cellNexusPy
June 9, 2026 · View on GitHub
Importing the package
from cellnexuspy import get_metadata, get_anndata, get_pseudobulk, join_census_table, keep_quality_cells, get_cell_communication_strength, get_metadata_url, SAMPLE_DATABASE_URL, CENSUS_SAMPLE_METADATA_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()
table = join_census_table(conn, table)
table
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┌─────────┬────────────────────┬──────────────────────────────────────┬──────────────────────────────────────────────┬──────────────────────────────────┬───────────────┬──────────────────┬─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┬──────────┬─────────────────────────────────────┬──────────────────────────────┬───────────────────┬───────────────┬────────────────────────────┬───────────┬──────────────────────┬──────────────────────┬────────────────────┬───────────────┬───────────────────┬──────────────┬────────────┬─────────────────────────┬───────────────────────────────────────────┬───────────────────────────────────────────┬───────────────────┬───────────────────────────┬─────────────────────────┬─────────┬───────────────────────────────────┬────────────────────────────────┬────────────────────────────┬──────────────────────────┬──────────────────────────┬───────────────────┬───────────────────┬──────────────────────┬────────────────────┬──────────────────────────────────────┬──────────────────────────────────────────────┬──────────────────────────────────────┬────────────────────────────┬───────────┬────────────────────────┬─────────────────────────┬────────────────────────────────────┬─────────┬──────────────────────────┬────────────┬─────────────────┬──────────────┬───────────────────────────┬─────────────────────────┬──────────────────────────────────────────┬─────────┬──────────────────────┬─────────────────────────┬─────────────────────────┬───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┬──────────────────────────────────────┬──────────────────────────────────────┬───────────────────┬──────────────┬───────────────────┬────────────┬────────────────────┬────────────────┬─────────────┬─────────────────────────────────────────────────────────────────────────────────┬───────────┬────────────────────────────┬──────────────────────────────────────────────────────────────────────────────┬────────────┬───────────────┬──────────────┬──────────┬─────────────────────┬─────────────────┬─────────────────────────────────────────────────────────────────────────────────────┐
│ cell_id │ observation_joinid │ dataset_id │ sample_id │ sample_ │ experiment___ │ run_from_cell_id │ sample_heuristic │ 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 │ sample_chunk │ cell_chunk │ sample_pseudobulk_chunk │ file_id_cellNexus_single_cell │ file_id_cellNexus_pseudobulk │ count_upper_bound │ nfeature_expressed_thresh │ inverse_transform │ alive │ cell_annotation_blueprint_singler │ cell_annotation_monaco_singler │ cell_annotation_azimuth_l2 │ ethnicity_flagging_score │ low_confidence_ethnicity │ .aggregated_cells │ imputed_ethnicity │ atlas_id │ observation_joinid │ dataset_id │ sample_id │ cell_type │ cell_type_ontology_term_id │ assay │ assay_ontology_term_id │ development_stage │ development_stage_ontology_term_id │ disease │ disease_ontology_term_id │ donor_id │ is_primary_data │ organism │ organism_ontology_term_id │ self_reported_ethnicity │ self_reported_ethnicity_ontology_term_id │ sex │ sex_ontology_term_id │ tissue │ tissue_ontology_term_id │ citation │ collection_id │ dataset_version_id │ default_embedding │ published_at │ raw_data_location │ revised_at │ primary_cell_count │ schema_version │ tissue_type │ title │ tombstone │ x_approximate_distribution │ explorer_url │ cell_count │ feature_count │ filesize │ filetype │ mean_genes_per_cell │ suspension_type │ url │
│ double │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ int32 │ varchar │ int32 │ double │ boolean │ varchar │ boolean │ int32 │ int32 │ boolean │ boolean │ varchar │ int32 │ int32 │ int32 │ varchar │ varchar │ double │ double │ varchar │ boolean │ varchar │ varchar │ varchar │ double │ varchar │ int32 │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ boolean │ varchar │ varchar │ int32 │ int32 │ double │ varchar │ double │ varchar │ varchar │
├─────────┼────────────────────┼──────────────────────────────────────┼──────────────────────────────────────────────┼──────────────────────────────────┼───────────────┼──────────────────┼─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┼──────────┼─────────────────────────────────────┼──────────────────────────────┼───────────────────┼───────────────┼────────────────────────────┼───────────┼──────────────────────┼──────────────────────┼────────────────────┼───────────────┼───────────────────┼──────────────┼────────────┼─────────────────────────┼───────────────────────────────────────────┼───────────────────────────────────────────┼───────────────────┼───────────────────────────┼─────────────────────────┼─────────┼───────────────────────────────────┼────────────────────────────────┼────────────────────────────┼──────────────────────────┼──────────────────────────┼───────────────────┼───────────────────┼──────────────────────┼────────────────────┼──────────────────────────────────────┼──────────────────────────────────────────────┼──────────────────────────────────────┼────────────────────────────┼───────────┼────────────────────────┼─────────────────────────┼────────────────────────────────────┼─────────┼──────────────────────────┼────────────┼─────────────────┼──────────────┼───────────────────────────┼─────────────────────────┼──────────────────────────────────────────┼─────────┼──────────────────────┼─────────────────────────┼─────────────────────────┼───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┼──────────────────────────────────────┼──────────────────────────────────────┼───────────────────┼──────────────┼───────────────────┼────────────┼────────────────────┼────────────────┼─────────────┼─────────────────────────────────────────────────────────────────────────────────┼───────────┼────────────────────────────┼──────────────────────────────────────────────────────────────────────────────┼────────────┼───────────────┼──────────────┼──────────┼─────────────────────┼─────────────────┼─────────────────────────────────────────────────────────────────────────────────────┤
│ 11934.0 │ tMa=76pr}S │ 4976b234-9028-4b4b-8a2f-8ac59d636219 │ 144da207531b7877c50d4aa306d967f3___10X237_1: │ 144da207531b7877c50d4aa306d967f3 │ │ NULL │ H19.30.001___cerebellum___42-year-old human stage___10x 3' v3______normal___TRUE │ 15330 │ brainstem and cerebellar structures │ 1701 │ 3003.0 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ 34b4a444f06d582c50b59e279e44b9a3___1.h5ad │ 83915546022d9c58bb1d23397d4e987c___1.h5ad │ 10.0 │ 200.0 │ identity_with_max_limit │ true │ Neurons │ Myeloid dendritic cells │ pDC │ NULL │ NULL │ 5093 │ European │ cellxgene_2024/0.4.0 │ tMa=76pr}S │ 4976b234-9028-4b4b-8a2f-8ac59d636219 │ 144da207531b7877c50d4aa306d967f3___10X237_1: │ neuron │ CL:0000540 │ 10x 3' v3 │ EFO:0009922 │ 42-year-old human stage │ HsapDv:0000136 │ normal │ PATO:0000461 │ H19.30.001 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ cerebellum │ UBERON:0002037 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/e9f575c0-bf54-4252-9551-1d4c69eda1bf.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/283d65eb-dd53-496d-adb7-7570c7caa443 │ 283d65eb-dd53-496d-adb7-7570c7caa443 │ e9f575c0-bf54-4252-9551-1d4c69eda1bf │ NULL │ 2022-12-08 │ X │ 2024-06-11 │ 71874 │ 5.1.0 │ tissue │ Dissection: Cerebellum (CB) - Cerebellar Vermis - CBV │ false │ NULL │ https://cellxgene.cziscience.com/e/4976b234-9028-4b4b-8a2f-8ac59d636219.cxg/ │ 71874 │ 59236 │ 438436612.0 │ H5AD │ 2560.6052536383113 │ nucleus │ https://datasets.cellxgene.cziscience.com/e9f575c0-bf54-4252-9551-1d4c69eda1bf.h5ad │
│ 11925.0 │ kNWk5U<kHP │ 4976b234-9028-4b4b-8a2f-8ac59d636219 │ 144da207531b7877c50d4aa306d967f3___10X237_1: │ 144da207531b7877c50d4aa306d967f3 │ │ NULL │ H19.30.001___cerebellum___42-year-old human stage___10x 3' v3______normal___TRUE │ 15330 │ brainstem and cerebellar structures │ 1518 │ 2913.0 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ 34b4a444f06d582c50b59e279e44b9a3___1.h5ad │ 83915546022d9c58bb1d23397d4e987c___1.h5ad │ 10.0 │ 200.0 │ identity_with_max_limit │ true │ Neurons │ Myeloid dendritic cells │ pDC │ NULL │ NULL │ 5093 │ European │ cellxgene_2024/0.4.0 │ kNWk5U<kHP │ 4976b234-9028-4b4b-8a2f-8ac59d636219 │ 144da207531b7877c50d4aa306d967f3___10X237_1: │ neuron │ CL:0000540 │ 10x 3' v3 │ EFO:0009922 │ 42-year-old human stage │ HsapDv:0000136 │ normal │ PATO:0000461 │ H19.30.001 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ cerebellum │ UBERON:0002037 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/e9f575c0-bf54-4252-9551-1d4c69eda1bf.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/283d65eb-dd53-496d-adb7-7570c7caa443 │ 283d65eb-dd53-496d-adb7-7570c7caa443 │ e9f575c0-bf54-4252-9551-1d4c69eda1bf │ NULL │ 2022-12-08 │ X │ 2024-06-11 │ 71874 │ 5.1.0 │ tissue │ Dissection: Cerebellum (CB) - Cerebellar Vermis - CBV │ false │ NULL │ https://cellxgene.cziscience.com/e/4976b234-9028-4b4b-8a2f-8ac59d636219.cxg/ │ 71874 │ 59236 │ 438436612.0 │ H5AD │ 2560.6052536383113 │ nucleus │ https://datasets.cellxgene.cziscience.com/e9f575c0-bf54-4252-9551-1d4c69eda1bf.h5ad │
│ 11993.0 │ 3gHkK@=&M6 │ 4976b234-9028-4b4b-8a2f-8ac59d636219 │ 144da207531b7877c50d4aa306d967f3___10X237_1: │ 144da207531b7877c50d4aa306d967f3 │ │ NULL │ H19.30.001___cerebellum___42-year-old human stage___10x 3' v3______normal___TRUE │ 15330 │ brainstem and cerebellar structures │ 1498 │ 2744.0 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ 34b4a444f06d582c50b59e279e44b9a3___1.h5ad │ 83915546022d9c58bb1d23397d4e987c___1.h5ad │ 10.0 │ 200.0 │ identity_with_max_limit │ true │ Neurons │ Myeloid dendritic cells │ pDC │ NULL │ NULL │ 5093 │ European │ cellxgene_2024/0.4.0 │ 3gHkK@=&M6 │ 4976b234-9028-4b4b-8a2f-8ac59d636219 │ 144da207531b7877c50d4aa306d967f3___10X237_1: │ neuron │ CL:0000540 │ 10x 3' v3 │ EFO:0009922 │ 42-year-old human stage │ HsapDv:0000136 │ normal │ PATO:0000461 │ H19.30.001 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ cerebellum │ UBERON:0002037 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/e9f575c0-bf54-4252-9551-1d4c69eda1bf.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/283d65eb-dd53-496d-adb7-7570c7caa443 │ 283d65eb-dd53-496d-adb7-7570c7caa443 │ e9f575c0-bf54-4252-9551-1d4c69eda1bf │ NULL │ 2022-12-08 │ X │ 2024-06-11 │ 71874 │ 5.1.0 │ tissue │ Dissection: Cerebellum (CB) - Cerebellar Vermis - CBV │ false │ NULL │ https://cellxgene.cziscience.com/e/4976b234-9028-4b4b-8a2f-8ac59d636219.cxg/ │ 71874 │ 59236 │ 438436612.0 │ H5AD │ 2560.6052536383113 │ nucleus │ https://datasets.cellxgene.cziscience.com/e9f575c0-bf54-4252-9551-1d4c69eda1bf.h5ad │
│ 14176.0 │ 6TUbfTwfb{ │ 4976b234-9028-4b4b-8a2f-8ac59d636219 │ 144da207531b7877c50d4aa306d967f3___10X237_1: │ 144da207531b7877c50d4aa306d967f3 │ │ NULL │ H19.30.001___cerebellum___42-year-old human stage___10x 3' v3______normal___TRUE │ 15330 │ brainstem and cerebellar structures │ 1654 │ 2887.0 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ 34b4a444f06d582c50b59e279e44b9a3___1.h5ad │ 83915546022d9c58bb1d23397d4e987c___1.h5ad │ 10.0 │ 200.0 │ identity_with_max_limit │ true │ Neurons │ Myeloid dendritic cells │ pDC │ NULL │ NULL │ 5093 │ European │ cellxgene_2024/0.4.0 │ 6TUbfTwfb{ │ 4976b234-9028-4b4b-8a2f-8ac59d636219 │ 144da207531b7877c50d4aa306d967f3___10X237_1: │ neuron │ CL:0000540 │ 10x 3' v3 │ EFO:0009922 │ 42-year-old human stage │ HsapDv:0000136 │ normal │ PATO:0000461 │ H19.30.001 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ cerebellum │ UBERON:0002037 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/e9f575c0-bf54-4252-9551-1d4c69eda1bf.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/283d65eb-dd53-496d-adb7-7570c7caa443 │ 283d65eb-dd53-496d-adb7-7570c7caa443 │ e9f575c0-bf54-4252-9551-1d4c69eda1bf │ NULL │ 2022-12-08 │ X │ 2024-06-11 │ 71874 │ 5.1.0 │ tissue │ Dissection: Cerebellum (CB) - Cerebellar Vermis - CBV │ false │ NULL │ https://cellxgene.cziscience.com/e/4976b234-9028-4b4b-8a2f-8ac59d636219.cxg/ │ 71874 │ 59236 │ 438436612.0 │ H5AD │ 2560.6052536383113 │ nucleus │ https://datasets.cellxgene.cziscience.com/e9f575c0-bf54-4252-9551-1d4c69eda1bf.h5ad │
