confidence_ethnicity', '.aggregated_cells', 'imputed_ethnicity'
Visualizing gene expression
Taking advantage of the AnnData object, we can use scanpy library to visualize gene expression gfor a groups of interest:
query = table.filter("""
cell_type_unified_ensemble = 'cd14 mono'
""")
adata = get_single_cell_experiment(query, assays = 'cpm')
from matplotlib.pyplot import rc_context
import scanpy as sc
with rc_context({"figure.figsize": (15, 5)}):
sc.pl.violin(adata, ["ENSG00000085265"], groupby="disease",rotation=90)
Furthermore, it is possible to use matplotlib to generate customized plots:
import matplotlib.pyplot as plt
gene = "ENSG00000085265"
group = "tissue"
# Compute mean expression per condition
mean_expr = adata.to_df()[gene].groupby(adata.obs[group]).mean()
# Plot
colors = plt.cm.tab20.colors[:len(mean_expr)]
plt.figure(figsize=(15,5))
plt.bar(mean_expr.index, mean_expr.values,color=colors)
plt.ylabel(f"Mean expression of {gene}")
plt.xticks(rotation=90)
plt.title(f"{gene} expression per {group}")
plt.show()
/tmp/ipykernel_28358/4092819108.py:7: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
mean_expr = adata.to_df()[gene].groupby(adata.obs[group]).mean()
Saving as H5AD
It is possible to save AnnData objects using the function write_h5ad:
adata.obs.index.name = None
adata.obs["run_from_cell_id"] = adata.obs["run_from_cell_id"].fillna("NA").astype(str)
adata.write_h5ad("myH5ADfile.h5ad")
Finishing Up
When you are finished, you should close the connection:
conn.close()
Cell metadata
Dataset-specific columns (definitions available at cellxgene.cziscience.com)
cell_count, collection_id, filetype, is_primary_data, mean_genes_per_cell, published_at, revised_at, schema_version, tombstone, x_normalization, explorer_url, dataset_id, dataset_version_id
Sample-specific columns (definitions available at cellxgene.cziscience.com)
sample_id, sample_, age_days, assay, assay_ontology_term_id, development_stage, development_stage_ontology_term_id, self_reported_ethnicity, self_reported_ethnicity_ontology_term_id, experiment___, organism, organism_ontology_term_id, sample_placeholder, sex, sex_ontology_term_id, tissue, tissue_type, tissue_ontology_term_id, tissue_groups, disease, disease_ontology_term_id, is_primary_data, donor_id, is_immune
Cell-specific columns (definitions available at cellxgene.cziscience.com)
cell_id, cell_type, cell_type_ontology_term_id, cell_annotation_azimuth_l2, cell_annotation_blueprint_singler, observation_joinid, empty_droplet, alive, scDblFinder.class
Through harmonisation and curation we introduced custom column, not present in the original CELLxGENE metadata
age_days: donors' age in dayscell_type_unified_ensemble: the consensus call identity (for immune cells) using the original and three novel annotations using Seurat Azimuth and SingleRcell_annotation_azimuth_l2: Azimuth cell annotationcell_annotation_blueprint_singler: SingleR cell annotation using Blueprint referencecell_annotation_blueprint_monaco: SingleR cell annotation using Monaco referencesample_heuristic: sample subdivision for internal usefile_id_cellNexus_single_cell: file subdivision for internal usefile_id_cellNexus_pseudobulk: file subdivision for internal usesample_id: sample IDnCount_RNA: total number of RNA detected in a cell per samplenFeature_expressed_in_sample: total number of genes expressed in a cell per sample
RNA abundance
The counts assay includes RNA abundance in the positive real scale (not transformed with non-linear functions, e.g. log sqrt). Originally CELLxGENE include a mix of scales and transformations specified in the x_normalization column.
The cpm assay includes counts per million.
Other representations
The rank assay is the representation of each cell’s gene expression profile where genes are ranked by expression intensity.
The pseudobulk assay includes aggregated RNA abundance for sample and cell type combination.
The metacell (e.g metacell_2, metacell_4, etc) assays represent hierarchical partitions of cells into metacell groups.
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