│ 13874.0 │ S9RRZO<P-$ │ 4976b234-9028-4b4b-8a2f-8ac59d636219 │ 144da207531b7877c50d4aa306d967f3___10X237_1: │ 144da207531b7877c50d4aa306d967f3 │ │ NULL │ H19.30.001___cerebellum___42-year-old human stage___10x 3' v3______normal___TRUE │ 15330 │ brainstem and cerebellar structures │ 1506 │ 2777.0 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ 34b4a444f06d582c50b59e279e44b9a3___1.h5ad │ 83915546022d9c58bb1d23397d4e987c___1.h5ad │ 10.0 │ 200.0 │ identity_with_max_limit │ true │ Neurons │ Plasmacytoid dendritic cells │ pDC │ NULL │ NULL │ 5093 │ European │ cellxgene_2024/0.4.0 │ S9RRZO<P-$ │ 4976b234-9028-4b4b-8a2f-8ac59d636219 │ 144da207531b7877c50d4aa306d967f3___10X237_1: │ neuron │ CL:0000540 │ 10x 3' v3 │ EFO:0009922 │ 42-year-old human stage │ HsapDv:0000136 │ normal │ PATO:0000461 │ H19.30.001 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ cerebellum │ UBERON:0002037 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/e9f575c0-bf54-4252-9551-1d4c69eda1bf.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/283d65eb-dd53-496d-adb7-7570c7caa443 │ 283d65eb-dd53-496d-adb7-7570c7caa443 │ e9f575c0-bf54-4252-9551-1d4c69eda1bf │ NULL │ 2022-12-08 │ X │ 2024-06-11 │ 71874 │ 5.1.0 │ tissue │ Dissection: Cerebellum (CB) - Cerebellar Vermis - CBV │ false │ NULL │ https://cellxgene.cziscience.com/e/4976b234-9028-4b4b-8a2f-8ac59d636219.cxg/ │ 71874 │ 59236 │ 438436612.0 │ H5AD │ 2560.6052536383113 │ nucleus │ https://datasets.cellxgene.cziscience.com/e9f575c0-bf54-4252-9551-1d4c69eda1bf.h5ad │
│ 13796.0 │ V&CgQ`0T}n │ 4976b234-9028-4b4b-8a2f-8ac59d636219 │ 144da207531b7877c50d4aa306d967f3___10X237_1: │ 144da207531b7877c50d4aa306d967f3 │ │ NULL │ H19.30.001___cerebellum___42-year-old human stage___10x 3' v3______normal___TRUE │ 15330 │ brainstem and cerebellar structures │ 1447 │ 2637.0 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ 34b4a444f06d582c50b59e279e44b9a3___1.h5ad │ 83915546022d9c58bb1d23397d4e987c___1.h5ad │ 10.0 │ 200.0 │ identity_with_max_limit │ true │ Neurons │ Progenitor cells │ pDC │ NULL │ NULL │ 5093 │ European │ cellxgene_2024/0.4.0 │ V&CgQ`0T}n │ 4976b234-9028-4b4b-8a2f-8ac59d636219 │ 144da207531b7877c50d4aa306d967f3___10X237_1: │ neuron │ CL:0000540 │ 10x 3' v3 │ EFO:0009922 │ 42-year-old human stage │ HsapDv:0000136 │ normal │ PATO:0000461 │ H19.30.001 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ cerebellum │ UBERON:0002037 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/e9f575c0-bf54-4252-9551-1d4c69eda1bf.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/283d65eb-dd53-496d-adb7-7570c7caa443 │ 283d65eb-dd53-496d-adb7-7570c7caa443 │ e9f575c0-bf54-4252-9551-1d4c69eda1bf │ NULL │ 2022-12-08 │ X │ 2024-06-11 │ 71874 │ 5.1.0 │ tissue │ Dissection: Cerebellum (CB) - Cerebellar Vermis - CBV │ false │ NULL │ https://cellxgene.cziscience.com/e/4976b234-9028-4b4b-8a2f-8ac59d636219.cxg/ │ 71874 │ 59236 │ 438436612.0 │ H5AD │ 2560.6052536383113 │ nucleus │ https://datasets.cellxgene.cziscience.com/e9f575c0-bf54-4252-9551-1d4c69eda1bf.h5ad │
│ 13889.0 │ Czj;=DLKX* │ 4976b234-9028-4b4b-8a2f-8ac59d636219 │ 144da207531b7877c50d4aa306d967f3___10X237_1: │ 144da207531b7877c50d4aa306d967f3 │ │ NULL │ H19.30.001___cerebellum___42-year-old human stage___10x 3' v3______normal___TRUE │ 15330 │ brainstem and cerebellar structures │ 1290 │ 2302.0 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ 34b4a444f06d582c50b59e279e44b9a3___1.h5ad │ 83915546022d9c58bb1d23397d4e987c___1.h5ad │ 10.0 │ 200.0 │ identity_with_max_limit │ true │ Neurons │ Myeloid dendritic cells │ pDC │ NULL │ NULL │ 5093 │ European │ cellxgene_2024/0.4.0 │ Czj;=DLKX* │ 4976b234-9028-4b4b-8a2f-8ac59d636219 │ 144da207531b7877c50d4aa306d967f3___10X237_1: │ neuron │ CL:0000540 │ 10x 3' v3 │ EFO:0009922 │ 42-year-old human stage │ HsapDv:0000136 │ normal │ PATO:0000461 │ H19.30.001 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ cerebellum │ UBERON:0002037 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/e9f575c0-bf54-4252-9551-1d4c69eda1bf.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/283d65eb-dd53-496d-adb7-7570c7caa443 │ 283d65eb-dd53-496d-adb7-7570c7caa443 │ e9f575c0-bf54-4252-9551-1d4c69eda1bf │ NULL │ 2022-12-08 │ X │ 2024-06-11 │ 71874 │ 5.1.0 │ tissue │ Dissection: Cerebellum (CB) - Cerebellar Vermis - CBV │ false │ NULL │ https://cellxgene.cziscience.com/e/4976b234-9028-4b4b-8a2f-8ac59d636219.cxg/ │ 71874 │ 59236 │ 438436612.0 │ H5AD │ 2560.6052536383113 │ nucleus │ https://datasets.cellxgene.cziscience.com/e9f575c0-bf54-4252-9551-1d4c69eda1bf.h5ad │
│ 12476.0 │ mkLgyEZ^9d │ 4976b234-9028-4b4b-8a2f-8ac59d636219 │ 144da207531b7877c50d4aa306d967f3___10X237_1: │ 144da207531b7877c50d4aa306d967f3 │ │ NULL │ H19.30.001___cerebellum___42-year-old human stage___10x 3' v3______normal___TRUE │ 15330 │ brainstem and cerebellar structures │ 1405 │ 2582.0 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ 34b4a444f06d582c50b59e279e44b9a3___1.h5ad │ 83915546022d9c58bb1d23397d4e987c___1.h5ad │ 10.0 │ 200.0 │ identity_with_max_limit │ true │ Neurons │ Myeloid dendritic cells │ pDC │ NULL │ NULL │ 5093 │ European │ cellxgene_2024/0.4.0 │ mkLgyEZ^9d │ 4976b234-9028-4b4b-8a2f-8ac59d636219 │ 144da207531b7877c50d4aa306d967f3___10X237_1: │ neuron │ CL:0000540 │ 10x 3' v3 │ EFO:0009922 │ 42-year-old human stage │ HsapDv:0000136 │ normal │ PATO:0000461 │ H19.30.001 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ cerebellum │ UBERON:0002037 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/e9f575c0-bf54-4252-9551-1d4c69eda1bf.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/283d65eb-dd53-496d-adb7-7570c7caa443 │ 283d65eb-dd53-496d-adb7-7570c7caa443 │ e9f575c0-bf54-4252-9551-1d4c69eda1bf │ NULL │ 2022-12-08 │ X │ 2024-06-11 │ 71874 │ 5.1.0 │ tissue │ Dissection: Cerebellum (CB) - Cerebellar Vermis - CBV │ false │ NULL │ https://cellxgene.cziscience.com/e/4976b234-9028-4b4b-8a2f-8ac59d636219.cxg/ │ 71874 │ 59236 │ 438436612.0 │ H5AD │ 2560.6052536383113 │ nucleus │ https://datasets.cellxgene.cziscience.com/e9f575c0-bf54-4252-9551-1d4c69eda1bf.h5ad │
│ 12441.0 │ h^?FBc|4>? │ 4976b234-9028-4b4b-8a2f-8ac59d636219 │ 144da207531b7877c50d4aa306d967f3___10X237_1: │ 144da207531b7877c50d4aa306d967f3 │ │ NULL │ H19.30.001___cerebellum___42-year-old human stage___10x 3' v3______normal___TRUE │ 15330 │ brainstem and cerebellar structures │ 1520 │ 2740.0 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ 34b4a444f06d582c50b59e279e44b9a3___1.h5ad │ 83915546022d9c58bb1d23397d4e987c___1.h5ad │ 10.0 │ 200.0 │ identity_with_max_limit │ true │ Neurons │ Myeloid dendritic cells │ pDC │ NULL │ NULL │ 5093 │ European │ cellxgene_2024/0.4.0 │ h^?FBc|4>? │ 4976b234-9028-4b4b-8a2f-8ac59d636219 │ 144da207531b7877c50d4aa306d967f3___10X237_1: │ neuron │ CL:0000540 │ 10x 3' v3 │ EFO:0009922 │ 42-year-old human stage │ HsapDv:0000136 │ normal │ PATO:0000461 │ H19.30.001 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ cerebellum │ UBERON:0002037 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/e9f575c0-bf54-4252-9551-1d4c69eda1bf.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/283d65eb-dd53-496d-adb7-7570c7caa443 │ 283d65eb-dd53-496d-adb7-7570c7caa443 │ e9f575c0-bf54-4252-9551-1d4c69eda1bf │ NULL │ 2022-12-08 │ X │ 2024-06-11 │ 71874 │ 5.1.0 │ tissue │ Dissection: Cerebellum (CB) - Cerebellar Vermis - CBV │ false │ NULL │ https://cellxgene.cziscience.com/e/4976b234-9028-4b4b-8a2f-8ac59d636219.cxg/ │ 71874 │ 59236 │ 438436612.0 │ H5AD │ 2560.6052536383113 │ nucleus │ https://datasets.cellxgene.cziscience.com/e9f575c0-bf54-4252-9551-1d4c69eda1bf.h5ad │
│ 13835.0 │ NAQ!sPRagS │ 4976b234-9028-4b4b-8a2f-8ac59d636219 │ 144da207531b7877c50d4aa306d967f3___10X237_1: │ 144da207531b7877c50d4aa306d967f3 │ │ NULL │ H19.30.001___cerebellum___42-year-old human stage___10x 3' v3______normal___TRUE │ 15330 │ brainstem and cerebellar structures │ 1414 │ 2398.0 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ 34b4a444f06d582c50b59e279e44b9a3___1.h5ad │ 83915546022d9c58bb1d23397d4e987c___1.h5ad │ 10.0 │ 200.0 │ identity_with_max_limit │ true │ Neurons │ Th2 cells │ pDC │ NULL │ NULL │ 5093 │ European │ cellxgene_2024/0.4.0 │ NAQ!sPRagS │ 4976b234-9028-4b4b-8a2f-8ac59d636219 │ 144da207531b7877c50d4aa306d967f3___10X237_1: │ neuron │ CL:0000540 │ 10x 3' v3 │ EFO:0009922 │ 42-year-old human stage │ HsapDv:0000136 │ normal │ PATO:0000461 │ H19.30.001 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ cerebellum │ UBERON:0002037 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/e9f575c0-bf54-4252-9551-1d4c69eda1bf.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/283d65eb-dd53-496d-adb7-7570c7caa443 │ 283d65eb-dd53-496d-adb7-7570c7caa443 │ e9f575c0-bf54-4252-9551-1d4c69eda1bf │ NULL │ 2022-12-08 │ X │ 2024-06-11 │ 71874 │ 5.1.0 │ tissue │ Dissection: Cerebellum (CB) - Cerebellar Vermis - CBV │ false │ NULL │ https://cellxgene.cziscience.com/e/4976b234-9028-4b4b-8a2f-8ac59d636219.cxg/ │ 71874 │ 59236 │ 438436612.0 │ H5AD │ 2560.6052536383113 │ nucleus │ https://datasets.cellxgene.cziscience.com/e9f575c0-bf54-4252-9551-1d4c69eda1bf.h5ad │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
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│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ 294.0 │ d<Qr`I#wl| │ b693123e-95e6-4331-8b50-f367489a767e │ 479b1e0f4ce28dffaa5c5fa629ed5ce8 │ 479b1e0f4ce28dffaa5c5fa629ed5ce8 │ │ NULL │ 354fb56c-1534-4a1f-8d33-9c17de10897b___donor_3___f0b58e0b-1485-4e90-83a9-9efa284dbbbb___edbf7426-f74b-4d8c-8b2d-d0238ec64447___ampulla of uterine tube___46-year-old human stage___10x 3' v3______normal___TRUE │ 16790 │ female reproductive system │ 2777 │ 7546.856679999938 │ false │ endothelial │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ 64d4a3da902a9a4143de4b60a52bf2e0___1.h5ad │ f1b1af79acdb0249ad1eeee7c7571724___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ mv Endothelial cells │ Progenitor cells │ Platelet │ 1.0 │ FALSE │ 290 │ European │ cellxgene_2024/0.4.0 │ d<Qr`I#wl| │ b693123e-95e6-4331-8b50-f367489a767e │ 479b1e0f4ce28dffaa5c5fa629ed5ce8 │ endothelial cell of lymphatic vessel │ CL:0002138 │ 10x 3' v3 │ EFO:0009922 │ 46-year-old human stage │ HsapDv:0000140 │ normal │ PATO:0000461 │ donor_3 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ European │ HANCESTRO:0005 │ female │ PATO:0000383 │ ampulla of uterine tube │ UBERON:0012648 │ Publication: https://doi.org/10.1101/2021.09.16.460628 Dataset Version: https://datasets.cellxgene.cziscience.com/7fa27624-7eda-454a-a066-4de49d5788bd.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/fc77d2ae-247d-44d7-aa24-3f4859254c2c │ fc77d2ae-247d-44d7-aa24-3f4859254c2c │ 7fa27624-7eda-454a-a066-4de49d5788bd │ X_umap │ 2022-01-23 │ raw.X │ 2024-06-11 │ 77536 │ 5.1.0 │ tissue │ scRNA-seq analysis of human fallopian tubes in healthy Vs. hydrosalphinx states │ false │ NULL │ https://cellxgene.cziscience.com/e/b693123e-95e6-4331-8b50-f367489a767e.cxg/ │ 77536 │ 36960 │ 1002296655.0 │ H5AD │ 2641.664426846884 │ cell │ https://datasets.cellxgene.cziscience.com/7fa27624-7eda-454a-a066-4de49d5788bd.h5ad │
│ 4685.0 │ Ul=NE=!mh3 │ b693123e-95e6-4331-8b50-f367489a767e │ 479b1e0f4ce28dffaa5c5fa629ed5ce8 │ 479b1e0f4ce28dffaa5c5fa629ed5ce8 │ │ NULL │ 354fb56c-1534-4a1f-8d33-9c17de10897b___donor_3___f0b58e0b-1485-4e90-83a9-9efa284dbbbb___edbf7426-f74b-4d8c-8b2d-d0238ec64447___ampulla of uterine tube___46-year-old human stage___10x 3' v3______normal___TRUE │ 16790 │ female reproductive system │ 4422 │ 6925.952869999976 │ false │ secretory │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ 4bfcce87f64ea52b1096d115e95428eb___1.h5ad │ f1b1af79acdb0249ad1eeee7c7571724___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Epithelial cells │ Myeloid dendritic cells │ Platelet │ 1.0 │ FALSE │ 198 │ European │ cellxgene_2024/0.4.0 │ Ul=NE=!mh3 │ b693123e-95e6-4331-8b50-f367489a767e │ 479b1e0f4ce28dffaa5c5fa629ed5ce8 │ secretory cell │ CL:0000151 │ 10x 3' v3 │ EFO:0009922 │ 46-year-old human stage │ HsapDv:0000140 │ normal │ PATO:0000461 │ donor_3 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ European │ HANCESTRO:0005 │ female │ PATO:0000383 │ ampulla of uterine tube │ UBERON:0012648 │ Publication: https://doi.org/10.1101/2021.09.16.460628 Dataset Version: https://datasets.cellxgene.cziscience.com/7fa27624-7eda-454a-a066-4de49d5788bd.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/fc77d2ae-247d-44d7-aa24-3f4859254c2c │ fc77d2ae-247d-44d7-aa24-3f4859254c2c │ 7fa27624-7eda-454a-a066-4de49d5788bd │ X_umap │ 2022-01-23 │ raw.X │ 2024-06-11 │ 77536 │ 5.1.0 │ tissue │ scRNA-seq analysis of human fallopian tubes in healthy Vs. hydrosalphinx states │ false │ NULL │ https://cellxgene.cziscience.com/e/b693123e-95e6-4331-8b50-f367489a767e.cxg/ │ 77536 │ 36960 │ 1002296655.0 │ H5AD │ 2641.664426846884 │ cell │ https://datasets.cellxgene.cziscience.com/7fa27624-7eda-454a-a066-4de49d5788bd.h5ad │
│ 2187.0 │ L)db-Kt3V@ │ b693123e-95e6-4331-8b50-f367489a767e │ 479b1e0f4ce28dffaa5c5fa629ed5ce8 │ 479b1e0f4ce28dffaa5c5fa629ed5ce8 │ │ NULL │ 354fb56c-1534-4a1f-8d33-9c17de10897b___donor_3___f0b58e0b-1485-4e90-83a9-9efa284dbbbb___edbf7426-f74b-4d8c-8b2d-d0238ec64447___ampulla of uterine tube___46-year-old human stage___10x 3' v3______normal___TRUE │ 16790 │ female reproductive system │ 3371 │ 6820.755330000038 │ false │ stromal │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ c202d2ed067f7b775e0666ac5cc84404___1.h5ad │ f1b1af79acdb0249ad1eeee7c7571724___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Fibroblasts │ Progenitor cells │ Platelet │ 1.0 │ FALSE │ 420 │ European │ cellxgene_2024/0.4.0 │ L)db-Kt3V@ │ b693123e-95e6-4331-8b50-f367489a767e │ 479b1e0f4ce28dffaa5c5fa629ed5ce8 │ myofibroblast cell │ CL:0000186 │ 10x 3' v3 │ EFO:0009922 │ 46-year-old human stage │ HsapDv:0000140 │ normal │ PATO:0000461 │ donor_3 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ European │ HANCESTRO:0005 │ female │ PATO:0000383 │ ampulla of uterine tube │ UBERON:0012648 │ Publication: https://doi.org/10.1101/2021.09.16.460628 Dataset Version: https://datasets.cellxgene.cziscience.com/7fa27624-7eda-454a-a066-4de49d5788bd.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/fc77d2ae-247d-44d7-aa24-3f4859254c2c │ fc77d2ae-247d-44d7-aa24-3f4859254c2c │ 7fa27624-7eda-454a-a066-4de49d5788bd │ X_umap │ 2022-01-23 │ raw.X │ 2024-06-11 │ 77536 │ 5.1.0 │ tissue │ scRNA-seq analysis of human fallopian tubes in healthy Vs. hydrosalphinx states │ false │ NULL │ https://cellxgene.cziscience.com/e/b693123e-95e6-4331-8b50-f367489a767e.cxg/ │ 77536 │ 36960 │ 1002296655.0 │ H5AD │ 2641.664426846884 │ cell │ https://datasets.cellxgene.cziscience.com/7fa27624-7eda-454a-a066-4de49d5788bd.h5ad │
│ 557.0 │ BwF`8u0$FY │ b693123e-95e6-4331-8b50-f367489a767e │ 479b1e0f4ce28dffaa5c5fa629ed5ce8 │ 479b1e0f4ce28dffaa5c5fa629ed5ce8 │ │ NULL │ 354fb56c-1534-4a1f-8d33-9c17de10897b___donor_3___f0b58e0b-1485-4e90-83a9-9efa284dbbbb___edbf7426-f74b-4d8c-8b2d-d0238ec64447___ampulla of uterine tube___46-year-old human stage___10x 3' v3______normal___TRUE │ 16790 │ female reproductive system │ 559 │ 9774.013200000007 │ false │ granulocyte │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ bcea410ed178c0dfa9b62dd31fa5a709___1.h5ad │ f1b1af79acdb0249ad1eeee7c7571724___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Neutrophils │ Low-density neutrophils │ Platelet │ 1.0 │ FALSE │ 75 │ European │ cellxgene_2024/0.4.0 │ BwF`8u0$FY │ b693123e-95e6-4331-8b50-f367489a767e │ 479b1e0f4ce28dffaa5c5fa629ed5ce8 │ macrophage │ CL:0000235 │ 10x 3' v3 │ EFO:0009922 │ 46-year-old human stage │ HsapDv:0000140 │ normal │ PATO:0000461 │ donor_3 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ European │ HANCESTRO:0005 │ female │ PATO:0000383 │ ampulla of uterine tube │ UBERON:0012648 │ Publication: https://doi.org/10.1101/2021.09.16.460628 Dataset Version: https://datasets.cellxgene.cziscience.com/7fa27624-7eda-454a-a066-4de49d5788bd.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/fc77d2ae-247d-44d7-aa24-3f4859254c2c │ fc77d2ae-247d-44d7-aa24-3f4859254c2c │ 7fa27624-7eda-454a-a066-4de49d5788bd │ X_umap │ 2022-01-23 │ raw.X │ 2024-06-11 │ 77536 │ 5.1.0 │ tissue │ scRNA-seq analysis of human fallopian tubes in healthy Vs. hydrosalphinx states │ false │ NULL │ https://cellxgene.cziscience.com/e/b693123e-95e6-4331-8b50-f367489a767e.cxg/ │ 77536 │ 36960 │ 1002296655.0 │ H5AD │ 2641.664426846884 │ cell │ https://datasets.cellxgene.cziscience.com/7fa27624-7eda-454a-a066-4de49d5788bd.h5ad │
│ 295.0 │ mpdtUlm-@u │ b693123e-95e6-4331-8b50-f367489a767e │ 479b1e0f4ce28dffaa5c5fa629ed5ce8 │ 479b1e0f4ce28dffaa5c5fa629ed5ce8 │ │ NULL │ 354fb56c-1534-4a1f-8d33-9c17de10897b___donor_3___f0b58e0b-1485-4e90-83a9-9efa284dbbbb___edbf7426-f74b-4d8c-8b2d-d0238ec64447___ampulla of uterine tube___46-year-old human stage___10x 3' v3______normal___TRUE │ 16790 │ female reproductive system │ 3056 │ 7131.659800000012 │ false │ endothelial │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ 64d4a3da902a9a4143de4b60a52bf2e0___1.h5ad │ f1b1af79acdb0249ad1eeee7c7571724___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ mv Endothelial cells │ Progenitor cells │ Platelet │ 1.0 │ FALSE │ 290 │ European │ cellxgene_2024/0.4.0 │ mpdtUlm-@u │ b693123e-95e6-4331-8b50-f367489a767e │ 479b1e0f4ce28dffaa5c5fa629ed5ce8 │ endothelial cell of lymphatic vessel │ CL:0002138 │ 10x 3' v3 │ EFO:0009922 │ 46-year-old human stage │ HsapDv:0000140 │ normal │ PATO:0000461 │ donor_3 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ European │ HANCESTRO:0005 │ female │ PATO:0000383 │ ampulla of uterine tube │ UBERON:0012648 │ Publication: https://doi.org/10.1101/2021.09.16.460628 Dataset Version: https://datasets.cellxgene.cziscience.com/7fa27624-7eda-454a-a066-4de49d5788bd.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/fc77d2ae-247d-44d7-aa24-3f4859254c2c │ fc77d2ae-247d-44d7-aa24-3f4859254c2c │ 7fa27624-7eda-454a-a066-4de49d5788bd │ X_umap │ 2022-01-23 │ raw.X │ 2024-06-11 │ 77536 │ 5.1.0 │ tissue │ scRNA-seq analysis of human fallopian tubes in healthy Vs. hydrosalphinx states │ false │ NULL │ https://cellxgene.cziscience.com/e/b693123e-95e6-4331-8b50-f367489a767e.cxg/ │ 77536 │ 36960 │ 1002296655.0 │ H5AD │ 2641.664426846884 │ cell │ https://datasets.cellxgene.cziscience.com/7fa27624-7eda-454a-a066-4de49d5788bd.h5ad │
│ 1040.0 │ ^uXQo67L*{ │ b693123e-95e6-4331-8b50-f367489a767e │ 479b1e0f4ce28dffaa5c5fa629ed5ce8 │ 479b1e0f4ce28dffaa5c5fa629ed5ce8 │ │ NULL │ 354fb56c-1534-4a1f-8d33-9c17de10897b___donor_3___f0b58e0b-1485-4e90-83a9-9efa284dbbbb___edbf7426-f74b-4d8c-8b2d-d0238ec64447___ampulla of uterine tube___46-year-old human stage___10x 3' v3______normal___TRUE │ 16790 │ female reproductive system │ 4171 │ 8248.187819999981 │ false │ progenitor │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ e086b99b339bbcd48d1beacad9e1985d___1.h5ad │ f1b1af79acdb0249ad1eeee7c7571724___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Fibroblasts │ Classical monocytes │ Platelet │ 1.0 │ FALSE │ 490 │ European │ cellxgene_2024/0.4.0 │ ^uXQo67L*{ │ b693123e-95e6-4331-8b50-f367489a767e │ 479b1e0f4ce28dffaa5c5fa629ed5ce8 │ fibroblast │ CL:0000057 │ 10x 3' v3 │ EFO:0009922 │ 46-year-old human stage │ HsapDv:0000140 │ normal │ PATO:0000461 │ donor_3 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ European │ HANCESTRO:0005 │ female │ PATO:0000383 │ ampulla of uterine tube │ UBERON:0012648 │ Publication: https://doi.org/10.1101/2021.09.16.460628 Dataset Version: https://datasets.cellxgene.cziscience.com/7fa27624-7eda-454a-a066-4de49d5788bd.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/fc77d2ae-247d-44d7-aa24-3f4859254c2c │ fc77d2ae-247d-44d7-aa24-3f4859254c2c │ 7fa27624-7eda-454a-a066-4de49d5788bd │ X_umap │ 2022-01-23 │ raw.X │ 2024-06-11 │ 77536 │ 5.1.0 │ tissue │ scRNA-seq analysis of human fallopian tubes in healthy Vs. hydrosalphinx states │ false │ NULL │ https://cellxgene.cziscience.com/e/b693123e-95e6-4331-8b50-f367489a767e.cxg/ │ 77536 │ 36960 │ 1002296655.0 │ H5AD │ 2641.664426846884 │ cell │ https://datasets.cellxgene.cziscience.com/7fa27624-7eda-454a-a066-4de49d5788bd.h5ad │
│ 4686.0 │ 22+Mrur{<i │ b693123e-95e6-4331-8b50-f367489a767e │ 479b1e0f4ce28dffaa5c5fa629ed5ce8 │ 479b1e0f4ce28dffaa5c5fa629ed5ce8 │ │ NULL │ 354fb56c-1534-4a1f-8d33-9c17de10897b___donor_3___f0b58e0b-1485-4e90-83a9-9efa284dbbbb___edbf7426-f74b-4d8c-8b2d-d0238ec64447___ampulla of uterine tube___46-year-old human stage___10x 3' v3______normal___TRUE │ 16790 │ female reproductive system │ 7173 │ 6976.518689999965 │ false │ secretory │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ 4bfcce87f64ea52b1096d115e95428eb___1.h5ad │ f1b1af79acdb0249ad1eeee7c7571724___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Epithelial cells │ Myeloid dendritic cells │ Platelet │ 1.0 │ FALSE │ 198 │ European │ cellxgene_2024/0.4.0 │ 22+Mrur{<i │ b693123e-95e6-4331-8b50-f367489a767e │ 479b1e0f4ce28dffaa5c5fa629ed5ce8 │ secretory cell │ CL:0000151 │ 10x 3' v3 │ EFO:0009922 │ 46-year-old human stage │ HsapDv:0000140 │ normal │ PATO:0000461 │ donor_3 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ European │ HANCESTRO:0005 │ female │ PATO:0000383 │ ampulla of uterine tube │ UBERON:0012648 │ Publication: https://doi.org/10.1101/2021.09.16.460628 Dataset Version: https://datasets.cellxgene.cziscience.com/7fa27624-7eda-454a-a066-4de49d5788bd.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/fc77d2ae-247d-44d7-aa24-3f4859254c2c │ fc77d2ae-247d-44d7-aa24-3f4859254c2c │ 7fa27624-7eda-454a-a066-4de49d5788bd │ X_umap │ 2022-01-23 │ raw.X │ 2024-06-11 │ 77536 │ 5.1.0 │ tissue │ scRNA-seq analysis of human fallopian tubes in healthy Vs. hydrosalphinx states │ false │ NULL │ https://cellxgene.cziscience.com/e/b693123e-95e6-4331-8b50-f367489a767e.cxg/ │ 77536 │ 36960 │ 1002296655.0 │ H5AD │ 2641.664426846884 │ cell │ https://datasets.cellxgene.cziscience.com/7fa27624-7eda-454a-a066-4de49d5788bd.h5ad │
│ 1041.0 │ `N0#f29ixc │ b693123e-95e6-4331-8b50-f367489a767e │ 479b1e0f4ce28dffaa5c5fa629ed5ce8 │ 479b1e0f4ce28dffaa5c5fa629ed5ce8 │ │ NULL │ 354fb56c-1534-4a1f-8d33-9c17de10897b___donor_3___f0b58e0b-1485-4e90-83a9-9efa284dbbbb___edbf7426-f74b-4d8c-8b2d-d0238ec64447___ampulla of uterine tube___46-year-old human stage___10x 3' v3______normal___TRUE │ 16790 │ female reproductive system │ 4578 │ 8129.233670000019 │ false │ progenitor │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ e086b99b339bbcd48d1beacad9e1985d___1.h5ad │ f1b1af79acdb0249ad1eeee7c7571724___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Fibroblasts │ Classical monocytes │ Platelet │ 1.0 │ FALSE │ 490 │ European │ cellxgene_2024/0.4.0 │ `N0#f29ixc │ b693123e-95e6-4331-8b50-f367489a767e │ 479b1e0f4ce28dffaa5c5fa629ed5ce8 │ fibroblast │ CL:0000057 │ 10x 3' v3 │ EFO:0009922 │ 46-year-old human stage │ HsapDv:0000140 │ normal │ PATO:0000461 │ donor_3 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ European │ HANCESTRO:0005 │ female │ PATO:0000383 │ ampulla of uterine tube │ UBERON:0012648 │ Publication: https://doi.org/10.1101/2021.09.16.460628 Dataset Version: https://datasets.cellxgene.cziscience.com/7fa27624-7eda-454a-a066-4de49d5788bd.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/fc77d2ae-247d-44d7-aa24-3f4859254c2c │ fc77d2ae-247d-44d7-aa24-3f4859254c2c │ 7fa27624-7eda-454a-a066-4de49d5788bd │ X_umap │ 2022-01-23 │ raw.X │ 2024-06-11 │ 77536 │ 5.1.0 │ tissue │ scRNA-seq analysis of human fallopian tubes in healthy Vs. hydrosalphinx states │ false │ NULL │ https://cellxgene.cziscience.com/e/b693123e-95e6-4331-8b50-f367489a767e.cxg/ │ 77536 │ 36960 │ 1002296655.0 │ H5AD │ 2641.664426846884 │ cell │ https://datasets.cellxgene.cziscience.com/7fa27624-7eda-454a-a066-4de49d5788bd.h5ad │
│ 558.0 │ N108C&z+r* │ b693123e-95e6-4331-8b50-f367489a767e │ 479b1e0f4ce28dffaa5c5fa629ed5ce8 │ 479b1e0f4ce28dffaa5c5fa629ed5ce8 │ │ NULL │ 354fb56c-1534-4a1f-8d33-9c17de10897b___donor_3___f0b58e0b-1485-4e90-83a9-9efa284dbbbb___edbf7426-f74b-4d8c-8b2d-d0238ec64447___ampulla of uterine tube___46-year-old human stage___10x 3' v3______normal___TRUE │ 16790 │ female reproductive system │ 2728 │ 7964.86221000001 │ false │ macrophage │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ bcea410ed178c0dfa9b62dd31fa5a709___1.h5ad │ f1b1af79acdb0249ad1eeee7c7571724___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Monocytes │ Classical monocytes │ Platelet │ 1.0 │ FALSE │ 178 │ European │ cellxgene_2024/0.4.0 │ N108C&z+r* │ b693123e-95e6-4331-8b50-f367489a767e │ 479b1e0f4ce28dffaa5c5fa629ed5ce8 │ macrophage │ CL:0000235 │ 10x 3' v3 │ EFO:0009922 │ 46-year-old human stage │ HsapDv:0000140 │ normal │ PATO:0000461 │ donor_3 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ European │ HANCESTRO:0005 │ female │ PATO:0000383 │ ampulla of uterine tube │ UBERON:0012648 │ Publication: https://doi.org/10.1101/2021.09.16.460628 Dataset Version: https://datasets.cellxgene.cziscience.com/7fa27624-7eda-454a-a066-4de49d5788bd.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/fc77d2ae-247d-44d7-aa24-3f4859254c2c │ fc77d2ae-247d-44d7-aa24-3f4859254c2c │ 7fa27624-7eda-454a-a066-4de49d5788bd │ X_umap │ 2022-01-23 │ raw.X │ 2024-06-11 │ 77536 │ 5.1.0 │ tissue │ scRNA-seq analysis of human fallopian tubes in healthy Vs. hydrosalphinx states │ false │ NULL │ https://cellxgene.cziscience.com/e/b693123e-95e6-4331-8b50-f367489a767e.cxg/ │ 77536 │ 36960 │ 1002296655.0 │ H5AD │ 2641.664426846884 │ cell │ https://datasets.cellxgene.cziscience.com/7fa27624-7eda-454a-a066-4de49d5788bd.h5ad │
│ 2188.0 │ sHv|-W)Q); │ b693123e-95e6-4331-8b50-f367489a767e │ 479b1e0f4ce28dffaa5c5fa629ed5ce8 │ 479b1e0f4ce28dffaa5c5fa629ed5ce8 │ │ NULL │ 354fb56c-1534-4a1f-8d33-9c17de10897b___donor_3___f0b58e0b-1485-4e90-83a9-9efa284dbbbb___edbf7426-f74b-4d8c-8b2d-d0238ec64447___ampulla of uterine tube___46-year-old human stage___10x 3' v3______normal___TRUE │ 16790 │ female reproductive system │ 2897 │ 7695.171710000061 │ false │ stromal │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ c202d2ed067f7b775e0666ac5cc84404___1.h5ad │ f1b1af79acdb0249ad1eeee7c7571724___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Fibroblasts │ Intermediate monocytes │ Platelet │ 1.0 │ FALSE │ 420 │ European │ cellxgene_2024/0.4.0 │ sHv|-W)Q); │ b693123e-95e6-4331-8b50-f367489a767e │ 479b1e0f4ce28dffaa5c5fa629ed5ce8 │ myofibroblast cell │ CL:0000186 │ 10x 3' v3 │ EFO:0009922 │ 46-year-old human stage │ HsapDv:0000140 │ normal │ PATO:0000461 │ donor_3 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ European │ HANCESTRO:0005 │ female │ PATO:0000383 │ ampulla of uterine tube │ UBERON:0012648 │ Publication: https://doi.org/10.1101/2021.09.16.460628 Dataset Version: https://datasets.cellxgene.cziscience.com/7fa27624-7eda-454a-a066-4de49d5788bd.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/fc77d2ae-247d-44d7-aa24-3f4859254c2c │ fc77d2ae-247d-44d7-aa24-3f4859254c2c │ 7fa27624-7eda-454a-a066-4de49d5788bd │ X_umap │ 2022-01-23 │ raw.X │ 2024-06-11 │ 77536 │ 5.1.0 │ tissue │ scRNA-seq analysis of human fallopian tubes in healthy Vs. hydrosalphinx states │ false │ NULL │ https://cellxgene.cziscience.com/e/b693123e-95e6-4331-8b50-f367489a767e.cxg/ │ 77536 │ 36960 │ 1002296655.0 │ H5AD │ 2641.664426846884 │ cell │ https://datasets.cellxgene.cziscience.com/7fa27624-7eda-454a-a066-4de49d5788bd.h5ad │
└─────────┴────────────────────┴──────────────────────────────────────┴──────────────────────────────────────────────┴──────────────────────────────────┴───────────────┴──────────────────┴─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┴──────────┴─────────────────────────────────────┴──────────────────────────────┴───────────────────┴───────────────┴────────────────────────────┴───────────┴──────────────────────┴──────────────────────┴────────────────────┴───────────────┴───────────────────┴──────────────┴────────────┴─────────────────────────┴───────────────────────────────────────────┴───────────────────────────────────────────┴───────────────────┴───────────────────────────┴─────────────────────────┴─────────┴───────────────────────────────────┴────────────────────────────────┴────────────────────────────┴──────────────────────────┴──────────────────────────┴───────────────────┴───────────────────┴──────────────────────┴────────────────────┴──────────────────────────────────────┴──────────────────────────────────────────────┴──────────────────────────────────────┴────────────────────────────┴───────────┴────────────────────────┴─────────────────────────┴────────────────────────────────────┴─────────┴──────────────────────────┴────────────┴─────────────────┴──────────────┴───────────────────────────┴─────────────────────────┴──────────────────────────────────────────┴─────────┴──────────────────────┴─────────────────────────┴─────────────────────────┴───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┴──────────────────────────────────────┴──────────────────────────────────────┴───────────────────┴──────────────┴───────────────────┴────────────┴────────────────────┴────────────────┴─────────────┴─────────────────────────────────────────────────────────────────────────────────┴───────────┴────────────────────────────┴──────────────────────────────────────────────────────────────────────────────┴────────────┴───────────────┴──────────────┴──────────┴─────────────────────┴─────────────────┴─────────────────────────────────────────────────────────────────────────────────────┘
? rows (>9999 rows, 20 shown) 79 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 │
├────────────────────────────────┼────────────────────────────┼────────┤
│ blood │ tgd │ 109332 │
│ dorsolateral prefrontal cortex │ endothelial │ 9365 │
│ dorsolateral prefrontal cortex │ pericyte │ 9332 │
│ fovea centralis │ neuron │ 144412 │
│ brain │ muscle │ 144 │
│ lung │ pericyte │ 16737 │
│ lung │ endothelial │ 147095 │
│ lung │ stromal │ 159983 │
│ ileum │ b │ 4028 │
│ ileum │ t cd4 │ 7073 │
│ · │ · │ · │
│ · │ · │ · │
│ · │ · │ · │
│ vein │ progenitor │ 199 │
│ arm skin │ ilc │ 22 │
│ arm skin │ mast │ 4 │
│ submucosa of ascending colon │ stromal │ 7132 │
│ temporoparietal junction │ cd8 tcm │ 3 │
│ temporoparietal junction │ cd4 th17 em │ 1 │
│ hepatic flexure of colon │ cd4 th2 em │ 2 │
│ respiratory airway │ erythrocyte │ 1 │
│ kidney │ cartilage │ 1 │
│ white matter of cerebellum │ Unknown │ 1 │
└────────────────────────────────┴────────────────────────────┴────────┘
6390 rows (20 shown) 3 columns
table.filter("self_reported_ethnicity == 'African'")
┌─────────┬────────────────────┬──────────────────────────────────────┬──────────────────────────────────────────────────┬──────────────────────────────────┬───────────────┬──────────────────┬──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┬──────────┬────────────────────┬──────────────────────────────┬───────────────────┬───────────────┬────────────────────────────┬───────────┬──────────────────────┬──────────────────────┬────────────────────┬───────────────┬───────────────────┬──────────────┬────────────┬─────────────────────────┬───────────────────────────────────────────┬───────────────────────────────────────────┬───────────────────┬───────────────────────────┬───────────────────┬─────────┬───────────────────────────────────┬────────────────────────────────┬────────────────────────────┬──────────────────────────┬──────────────────────────┬───────────────────┬───────────────────┬──────────────────────┬────────────────────┬──────────────────────────────────────┬──────────────────────────────────────────────────┬────────────────────────────────────────────────────────────┬────────────────────────────┬───────────┬────────────────────────┬─────────────────────────┬────────────────────────────────────┬─────────┬──────────────────────────┬───────────────────────────────────────────────────────────────────────────┬─────────────────┬──────────────┬───────────────────────────┬─────────────────────────┬──────────────────────────────────────────┬─────────┬──────────────────────┬─────────────────┬─────────────────────────┬────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┬──────────────────────────────────────┬──────────────────────────────────────┬───────────────────┬──────────────┬───────────────────┬────────────┬────────────────────┬────────────────┬─────────────┬─────────────────────────────────────────────────────────────────────────┬───────────┬────────────────────────────┬──────────────────────────────────────────────────────────────────────────────┬────────────┬───────────────┬───────────────┬──────────┬─────────────────────┬─────────────────┬─────────────────────────────────────────────────────────────────────────────────────┐
│ cell_id │ observation_joinid │ dataset_id │ sample_id │ sample_ │ experiment___ │ run_from_cell_id │ sample_heuristic │ 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 │ sample_chunk │ cell_chunk │ sample_pseudobulk_chunk │ file_id_cellNexus_single_cell │ file_id_cellNexus_pseudobulk │ count_upper_bound │ nfeature_expressed_thresh │ inverse_transform │ alive │ cell_annotation_blueprint_singler │ cell_annotation_monaco_singler │ cell_annotation_azimuth_l2 │ ethnicity_flagging_score │ low_confidence_ethnicity │ .aggregated_cells │ imputed_ethnicity │ atlas_id │ observation_joinid │ dataset_id │ sample_id │ cell_type │ cell_type_ontology_term_id │ assay │ assay_ontology_term_id │ development_stage │ development_stage_ontology_term_id │ disease │ disease_ontology_term_id │ donor_id │ is_primary_data │ organism │ organism_ontology_term_id │ self_reported_ethnicity │ self_reported_ethnicity_ontology_term_id │ sex │ sex_ontology_term_id │ tissue │ tissue_ontology_term_id │ citation │ collection_id │ dataset_version_id │ default_embedding │ published_at │ raw_data_location │ revised_at │ primary_cell_count │ schema_version │ tissue_type │ title │ tombstone │ x_approximate_distribution │ explorer_url │ cell_count │ feature_count │ filesize │ filetype │ mean_genes_per_cell │ suspension_type │ url │
│ double │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ int32 │ varchar │ int32 │ double │ boolean │ varchar │ boolean │ int32 │ int32 │ boolean │ boolean │ varchar │ int32 │ int32 │ int32 │ varchar │ varchar │ double │ double │ varchar │ boolean │ varchar │ varchar │ varchar │ double │ varchar │ int32 │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ boolean │ varchar │ varchar │ int32 │ int32 │ double │ varchar │ double │ varchar │ varchar │
├─────────┼────────────────────┼──────────────────────────────────────┼──────────────────────────────────────────────────┼──────────────────────────────────┼───────────────┼──────────────────┼──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┼──────────┼────────────────────┼──────────────────────────────┼───────────────────┼───────────────┼────────────────────────────┼───────────┼──────────────────────┼──────────────────────┼────────────────────┼───────────────┼───────────────────┼──────────────┼────────────┼─────────────────────────┼───────────────────────────────────────────┼───────────────────────────────────────────┼───────────────────┼───────────────────────────┼───────────────────┼─────────┼───────────────────────────────────┼────────────────────────────────┼────────────────────────────┼──────────────────────────┼──────────────────────────┼───────────────────┼───────────────────┼──────────────────────┼────────────────────┼──────────────────────────────────────┼──────────────────────────────────────────────────┼────────────────────────────────────────────────────────────┼────────────────────────────┼───────────┼────────────────────────┼─────────────────────────┼────────────────────────────────────┼─────────┼──────────────────────────┼───────────────────────────────────────────────────────────────────────────┼─────────────────┼──────────────┼───────────────────────────┼─────────────────────────┼──────────────────────────────────────────┼─────────┼──────────────────────┼─────────────────┼─────────────────────────┼────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┼──────────────────────────────────────┼──────────────────────────────────────┼───────────────────┼──────────────┼───────────────────┼────────────┼────────────────────┼────────────────┼─────────────┼─────────────────────────────────────────────────────────────────────────┼───────────┼────────────────────────────┼──────────────────────────────────────────────────────────────────────────────┼────────────┼───────────────┼───────────────┼──────────┼─────────────────────┼─────────────────┼─────────────────────────────────────────────────────────────────────────────────────┤
│ 1853.0 │ XD$kqRjl`= │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP87_1_duong │ 9c8fa5a8d2ae37179b579a0217670512 │ │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239___lung parenchyma___37-year-old human stage___10x 3' v3______normal___TRUE │ 13505 │ respiratory system │ 486 │ 7604.303520000003 │ false │ cd14 mono │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 6 │ 2 │ d172a7edacd12a94fa015f141db87852___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Neutrophils │ Low-density neutrophils │ CD14 Mono │ 1.0 │ FALSE │ 252 │ African │ cellxgene_2024/0.4.0 │ XD$kqRjl`= │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP87_1_duong │ classical monocyte │ CL:0000860 │ 10x 3' v3 │ EFO:0009922 │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ lung parenchyma │ UBERON:0008946 │ 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 │ 2023-05-08 │ raw.X │ 2024-06-11 │ 1959503 │ 5.1.0 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ NULL │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 2282447 │ 56239 │ 21851725645.0 │ H5AD │ 1760.6743113859818 │ NULL │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │
│ 3999.0 │ n8_c{oOpKl │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP87_1_duong │ 9c8fa5a8d2ae37179b579a0217670512 │ │ 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 │ 13505 │ respiratory system │ 2630 │ 7619.86868999999 │ false │ other │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 6 │ 2 │ 8612194bc96cde5a7ec8990c3b4650b1___2.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___2.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ HSC │ Plasmacytoid dendritic cells │ CD14 Mono │ 1.0 │ FALSE │ 1029 │ African │ cellxgene_2024/0.4.0 │ n8_c{oOpKl │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP87_1_duong │ unknown │ unknown │ 10x 3' v3 │ EFO:0009922 │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ lung parenchyma │ UBERON:0008946 │ 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 │ 2023-05-08 │ raw.X │ 2024-06-11 │ 1959503 │ 5.1.0 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ NULL │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 2282447 │ 56239 │ 21851725645.0 │ H5AD │ 1760.6743113859818 │ NULL │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │
│ 121.0 │ <O6V_D`RJ7 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP87_1_duong │ 9c8fa5a8d2ae37179b579a0217670512 │ │ 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 │ 13505 │ respiratory system │ 1286 │ 7628.085160000006 │ false │ pericyte │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 6 │ 2 │ bb65e61557ccedd4ae94bfdabd6be26a___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Adipocytes │ Myeloid dendritic cells │ CD14 Mono │ 1.0 │ FALSE │ 51 │ African │ cellxgene_2024/0.4.0 │ <O6V_D`RJ7 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP87_1_duong │ lung pericyte │ CL:0009089 │ 10x 3' v3 │ EFO:0009922 │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ lung parenchyma │ UBERON:0008946 │ 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 │ 2023-05-08 │ raw.X │ 2024-06-11 │ 1959503 │ 5.1.0 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ NULL │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 2282447 │ 56239 │ 21851725645.0 │ H5AD │ 1760.6743113859818 │ NULL │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │
│ 188.0 │ RQLpOI~QU& │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP87_1_duong │ 9c8fa5a8d2ae37179b579a0217670512 │ │ 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 │ 13505 │ respiratory system │ 2729 │ 7657.642730000015 │ false │ pneumocyte │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 6 │ 2 │ 22f433b222bdf21fc2e5f9172d1ffee5___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Epithelial cells │ Myeloid dendritic cells │ CD14 Mono │ 1.0 │ FALSE │ 781 │ African │ cellxgene_2024/0.4.0 │ RQLpOI~QU& │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP87_1_duong │ type I pneumocyte │ CL:0002062 │ 10x 3' v3 │ EFO:0009922 │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ lung parenchyma │ UBERON:0008946 │ 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 │ 2023-05-08 │ raw.X │ 2024-06-11 │ 1959503 │ 5.1.0 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ NULL │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 2282447 │ 56239 │ 21851725645.0 │ H5AD │ 1760.6743113859818 │ NULL │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │
│ 343.0 │ @@|r;oqpU= │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP87_1_duong │ 9c8fa5a8d2ae37179b579a0217670512 │ │ 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 │ 13505 │ respiratory system │ 2603 │ 7653.08804999999 │ false │ pneumocyte │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 6 │ 2 │ 22f433b222bdf21fc2e5f9172d1ffee5___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Epithelial cells │ Plasmacytoid dendritic cells │ CD14 Mono │ 1.0 │ FALSE │ 781 │ African │ cellxgene_2024/0.4.0 │ @@|r;oqpU= │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP87_1_duong │ type I pneumocyte │ CL:0002062 │ 10x 3' v3 │ EFO:0009922 │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ lung parenchyma │ UBERON:0008946 │ 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 │ 2023-05-08 │ raw.X │ 2024-06-11 │ 1959503 │ 5.1.0 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ NULL │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 2282447 │ 56239 │ 21851725645.0 │ H5AD │ 1760.6743113859818 │ NULL │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │
│ 3298.0 │ dF6bijTtJF │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP87_1_duong │ 9c8fa5a8d2ae37179b579a0217670512 │ │ 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 │ 13505 │ respiratory system │ 747 │ 7510.242950000011 │ false │ other │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 6 │ 2 │ 8612194bc96cde5a7ec8990c3b4650b1___2.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___2.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Adipocytes │ Non classical monocytes │ CD14 Mono │ 1.0 │ FALSE │ 1029 │ African │ cellxgene_2024/0.4.0 │ dF6bijTtJF │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP87_1_duong │ unknown │ unknown │ 10x 3' v3 │ EFO:0009922 │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ lung parenchyma │ UBERON:0008946 │ 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 │ 2023-05-08 │ raw.X │ 2024-06-11 │ 1959503 │ 5.1.0 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ NULL │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 2282447 │ 56239 │ 21851725645.0 │ H5AD │ 1760.6743113859818 │ NULL │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │
│ 321.0 │ !+(-*p>Y9F │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP87_1_duong │ 9c8fa5a8d2ae37179b579a0217670512 │ │ 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 │ 13505 │ respiratory system │ 1373 │ 7638.290979999999 │ false │ progenitor │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 6 │ 2 │ 519f026adfa0a26f731bb941e29e3588___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Adipocytes │ Progenitor cells │ CD14 Mono │ 1.0 │ FALSE │ 230 │ African │ cellxgene_2024/0.4.0 │ !+(-*p>Y9F │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP87_1_duong │ alveolar type 1 fibroblast cell │ CL:4028004 │ 10x 3' v3 │ EFO:0009922 │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ lung parenchyma │ UBERON:0008946 │ 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 │ 2023-05-08 │ raw.X │ 2024-06-11 │ 1959503 │ 5.1.0 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ NULL │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 2282447 │ 56239 │ 21851725645.0 │ H5AD │ 1760.6743113859818 │ NULL │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │
│ 370.0 │ P8Fj^XE$Hj │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP87_1_duong │ 9c8fa5a8d2ae37179b579a0217670512 │ │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239___lung parenchyma___37-year-old human stage___10x 3' v3______normal___TRUE │ 13505 │ respiratory system │ 2077 │ 7652.269010000013 │ false │ pneumocyte │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 6 │ 2 │ 22f433b222bdf21fc2e5f9172d1ffee5___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Epithelial cells │ Myeloid dendritic cells │ CD14 Mono │ 1.0 │ FALSE │ 781 │ African │ cellxgene_2024/0.4.0 │ P8Fj^XE$Hj │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP87_1_duong │ type I pneumocyte │ CL:0002062 │ 10x 3' v3 │ EFO:0009922 │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ lung parenchyma │ UBERON:0008946 │ 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 │ 2023-05-08 │ raw.X │ 2024-06-11 │ 1959503 │ 5.1.0 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ NULL │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 2282447 │ 56239 │ 21851725645.0 │ H5AD │ 1760.6743113859818 │ NULL │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │
│ 1767.0 │ c(5W4Oou9d │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP87_1_duong │ 9c8fa5a8d2ae37179b579a0217670512 │ │ 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 │ 13505 │ respiratory system │ 461 │ 7603.82414 │ false │ cd14 mono │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 6 │ 2 │ d172a7edacd12a94fa015f141db87852___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Neutrophils │ Low-density neutrophils │ CD14 Mono │ 1.0 │ FALSE │ 252 │ African │ cellxgene_2024/0.4.0 │ c(5W4Oou9d │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP87_1_duong │ classical monocyte │ CL:0000860 │ 10x 3' v3 │ EFO:0009922 │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ lung parenchyma │ UBERON:0008946 │ 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 │ 2023-05-08 │ raw.X │ 2024-06-11 │ 1959503 │ 5.1.0 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ NULL │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 2282447 │ 56239 │ 21851725645.0 │ H5AD │ 1760.6743113859818 │ NULL │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │
│ 3599.0 │ &N}bSaSaen │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP87_1_duong │ 9c8fa5a8d2ae37179b579a0217670512 │ │ 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 │ 13505 │ respiratory system │ 465 │ 7611.227539999995 │ false │ other │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 6 │ 2 │ 8612194bc96cde5a7ec8990c3b4650b1___2.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___2.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Myocytes │ Progenitor cells │ CD14 Mono │ 1.0 │ FALSE │ 1029 │ African │ cellxgene_2024/0.4.0 │ &N}bSaSaen │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP87_1_duong │ unknown │ unknown │ 10x 3' v3 │ EFO:0009922 │ 37-year-old human stage │ HsapDv:0000131 │ normal │ PATO:0000461 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747D239 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ African │ HANCESTRO:0010 │ male │ PATO:0000384 │ lung parenchyma │ UBERON:0008946 │ 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 │ 2023-05-08 │ raw.X │ 2024-06-11 │ 1959503 │ 5.1.0 │ tissue │ An integrated cell atlas of the human lung in health and disease (full) │ false │ NULL │ https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ │ 2282447 │ 56239 │ 21851725645.0 │ H5AD │ 1760.6743113859818 │ NULL │ https://datasets.cellxgene.cziscience.com/8d84ba15-d367-4dce-979c-85da70b868a2.h5ad │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ 427.0 │ PJXyb=HE?z │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 36d69323b8acd4f222cc94333b7b34e2 │ 36d69323b8acd4f222cc94333b7b34e2 │ │ NULL │ HBCA_Donor_2___SLX-20005-20446_SIGAG12___breast___33-year-old human stage___10x 3' v3______normal___TRUE │ 12045 │ breast │ 1039 │ 8841.184599999995 │ false │ myoepithelial │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 4 │ 1 │ 323a3de37656865fcec3f8ac0d6ff186___1.h5ad │ c0c024db188c173eeb0af3bb5f030156___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Epithelial cells │ Progenitor cells │ CD8 TCM │ NULL │ NULL │ 930 │ African │ cellxgene_2024/0.4.0 │ PJXyb=HE?z │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 36d69323b8acd4f222cc94333b7b34e2 │ myoepithelial cell of mammary gland │ CL:0002324 │ 10x 3' v3 │ EFO:0009922 │ 33-year-old human stage │ HsapDv:0000127 │ normal │ PATO:0000461 │ HBCA_Donor_2 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ breast │ UBERON:0000310 │ Publication: https://doi.org/10.1038/s41588-024-01688-9 Dataset Version: https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/48259aa8-f168-4bf5-b797-af8e88da6637 │ 48259aa8-f168-4bf5-b797-af8e88da6637 │ 5a611776-aae0-41b9-9f2b-aaf5f83771a3 │ NULL │ 2023-04-24 │ raw.X │ 2024-06-11 │ 803283 │ 5.1.0 │ tissue │ HBCA - global │ false │ NULL │ https://cellxgene.cziscience.com/e/0ba636a1-4754-4786-a8be-7ab3cf760fd6.cxg/ │ 803283 │ 34455 │ 8493125588.0 │ H5AD │ 2057.3174435410683 │ cell │ https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad │
│ 1086.0 │ xQ*lYXDun% │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 36d69323b8acd4f222cc94333b7b34e2 │ 36d69323b8acd4f222cc94333b7b34e2 │ │ NULL │ HBCA_Donor_2___SLX-20005-20446_SIGAG12___breast___33-year-old human stage___10x 3' v3______normal___TRUE │ 12045 │ breast │ 1279 │ 6757.374889999996 │ false │ progenitor │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 4 │ 1 │ 5366b7abd3a51cda6af161e7bb4d5000___2.h5ad │ c0c024db188c173eeb0af3bb5f030156___2.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Epithelial cells │ Myeloid dendritic cells │ CD8 TCM │ NULL │ NULL │ 2393 │ African │ cellxgene_2024/0.4.0 │ xQ*lYXDun% │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 36d69323b8acd4f222cc94333b7b34e2 │ luminal adaptive secretory precursor cell of mammary gland │ CL:4033057 │ 10x 3' v3 │ EFO:0009922 │ 33-year-old human stage │ HsapDv:0000127 │ normal │ PATO:0000461 │ HBCA_Donor_2 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ breast │ UBERON:0000310 │ Publication: https://doi.org/10.1038/s41588-024-01688-9 Dataset Version: https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/48259aa8-f168-4bf5-b797-af8e88da6637 │ 48259aa8-f168-4bf5-b797-af8e88da6637 │ 5a611776-aae0-41b9-9f2b-aaf5f83771a3 │ NULL │ 2023-04-24 │ raw.X │ 2024-06-11 │ 803283 │ 5.1.0 │ tissue │ HBCA - global │ false │ NULL │ https://cellxgene.cziscience.com/e/0ba636a1-4754-4786-a8be-7ab3cf760fd6.cxg/ │ 803283 │ 34455 │ 8493125588.0 │ H5AD │ 2057.3174435410683 │ cell │ https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad │
│ 8189.0 │ mjzEbjox4` │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 36d69323b8acd4f222cc94333b7b34e2 │ 36d69323b8acd4f222cc94333b7b34e2 │ │ NULL │ HBCA_Donor_2___SLX-20005-20446_SIGAG12___breast___33-year-old human stage___10x 3' v3______normal___TRUE │ 12045 │ breast │ 2238 │ 5666.45579 │ false │ progenitor │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 4 │ 1 │ 5366b7abd3a51cda6af161e7bb4d5000___2.h5ad │ c0c024db188c173eeb0af3bb5f030156___2.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Epithelial cells │ Classical monocytes │ CD8 TCM │ NULL │ NULL │ 2393 │ African │ cellxgene_2024/0.4.0 │ mjzEbjox4` │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 36d69323b8acd4f222cc94333b7b34e2 │ luminal adaptive secretory precursor cell of mammary gland │ CL:4033057 │ 10x 3' v3 │ EFO:0009922 │ 33-year-old human stage │ HsapDv:0000127 │ normal │ PATO:0000461 │ HBCA_Donor_2 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ breast │ UBERON:0000310 │ Publication: https://doi.org/10.1038/s41588-024-01688-9 Dataset Version: https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/48259aa8-f168-4bf5-b797-af8e88da6637 │ 48259aa8-f168-4bf5-b797-af8e88da6637 │ 5a611776-aae0-41b9-9f2b-aaf5f83771a3 │ NULL │ 2023-04-24 │ raw.X │ 2024-06-11 │ 803283 │ 5.1.0 │ tissue │ HBCA - global │ false │ NULL │ https://cellxgene.cziscience.com/e/0ba636a1-4754-4786-a8be-7ab3cf760fd6.cxg/ │ 803283 │ 34455 │ 8493125588.0 │ H5AD │ 2057.3174435410683 │ cell │ https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad │
│ 8404.0 │ lBf%Mu*)|H │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 36d69323b8acd4f222cc94333b7b34e2 │ 36d69323b8acd4f222cc94333b7b34e2 │ │ NULL │ HBCA_Donor_2___SLX-20005-20446_SIGAG12___breast___33-year-old human stage___10x 3' v3______normal___TRUE │ 12045 │ breast │ 2057 │ 8507.31074000001 │ false │ endocrine │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 4 │ 1 │ 9721d26d10409a23b3d7a090d03366f4___1.h5ad │ c0c024db188c173eeb0af3bb5f030156___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Epithelial cells │ Myeloid dendritic cells │ CD8 TCM │ NULL │ NULL │ 1632 │ African │ cellxgene_2024/0.4.0 │ lBf%Mu*)|H │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 36d69323b8acd4f222cc94333b7b34e2 │ luminal hormone-sensing cell of mammary gland │ CL:4033058 │ 10x 3' v3 │ EFO:0009922 │ 33-year-old human stage │ HsapDv:0000127 │ normal │ PATO:0000461 │ HBCA_Donor_2 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ breast │ UBERON:0000310 │ Publication: https://doi.org/10.1038/s41588-024-01688-9 Dataset Version: https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/48259aa8-f168-4bf5-b797-af8e88da6637 │ 48259aa8-f168-4bf5-b797-af8e88da6637 │ 5a611776-aae0-41b9-9f2b-aaf5f83771a3 │ NULL │ 2023-04-24 │ raw.X │ 2024-06-11 │ 803283 │ 5.1.0 │ tissue │ HBCA - global │ false │ NULL │ https://cellxgene.cziscience.com/e/0ba636a1-4754-4786-a8be-7ab3cf760fd6.cxg/ │ 803283 │ 34455 │ 8493125588.0 │ H5AD │ 2057.3174435410683 │ cell │ https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad │
│ 5100.0 │ gD7YieXX34 │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 36d69323b8acd4f222cc94333b7b34e2 │ 36d69323b8acd4f222cc94333b7b34e2 │ │ NULL │ HBCA_Donor_2___SLX-20005-20446_SIGAG12___breast___33-year-old human stage___10x 3' v3______normal___TRUE │ 12045 │ breast │ 2539 │ 6299.737090000004 │ false │ progenitor │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 4 │ 1 │ 5366b7abd3a51cda6af161e7bb4d5000___2.h5ad │ c0c024db188c173eeb0af3bb5f030156___2.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Epithelial cells │ Classical monocytes │ CD8 TCM │ NULL │ NULL │ 2393 │ African │ cellxgene_2024/0.4.0 │ gD7YieXX34 │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 36d69323b8acd4f222cc94333b7b34e2 │ luminal adaptive secretory precursor cell of mammary gland │ CL:4033057 │ 10x 3' v3 │ EFO:0009922 │ 33-year-old human stage │ HsapDv:0000127 │ normal │ PATO:0000461 │ HBCA_Donor_2 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ breast │ UBERON:0000310 │ Publication: https://doi.org/10.1038/s41588-024-01688-9 Dataset Version: https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/48259aa8-f168-4bf5-b797-af8e88da6637 │ 48259aa8-f168-4bf5-b797-af8e88da6637 │ 5a611776-aae0-41b9-9f2b-aaf5f83771a3 │ NULL │ 2023-04-24 │ raw.X │ 2024-06-11 │ 803283 │ 5.1.0 │ tissue │ HBCA - global │ false │ NULL │ https://cellxgene.cziscience.com/e/0ba636a1-4754-4786-a8be-7ab3cf760fd6.cxg/ │ 803283 │ 34455 │ 8493125588.0 │ H5AD │ 2057.3174435410683 │ cell │ https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad │
│ 2280.0 │ <|6=~j1d1J │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 36d69323b8acd4f222cc94333b7b34e2 │ 36d69323b8acd4f222cc94333b7b34e2 │ │ NULL │ HBCA_Donor_2___SLX-20005-20446_SIGAG12___breast___33-year-old human stage___10x 3' v3______normal___TRUE │ 12045 │ breast │ 1437 │ 8522.00811 │ false │ myoepithelial │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 4 │ 1 │ 323a3de37656865fcec3f8ac0d6ff186___1.h5ad │ c0c024db188c173eeb0af3bb5f030156___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Keratinocytes │ Classical monocytes │ CD8 TCM │ NULL │ NULL │ 930 │ African │ cellxgene_2024/0.4.0 │ <|6=~j1d1J │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 36d69323b8acd4f222cc94333b7b34e2 │ myoepithelial cell of mammary gland │ CL:0002324 │ 10x 3' v3 │ EFO:0009922 │ 33-year-old human stage │ HsapDv:0000127 │ normal │ PATO:0000461 │ HBCA_Donor_2 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ breast │ UBERON:0000310 │ Publication: https://doi.org/10.1038/s41588-024-01688-9 Dataset Version: https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/48259aa8-f168-4bf5-b797-af8e88da6637 │ 48259aa8-f168-4bf5-b797-af8e88da6637 │ 5a611776-aae0-41b9-9f2b-aaf5f83771a3 │ NULL │ 2023-04-24 │ raw.X │ 2024-06-11 │ 803283 │ 5.1.0 │ tissue │ HBCA - global │ false │ NULL │ https://cellxgene.cziscience.com/e/0ba636a1-4754-4786-a8be-7ab3cf760fd6.cxg/ │ 803283 │ 34455 │ 8493125588.0 │ H5AD │ 2057.3174435410683 │ cell │ https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad │
│ 655.0 │ &f9eh@col} │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 36d69323b8acd4f222cc94333b7b34e2 │ 36d69323b8acd4f222cc94333b7b34e2 │ │ NULL │ HBCA_Donor_2___SLX-20005-20446_SIGAG12___breast___33-year-old human stage___10x 3' v3______normal___TRUE │ 12045 │ breast │ 1243 │ 8091.328510000004 │ false │ endothelial │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 4 │ 1 │ c16b262e4f10269c80eb743b56eafe85___1.h5ad │ c0c024db188c173eeb0af3bb5f030156___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ mv Endothelial cells │ Progenitor cells │ CD8 TCM │ NULL │ NULL │ 337 │ African │ cellxgene_2024/0.4.0 │ &f9eh@col} │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 36d69323b8acd4f222cc94333b7b34e2 │ blood vessel endothelial cell │ CL:0000071 │ 10x 3' v3 │ EFO:0009922 │ 33-year-old human stage │ HsapDv:0000127 │ normal │ PATO:0000461 │ HBCA_Donor_2 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ breast │ UBERON:0000310 │ Publication: https://doi.org/10.1038/s41588-024-01688-9 Dataset Version: https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/48259aa8-f168-4bf5-b797-af8e88da6637 │ 48259aa8-f168-4bf5-b797-af8e88da6637 │ 5a611776-aae0-41b9-9f2b-aaf5f83771a3 │ NULL │ 2023-04-24 │ raw.X │ 2024-06-11 │ 803283 │ 5.1.0 │ tissue │ HBCA - global │ false │ NULL │ https://cellxgene.cziscience.com/e/0ba636a1-4754-4786-a8be-7ab3cf760fd6.cxg/ │ 803283 │ 34455 │ 8493125588.0 │ H5AD │ 2057.3174435410683 │ cell │ https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad │
│ 839.0 │ fGXeE3>7vN │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 36d69323b8acd4f222cc94333b7b34e2 │ 36d69323b8acd4f222cc94333b7b34e2 │ │ NULL │ HBCA_Donor_2___SLX-20005-20446_SIGAG12___breast___33-year-old human stage___10x 3' v3______normal___TRUE │ 12045 │ breast │ 2766 │ 8523.722500000013 │ false │ myoepithelial │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 4 │ 1 │ 323a3de37656865fcec3f8ac0d6ff186___1.h5ad │ c0c024db188c173eeb0af3bb5f030156___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Epithelial cells │ Classical monocytes │ CD8 TCM │ NULL │ NULL │ 930 │ African │ cellxgene_2024/0.4.0 │ fGXeE3>7vN │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 36d69323b8acd4f222cc94333b7b34e2 │ myoepithelial cell of mammary gland │ CL:0002324 │ 10x 3' v3 │ EFO:0009922 │ 33-year-old human stage │ HsapDv:0000127 │ normal │ PATO:0000461 │ HBCA_Donor_2 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ breast │ UBERON:0000310 │ Publication: https://doi.org/10.1038/s41588-024-01688-9 Dataset Version: https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/48259aa8-f168-4bf5-b797-af8e88da6637 │ 48259aa8-f168-4bf5-b797-af8e88da6637 │ 5a611776-aae0-41b9-9f2b-aaf5f83771a3 │ NULL │ 2023-04-24 │ raw.X │ 2024-06-11 │ 803283 │ 5.1.0 │ tissue │ HBCA - global │ false │ NULL │ https://cellxgene.cziscience.com/e/0ba636a1-4754-4786-a8be-7ab3cf760fd6.cxg/ │ 803283 │ 34455 │ 8493125588.0 │ H5AD │ 2057.3174435410683 │ cell │ https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad │
│ 907.0 │ 5DL5AOd2&K │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 36d69323b8acd4f222cc94333b7b34e2 │ 36d69323b8acd4f222cc94333b7b34e2 │ │ NULL │ HBCA_Donor_2___SLX-20005-20446_SIGAG12___breast___33-year-old human stage___10x 3' v3______normal___TRUE │ 12045 │ breast │ 1906 │ 8293.194120000018 │ false │ stromal │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 4 │ 1 │ c16a062ca68faac78b6fc80e130ea3a0___2.h5ad │ c0c024db188c173eeb0af3bb5f030156___2.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Fibroblasts │ Intermediate monocytes │ CD8 TCM │ NULL │ NULL │ 847 │ African │ cellxgene_2024/0.4.0 │ 5DL5AOd2&K │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 36d69323b8acd4f222cc94333b7b34e2 │ fibroblast of mammary gland │ CL:0002555 │ 10x 3' v3 │ EFO:0009922 │ 33-year-old human stage │ HsapDv:0000127 │ normal │ PATO:0000461 │ HBCA_Donor_2 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ breast │ UBERON:0000310 │ Publication: https://doi.org/10.1038/s41588-024-01688-9 Dataset Version: https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/48259aa8-f168-4bf5-b797-af8e88da6637 │ 48259aa8-f168-4bf5-b797-af8e88da6637 │ 5a611776-aae0-41b9-9f2b-aaf5f83771a3 │ NULL │ 2023-04-24 │ raw.X │ 2024-06-11 │ 803283 │ 5.1.0 │ tissue │ HBCA - global │ false │ NULL │ https://cellxgene.cziscience.com/e/0ba636a1-4754-4786-a8be-7ab3cf760fd6.cxg/ │ 803283 │ 34455 │ 8493125588.0 │ H5AD │ 2057.3174435410683 │ cell │ https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad │
│ 10416.0 │ SM7tH?1aNw │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 36d69323b8acd4f222cc94333b7b34e2 │ 36d69323b8acd4f222cc94333b7b34e2 │ │ NULL │ HBCA_Donor_2___SLX-20005-20446_SIGAG12___breast___33-year-old human stage___10x 3' v3______normal___TRUE │ 12045 │ breast │ 1322 │ 8101.23688 │ false │ pericyte │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 4 │ 1 │ cf7ad9a9b464d5da6bd087fbb2a7f028___1.h5ad │ c0c024db188c173eeb0af3bb5f030156___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Fibroblasts │ Progenitor cells │ CD8 TCM │ NULL │ NULL │ 226 │ African │ cellxgene_2024/0.4.0 │ SM7tH?1aNw │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 36d69323b8acd4f222cc94333b7b34e2 │ perivascular cell │ CL:4033054 │ 10x 3' v3 │ EFO:0009922 │ 33-year-old human stage │ HsapDv:0000127 │ normal │ PATO:0000461 │ HBCA_Donor_2 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ breast │ UBERON:0000310 │ Publication: https://doi.org/10.1038/s41588-024-01688-9 Dataset Version: https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/48259aa8-f168-4bf5-b797-af8e88da6637 │ 48259aa8-f168-4bf5-b797-af8e88da6637 │ 5a611776-aae0-41b9-9f2b-aaf5f83771a3 │ NULL │ 2023-04-24 │ raw.X │ 2024-06-11 │ 803283 │ 5.1.0 │ tissue │ HBCA - global │ false │ NULL │ https://cellxgene.cziscience.com/e/0ba636a1-4754-4786-a8be-7ab3cf760fd6.cxg/ │ 803283 │ 34455 │ 8493125588.0 │ H5AD │ 2057.3174435410683 │ cell │ https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad │
└─────────┴────────────────────┴──────────────────────────────────────┴──────────────────────────────────────────────────┴──────────────────────────────────┴───────────────┴──────────────────┴──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┴──────────┴────────────────────┴──────────────────────────────┴───────────────────┴───────────────┴────────────────────────────┴───────────┴──────────────────────┴──────────────────────┴────────────────────┴───────────────┴───────────────────┴──────────────┴────────────┴─────────────────────────┴───────────────────────────────────────────┴───────────────────────────────────────────┴───────────────────┴───────────────────────────┴───────────────────┴─────────┴───────────────────────────────────┴────────────────────────────────┴────────────────────────────┴──────────────────────────┴──────────────────────────┴───────────────────┴───────────────────┴──────────────────────┴────────────────────┴──────────────────────────────────────┴──────────────────────────────────────────────────┴────────────────────────────────────────────────────────────┴────────────────────────────┴───────────┴────────────────────────┴─────────────────────────┴────────────────────────────────────┴─────────┴──────────────────────────┴───────────────────────────────────────────────────────────────────────────┴─────────────────┴──────────────┴───────────────────────────┴─────────────────────────┴──────────────────────────────────────────┴─────────┴──────────────────────┴─────────────────┴─────────────────────────┴────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┴──────────────────────────────────────┴──────────────────────────────────────┴───────────────────┴──────────────┴───────────────────┴────────────┴────────────────────┴────────────────┴─────────────┴─────────────────────────────────────────────────────────────────────────┴───────────┴────────────────────────────┴──────────────────────────────────────────────────────────────────────────────┴────────────┴───────────────┴───────────────┴──────────┴─────────────────────┴─────────────────┴─────────────────────────────────────────────────────────────────────────────────────┘
? rows (>9999 rows, 20 shown) 79 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 = keep_quality_cells(table)
table = table.filter('feature_count >= 5000')
table
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│ cell_id │ observation_joinid │ dataset_id │ sample_id │ sample_ │ experiment___ │ run_from_cell_id │ sample_heuristic │ 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 │ sample_chunk │ cell_chunk │ sample_pseudobulk_chunk │ file_id_cellNexus_single_cell │ file_id_cellNexus_pseudobulk │ count_upper_bound │ nfeature_expressed_thresh │ inverse_transform │ alive │ cell_annotation_blueprint_singler │ cell_annotation_monaco_singler │ cell_annotation_azimuth_l2 │ ethnicity_flagging_score │ low_confidence_ethnicity │ .aggregated_cells │ imputed_ethnicity │ atlas_id │ observation_joinid │ dataset_id │ sample_id │ cell_type │ cell_type_ontology_term_id │ assay │ assay_ontology_term_id │ development_stage │ development_stage_ontology_term_id │ disease │ disease_ontology_term_id │ donor_id │ is_primary_data │ organism │ organism_ontology_term_id │ self_reported_ethnicity │ self_reported_ethnicity_ontology_term_id │ sex │ sex_ontology_term_id │ tissue │ tissue_ontology_term_id │ citation │ collection_id │ dataset_version_id │ default_embedding │ published_at │ raw_data_location │ revised_at │ primary_cell_count │ schema_version │ tissue_type │ title │ tombstone │ x_approximate_distribution │ explorer_url │ cell_count │ feature_count │ filesize │ filetype │ mean_genes_per_cell │ suspension_type │ url │
│ double │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ int32 │ varchar │ int32 │ double │ boolean │ varchar │ boolean │ int32 │ int32 │ boolean │ boolean │ varchar │ int32 │ int32 │ int32 │ varchar │ varchar │ double │ double │ varchar │ boolean │ varchar │ varchar │ varchar │ double │ varchar │ int32 │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ varchar │ boolean │ varchar │ varchar │ int32 │ int32 │ double │ varchar │ double │ varchar │ varchar │
├─────────┼────────────────────┼──────────────────────────────────────┼──────────────────────────────────┼──────────────────────────────────┼───────────────┼──────────────────┼──────────────────────────────────────────────────────────────────────────────────────────────────────────┼──────────┼───────────────────────────────────┼──────────────────────────────┼────────────────────┼───────────────┼────────────────────────────┼───────────┼──────────────────────┼──────────────────────┼────────────────────┼───────────────┼───────────────────┼──────────────┼────────────┼─────────────────────────┼───────────────────────────────────────────┼───────────────────────────────────────────┼───────────────────┼───────────────────────────┼─────────────────────────┼─────────┼───────────────────────────────────┼────────────────────────────────┼────────────────────────────┼──────────────────────────┼──────────────────────────┼───────────────────┼───────────────────┼──────────────────────┼────────────────────┼──────────────────────────────────────┼──────────────────────────────────┼───────────────────────────────────────────────┼────────────────────────────┼───────────┼────────────────────────┼─────────────────────────┼────────────────────────────────────┼─────────┼──────────────────────────┼───────────────┼─────────────────┼──────────────┼───────────────────────────┼─────────────────────────┼──────────────────────────────────────────┼─────────┼──────────────────────┼─────────────────┼─────────────────────────┼────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┼──────────────────────────────────────┼──────────────────────────────────────┼───────────────────┼──────────────┼───────────────────┼────────────┼────────────────────┼────────────────┼─────────────┼─────────────────────────────────────────────────────────────────────────────────────────┼───────────┼────────────────────────────┼──────────────────────────────────────────────────────────────────────────────┼────────────┼───────────────┼──────────────┼──────────┼─────────────────────┼─────────────────┼─────────────────────────────────────────────────────────────────────────────────────┤
│ 18599.0 │ 2a6`X+5!F9 │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 080110f3f267b3d6291c4d8b72f5b372 │ 080110f3f267b3d6291c4d8b72f5b372 │ │ NULL │ HBCA_Donor_35___SLX-20261-20448_SIGAG6___breast___46-year-old human stage___10x 3' v3______normal___TRUE │ 16790 │ breast │ 1558 │ 8171.269290000017 │ false │ endothelial │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 8 │ 1 │ d88d461bbd8c0c258eb36a80160fed83___1.h5ad │ c0c024db188c173eeb0af3bb5f030156___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ mv Endothelial cells │ Non classical monocytes │ Platelet │ NULL │ NULL │ 4677 │ British │ cellxgene_2024/0.4.0 │ 2a6`X+5!F9 │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 080110f3f267b3d6291c4d8b72f5b372 │ blood vessel endothelial cell │ CL:0000071 │ 10x 3' v3 │ EFO:0009922 │ 46-year-old human stage │ HsapDv:0000140 │ normal │ PATO:0000461 │ HBCA_Donor_35 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ British │ HANCESTRO:0462 │ female │ PATO:0000383 │ breast │ UBERON:0000310 │ Publication: https://doi.org/10.1038/s41588-024-01688-9 Dataset Version: https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/48259aa8-f168-4bf5-b797-af8e88da6637 │ 48259aa8-f168-4bf5-b797-af8e88da6637 │ 5a611776-aae0-41b9-9f2b-aaf5f83771a3 │ NULL │ 2023-04-24 │ raw.X │ 2024-06-11 │ 803283 │ 5.1.0 │ tissue │ HBCA - global │ false │ NULL │ https://cellxgene.cziscience.com/e/0ba636a1-4754-4786-a8be-7ab3cf760fd6.cxg/ │ 803283 │ 34455 │ 8493125588.0 │ H5AD │ 2057.3174435410683 │ cell │ https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad │
│ 6847.0 │ e^*mI`qSS% │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 080110f3f267b3d6291c4d8b72f5b372 │ 080110f3f267b3d6291c4d8b72f5b372 │ │ NULL │ HBCA_Donor_35___SLX-20261-20448_SIGAG6___breast___46-year-old human stage___10x 3' v3______normal___TRUE │ 16790 │ breast │ 1690 │ 6423.733250000009 │ false │ pericyte │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 8 │ 1 │ d6a190604d86ea52302a6c8e39b41fca___1.h5ad │ c0c024db188c173eeb0af3bb5f030156___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Adipocytes │ Classical monocytes │ Platelet │ NULL │ NULL │ 3036 │ British │ cellxgene_2024/0.4.0 │ e^*mI`qSS% │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 080110f3f267b3d6291c4d8b72f5b372 │ perivascular cell │ CL:4033054 │ 10x 3' v3 │ EFO:0009922 │ 46-year-old human stage │ HsapDv:0000140 │ normal │ PATO:0000461 │ HBCA_Donor_35 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ British │ HANCESTRO:0462 │ female │ PATO:0000383 │ breast │ UBERON:0000310 │ Publication: https://doi.org/10.1038/s41588-024-01688-9 Dataset Version: https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/48259aa8-f168-4bf5-b797-af8e88da6637 │ 48259aa8-f168-4bf5-b797-af8e88da6637 │ 5a611776-aae0-41b9-9f2b-aaf5f83771a3 │ NULL │ 2023-04-24 │ raw.X │ 2024-06-11 │ 803283 │ 5.1.0 │ tissue │ HBCA - global │ false │ NULL │ https://cellxgene.cziscience.com/e/0ba636a1-4754-4786-a8be-7ab3cf760fd6.cxg/ │ 803283 │ 34455 │ 8493125588.0 │ H5AD │ 2057.3174435410683 │ cell │ https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad │
│ 5486.0 │ V%CDcq|XnR │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 080110f3f267b3d6291c4d8b72f5b372 │ 080110f3f267b3d6291c4d8b72f5b372 │ │ NULL │ HBCA_Donor_35___SLX-20261-20448_SIGAG6___breast___46-year-old human stage___10x 3' v3______normal___TRUE │ 16790 │ breast │ 1460 │ 7448.898930000004 │ false │ pericyte │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 8 │ 1 │ d6a190604d86ea52302a6c8e39b41fca___1.h5ad │ c0c024db188c173eeb0af3bb5f030156___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Myocytes │ Classical monocytes │ Platelet │ NULL │ NULL │ 3036 │ British │ cellxgene_2024/0.4.0 │ V%CDcq|XnR │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 080110f3f267b3d6291c4d8b72f5b372 │ perivascular cell │ CL:4033054 │ 10x 3' v3 │ EFO:0009922 │ 46-year-old human stage │ HsapDv:0000140 │ normal │ PATO:0000461 │ HBCA_Donor_35 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ British │ HANCESTRO:0462 │ female │ PATO:0000383 │ breast │ UBERON:0000310 │ Publication: https://doi.org/10.1038/s41588-024-01688-9 Dataset Version: https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/48259aa8-f168-4bf5-b797-af8e88da6637 │ 48259aa8-f168-4bf5-b797-af8e88da6637 │ 5a611776-aae0-41b9-9f2b-aaf5f83771a3 │ NULL │ 2023-04-24 │ raw.X │ 2024-06-11 │ 803283 │ 5.1.0 │ tissue │ HBCA - global │ false │ NULL │ https://cellxgene.cziscience.com/e/0ba636a1-4754-4786-a8be-7ab3cf760fd6.cxg/ │ 803283 │ 34455 │ 8493125588.0 │ H5AD │ 2057.3174435410683 │ cell │ https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad │
│ 4688.0 │ k<-O8Sc{H) │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 080110f3f267b3d6291c4d8b72f5b372 │ 080110f3f267b3d6291c4d8b72f5b372 │ │ NULL │ HBCA_Donor_35___SLX-20261-20448_SIGAG6___breast___46-year-old human stage___10x 3' v3______normal___TRUE │ 16790 │ breast │ 847 │ 8575.688839999993 │ false │ pericyte │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 8 │ 1 │ d6a190604d86ea52302a6c8e39b41fca___1.h5ad │ c0c024db188c173eeb0af3bb5f030156___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Adipocytes │ Classical monocytes │ Platelet │ NULL │ NULL │ 3036 │ British │ cellxgene_2024/0.4.0 │ k<-O8Sc{H) │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 080110f3f267b3d6291c4d8b72f5b372 │ perivascular cell │ CL:4033054 │ 10x 3' v3 │ EFO:0009922 │ 46-year-old human stage │ HsapDv:0000140 │ normal │ PATO:0000461 │ HBCA_Donor_35 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ British │ HANCESTRO:0462 │ female │ PATO:0000383 │ breast │ UBERON:0000310 │ Publication: https://doi.org/10.1038/s41588-024-01688-9 Dataset Version: https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/48259aa8-f168-4bf5-b797-af8e88da6637 │ 48259aa8-f168-4bf5-b797-af8e88da6637 │ 5a611776-aae0-41b9-9f2b-aaf5f83771a3 │ NULL │ 2023-04-24 │ raw.X │ 2024-06-11 │ 803283 │ 5.1.0 │ tissue │ HBCA - global │ false │ NULL │ https://cellxgene.cziscience.com/e/0ba636a1-4754-4786-a8be-7ab3cf760fd6.cxg/ │ 803283 │ 34455 │ 8493125588.0 │ H5AD │ 2057.3174435410683 │ cell │ https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad │
│ 4283.0 │ Pmzw2)tRq? │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 080110f3f267b3d6291c4d8b72f5b372 │ 080110f3f267b3d6291c4d8b72f5b372 │ │ NULL │ HBCA_Donor_35___SLX-20261-20448_SIGAG6___breast___46-year-old human stage___10x 3' v3______normal___TRUE │ 16790 │ breast │ 2050 │ 7100.951800000012 │ false │ endothelial │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 8 │ 1 │ d88d461bbd8c0c258eb36a80160fed83___1.h5ad │ c0c024db188c173eeb0af3bb5f030156___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ mv Endothelial cells │ Intermediate monocytes │ Platelet │ NULL │ NULL │ 4677 │ British │ cellxgene_2024/0.4.0 │ Pmzw2)tRq? │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 080110f3f267b3d6291c4d8b72f5b372 │ blood vessel endothelial cell │ CL:0000071 │ 10x 3' v3 │ EFO:0009922 │ 46-year-old human stage │ HsapDv:0000140 │ normal │ PATO:0000461 │ HBCA_Donor_35 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ British │ HANCESTRO:0462 │ female │ PATO:0000383 │ breast │ UBERON:0000310 │ Publication: https://doi.org/10.1038/s41588-024-01688-9 Dataset Version: https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/48259aa8-f168-4bf5-b797-af8e88da6637 │ 48259aa8-f168-4bf5-b797-af8e88da6637 │ 5a611776-aae0-41b9-9f2b-aaf5f83771a3 │ NULL │ 2023-04-24 │ raw.X │ 2024-06-11 │ 803283 │ 5.1.0 │ tissue │ HBCA - global │ false │ NULL │ https://cellxgene.cziscience.com/e/0ba636a1-4754-4786-a8be-7ab3cf760fd6.cxg/ │ 803283 │ 34455 │ 8493125588.0 │ H5AD │ 2057.3174435410683 │ cell │ https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad │
│ 13396.0 │ )0aYk3tzKS │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 080110f3f267b3d6291c4d8b72f5b372 │ 080110f3f267b3d6291c4d8b72f5b372 │ │ NULL │ HBCA_Donor_35___SLX-20261-20448_SIGAG6___breast___46-year-old human stage___10x 3' v3______normal___TRUE │ 16790 │ breast │ 1422 │ 7371.200010000009 │ false │ pericyte │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 8 │ 1 │ d6a190604d86ea52302a6c8e39b41fca___1.h5ad │ c0c024db188c173eeb0af3bb5f030156___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Adipocytes │ Myeloid dendritic cells │ Platelet │ NULL │ NULL │ 3036 │ British │ cellxgene_2024/0.4.0 │ )0aYk3tzKS │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 080110f3f267b3d6291c4d8b72f5b372 │ perivascular cell │ CL:4033054 │ 10x 3' v3 │ EFO:0009922 │ 46-year-old human stage │ HsapDv:0000140 │ normal │ PATO:0000461 │ HBCA_Donor_35 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ British │ HANCESTRO:0462 │ female │ PATO:0000383 │ breast │ UBERON:0000310 │ Publication: https://doi.org/10.1038/s41588-024-01688-9 Dataset Version: https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/48259aa8-f168-4bf5-b797-af8e88da6637 │ 48259aa8-f168-4bf5-b797-af8e88da6637 │ 5a611776-aae0-41b9-9f2b-aaf5f83771a3 │ NULL │ 2023-04-24 │ raw.X │ 2024-06-11 │ 803283 │ 5.1.0 │ tissue │ HBCA - global │ false │ NULL │ https://cellxgene.cziscience.com/e/0ba636a1-4754-4786-a8be-7ab3cf760fd6.cxg/ │ 803283 │ 34455 │ 8493125588.0 │ H5AD │ 2057.3174435410683 │ cell │ https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad │
│ 8244.0 │ ^gLd?g$cVJ │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 080110f3f267b3d6291c4d8b72f5b372 │ 080110f3f267b3d6291c4d8b72f5b372 │ │ NULL │ HBCA_Donor_35___SLX-20261-20448_SIGAG6___breast___46-year-old human stage___10x 3' v3______normal___TRUE │ 16790 │ breast │ 1478 │ 7174.088100000005 │ false │ pericyte │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 8 │ 1 │ d6a190604d86ea52302a6c8e39b41fca___1.h5ad │ c0c024db188c173eeb0af3bb5f030156___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Adipocytes │ Myeloid dendritic cells │ Platelet │ NULL │ NULL │ 3036 │ British │ cellxgene_2024/0.4.0 │ ^gLd?g$cVJ │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 080110f3f267b3d6291c4d8b72f5b372 │ perivascular cell │ CL:4033054 │ 10x 3' v3 │ EFO:0009922 │ 46-year-old human stage │ HsapDv:0000140 │ normal │ PATO:0000461 │ HBCA_Donor_35 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ British │ HANCESTRO:0462 │ female │ PATO:0000383 │ breast │ UBERON:0000310 │ Publication: https://doi.org/10.1038/s41588-024-01688-9 Dataset Version: https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/48259aa8-f168-4bf5-b797-af8e88da6637 │ 48259aa8-f168-4bf5-b797-af8e88da6637 │ 5a611776-aae0-41b9-9f2b-aaf5f83771a3 │ NULL │ 2023-04-24 │ raw.X │ 2024-06-11 │ 803283 │ 5.1.0 │ tissue │ HBCA - global │ false │ NULL │ https://cellxgene.cziscience.com/e/0ba636a1-4754-4786-a8be-7ab3cf760fd6.cxg/ │ 803283 │ 34455 │ 8493125588.0 │ H5AD │ 2057.3174435410683 │ cell │ https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad │
│ 11282.0 │ U_{jyc+Q&| │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 080110f3f267b3d6291c4d8b72f5b372 │ 080110f3f267b3d6291c4d8b72f5b372 │ │ NULL │ HBCA_Donor_35___SLX-20261-20448_SIGAG6___breast___46-year-old human stage___10x 3' v3______normal___TRUE │ 16790 │ breast │ 1321 │ 8695.37884 │ false │ endocrine │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 8 │ 1 │ e1097c5223497c92e1d3a1f4aab841d2___1.h5ad │ c0c024db188c173eeb0af3bb5f030156___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Epithelial cells │ Myeloid dendritic cells │ Platelet │ NULL │ NULL │ 231 │ British │ cellxgene_2024/0.4.0 │ U_{jyc+Q&| │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 080110f3f267b3d6291c4d8b72f5b372 │ luminal hormone-sensing cell of mammary gland │ CL:4033058 │ 10x 3' v3 │ EFO:0009922 │ 46-year-old human stage │ HsapDv:0000140 │ normal │ PATO:0000461 │ HBCA_Donor_35 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ British │ HANCESTRO:0462 │ female │ PATO:0000383 │ breast │ UBERON:0000310 │ Publication: https://doi.org/10.1038/s41588-024-01688-9 Dataset Version: https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/48259aa8-f168-4bf5-b797-af8e88da6637 │ 48259aa8-f168-4bf5-b797-af8e88da6637 │ 5a611776-aae0-41b9-9f2b-aaf5f83771a3 │ NULL │ 2023-04-24 │ raw.X │ 2024-06-11 │ 803283 │ 5.1.0 │ tissue │ HBCA - global │ false │ NULL │ https://cellxgene.cziscience.com/e/0ba636a1-4754-4786-a8be-7ab3cf760fd6.cxg/ │ 803283 │ 34455 │ 8493125588.0 │ H5AD │ 2057.3174435410683 │ cell │ https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad │
│ 18483.0 │ A(-V1jtou) │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 080110f3f267b3d6291c4d8b72f5b372 │ 080110f3f267b3d6291c4d8b72f5b372 │ │ NULL │ HBCA_Donor_35___SLX-20261-20448_SIGAG6___breast___46-year-old human stage___10x 3' v3______normal___TRUE │ 16790 │ breast │ 1938 │ 8411.673580000015 │ false │ endothelial │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 8 │ 1 │ d88d461bbd8c0c258eb36a80160fed83___1.h5ad │ c0c024db188c173eeb0af3bb5f030156___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Adipocytes │ Myeloid dendritic cells │ Platelet │ NULL │ NULL │ 4677 │ British │ cellxgene_2024/0.4.0 │ A(-V1jtou) │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 080110f3f267b3d6291c4d8b72f5b372 │ blood vessel endothelial cell │ CL:0000071 │ 10x 3' v3 │ EFO:0009922 │ 46-year-old human stage │ HsapDv:0000140 │ normal │ PATO:0000461 │ HBCA_Donor_35 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ British │ HANCESTRO:0462 │ female │ PATO:0000383 │ breast │ UBERON:0000310 │ Publication: https://doi.org/10.1038/s41588-024-01688-9 Dataset Version: https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/48259aa8-f168-4bf5-b797-af8e88da6637 │ 48259aa8-f168-4bf5-b797-af8e88da6637 │ 5a611776-aae0-41b9-9f2b-aaf5f83771a3 │ NULL │ 2023-04-24 │ raw.X │ 2024-06-11 │ 803283 │ 5.1.0 │ tissue │ HBCA - global │ false │ NULL │ https://cellxgene.cziscience.com/e/0ba636a1-4754-4786-a8be-7ab3cf760fd6.cxg/ │ 803283 │ 34455 │ 8493125588.0 │ H5AD │ 2057.3174435410683 │ cell │ https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad │
│ 10276.0 │ B3Xt^?%n(! │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 080110f3f267b3d6291c4d8b72f5b372 │ 080110f3f267b3d6291c4d8b72f5b372 │ │ NULL │ HBCA_Donor_35___SLX-20261-20448_SIGAG6___breast___46-year-old human stage___10x 3' v3______normal___TRUE │ 16790 │ breast │ 2232 │ 7342.8573899999865 │ false │ endothelial │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 8 │ 1 │ d88d461bbd8c0c258eb36a80160fed83___1.h5ad │ c0c024db188c173eeb0af3bb5f030156___1.h5ad │ 10.0 │ 200.0 │ expm1 │ true │ Adipocytes │ Classical monocytes │ Platelet │ NULL │ NULL │ 4677 │ British │ cellxgene_2024/0.4.0 │ B3Xt^?%n(! │ 0ba636a1-4754-4786-a8be-7ab3cf760fd6 │ 080110f3f267b3d6291c4d8b72f5b372 │ blood vessel endothelial cell │ CL:0000071 │ 10x 3' v3 │ EFO:0009922 │ 46-year-old human stage │ HsapDv:0000140 │ normal │ PATO:0000461 │ HBCA_Donor_35 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ British │ HANCESTRO:0462 │ female │ PATO:0000383 │ breast │ UBERON:0000310 │ Publication: https://doi.org/10.1038/s41588-024-01688-9 Dataset Version: https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/48259aa8-f168-4bf5-b797-af8e88da6637 │ 48259aa8-f168-4bf5-b797-af8e88da6637 │ 5a611776-aae0-41b9-9f2b-aaf5f83771a3 │ NULL │ 2023-04-24 │ raw.X │ 2024-06-11 │ 803283 │ 5.1.0 │ tissue │ HBCA - global │ false │ NULL │ https://cellxgene.cziscience.com/e/0ba636a1-4754-4786-a8be-7ab3cf760fd6.cxg/ │ 803283 │ 34455 │ 8493125588.0 │ H5AD │ 2057.3174435410683 │ cell │ https://datasets.cellxgene.cziscience.com/5a611776-aae0-41b9-9f2b-aaf5f83771a3.h5ad │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ 11411.0 │ Cd<hi8j|oz │ f32c2c13-bb1a-4ffd-a457-60b64ecfa4cb │ 7296de260dac42b70a8e469d2ea1aac0 │ 7296de260dac42b70a8e469d2ea1aac0 │ │ NULL │ H19.30.002___cerebral cortex___29-year-old human stage___10x 3' v3______normal___TRUE │ 10585 │ cerebral lobes and cortical areas │ 3697 │ 8891.0 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 2 │ 1 │ a98df8d62ba814166c54c3729511a2ad___1.h5ad │ c6e5f05427ee78b65182f93dc5858cf1___1.h5ad │ 10.0 │ 200.0 │ identity_with_max_limit │ true │ Neurons │ Plasmacytoid dendritic cells │ HSPC │ NULL │ NULL │ 11475 │ European │ cellxgene_2024/0.4.0 │ Cd<hi8j|oz │ f32c2c13-bb1a-4ffd-a457-60b64ecfa4cb │ 7296de260dac42b70a8e469d2ea1aac0 │ neuron │ CL:0000540 │ 10x 3' v3 │ EFO:0009922 │ 29-year-old human stage │ HsapDv:0000123 │ normal │ PATO:0000461 │ H19.30.002 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ cerebral cortex │ UBERON:0000956 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/73ec94b8-e1c8-4de8-966a-8dea2842b068.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/283d65eb-dd53-496d-adb7-7570c7caa443 │ 283d65eb-dd53-496d-adb7-7570c7caa443 │ 73ec94b8-e1c8-4de8-966a-8dea2842b068 │ NULL │ 2022-12-08 │ X │ 2024-06-11 │ 116576 │ 5.1.0 │ tissue │ Dissection: Cerebral cortex (Cx) - Precentral gyrus (PrCG) - Primary motor cortex - M1C │ false │ NULL │ https://cellxgene.cziscience.com/e/f32c2c13-bb1a-4ffd-a457-60b64ecfa4cb.cxg/ │ 116576 │ 59236 │ 1418111189.0 │ H5AD │ 5574.439138416141 │ nucleus │ https://datasets.cellxgene.cziscience.com/73ec94b8-e1c8-4de8-966a-8dea2842b068.h5ad │
│ 6714.0 │ Se7Rxt|)C< │ f32c2c13-bb1a-4ffd-a457-60b64ecfa4cb │ 7296de260dac42b70a8e469d2ea1aac0 │ 7296de260dac42b70a8e469d2ea1aac0 │ │ NULL │ H19.30.002___cerebral cortex___29-year-old human stage___10x 3' v3______normal___TRUE │ 10585 │ cerebral lobes and cortical areas │ 1969 │ 3285.0 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 2 │ 1 │ a98df8d62ba814166c54c3729511a2ad___1.h5ad │ c6e5f05427ee78b65182f93dc5858cf1___1.h5ad │ 10.0 │ 200.0 │ identity_with_max_limit │ true │ Neurons │ Progenitor cells │ HSPC │ NULL │ NULL │ 11475 │ European │ cellxgene_2024/0.4.0 │ Se7Rxt|)C< │ f32c2c13-bb1a-4ffd-a457-60b64ecfa4cb │ 7296de260dac42b70a8e469d2ea1aac0 │ neuron │ CL:0000540 │ 10x 3' v3 │ EFO:0009922 │ 29-year-old human stage │ HsapDv:0000123 │ normal │ PATO:0000461 │ H19.30.002 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ cerebral cortex │ UBERON:0000956 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/73ec94b8-e1c8-4de8-966a-8dea2842b068.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/283d65eb-dd53-496d-adb7-7570c7caa443 │ 283d65eb-dd53-496d-adb7-7570c7caa443 │ 73ec94b8-e1c8-4de8-966a-8dea2842b068 │ NULL │ 2022-12-08 │ X │ 2024-06-11 │ 116576 │ 5.1.0 │ tissue │ Dissection: Cerebral cortex (Cx) - Precentral gyrus (PrCG) - Primary motor cortex - M1C │ false │ NULL │ https://cellxgene.cziscience.com/e/f32c2c13-bb1a-4ffd-a457-60b64ecfa4cb.cxg/ │ 116576 │ 59236 │ 1418111189.0 │ H5AD │ 5574.439138416141 │ nucleus │ https://datasets.cellxgene.cziscience.com/73ec94b8-e1c8-4de8-966a-8dea2842b068.h5ad │
│ 10279.0 │ 1NS=+aBY*> │ f32c2c13-bb1a-4ffd-a457-60b64ecfa4cb │ 7296de260dac42b70a8e469d2ea1aac0 │ 7296de260dac42b70a8e469d2ea1aac0 │ │ NULL │ H19.30.002___cerebral cortex___29-year-old human stage___10x 3' v3______normal___TRUE │ 10585 │ cerebral lobes and cortical areas │ 5396 │ 16127.0 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 2 │ 1 │ a98df8d62ba814166c54c3729511a2ad___1.h5ad │ c6e5f05427ee78b65182f93dc5858cf1___1.h5ad │ 10.0 │ 200.0 │ identity_with_max_limit │ true │ Neurons │ Progenitor cells │ HSPC │ NULL │ NULL │ 11475 │ European │ cellxgene_2024/0.4.0 │ 1NS=+aBY*> │ f32c2c13-bb1a-4ffd-a457-60b64ecfa4cb │ 7296de260dac42b70a8e469d2ea1aac0 │ neuron │ CL:0000540 │ 10x 3' v3 │ EFO:0009922 │ 29-year-old human stage │ HsapDv:0000123 │ normal │ PATO:0000461 │ H19.30.002 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ cerebral cortex │ UBERON:0000956 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/73ec94b8-e1c8-4de8-966a-8dea2842b068.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/283d65eb-dd53-496d-adb7-7570c7caa443 │ 283d65eb-dd53-496d-adb7-7570c7caa443 │ 73ec94b8-e1c8-4de8-966a-8dea2842b068 │ NULL │ 2022-12-08 │ X │ 2024-06-11 │ 116576 │ 5.1.0 │ tissue │ Dissection: Cerebral cortex (Cx) - Precentral gyrus (PrCG) - Primary motor cortex - M1C │ false │ NULL │ https://cellxgene.cziscience.com/e/f32c2c13-bb1a-4ffd-a457-60b64ecfa4cb.cxg/ │ 116576 │ 59236 │ 1418111189.0 │ H5AD │ 5574.439138416141 │ nucleus │ https://datasets.cellxgene.cziscience.com/73ec94b8-e1c8-4de8-966a-8dea2842b068.h5ad │
│ 2441.0 │ o0<p(qisI? │ f32c2c13-bb1a-4ffd-a457-60b64ecfa4cb │ 7296de260dac42b70a8e469d2ea1aac0 │ 7296de260dac42b70a8e469d2ea1aac0 │ │ NULL │ H19.30.002___cerebral cortex___29-year-old human stage___10x 3' v3______normal___TRUE │ 10585 │ cerebral lobes and cortical areas │ 4374 │ 10889.0 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 2 │ 1 │ a98df8d62ba814166c54c3729511a2ad___1.h5ad │ c6e5f05427ee78b65182f93dc5858cf1___1.h5ad │ 10.0 │ 200.0 │ identity_with_max_limit │ true │ Neurons │ Myeloid dendritic cells │ HSPC │ NULL │ NULL │ 11475 │ European │ cellxgene_2024/0.4.0 │ o0<p(qisI? │ f32c2c13-bb1a-4ffd-a457-60b64ecfa4cb │ 7296de260dac42b70a8e469d2ea1aac0 │ neuron │ CL:0000540 │ 10x 3' v3 │ EFO:0009922 │ 29-year-old human stage │ HsapDv:0000123 │ normal │ PATO:0000461 │ H19.30.002 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ cerebral cortex │ UBERON:0000956 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/73ec94b8-e1c8-4de8-966a-8dea2842b068.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/283d65eb-dd53-496d-adb7-7570c7caa443 │ 283d65eb-dd53-496d-adb7-7570c7caa443 │ 73ec94b8-e1c8-4de8-966a-8dea2842b068 │ NULL │ 2022-12-08 │ X │ 2024-06-11 │ 116576 │ 5.1.0 │ tissue │ Dissection: Cerebral cortex (Cx) - Precentral gyrus (PrCG) - Primary motor cortex - M1C │ false │ NULL │ https://cellxgene.cziscience.com/e/f32c2c13-bb1a-4ffd-a457-60b64ecfa4cb.cxg/ │ 116576 │ 59236 │ 1418111189.0 │ H5AD │ 5574.439138416141 │ nucleus │ https://datasets.cellxgene.cziscience.com/73ec94b8-e1c8-4de8-966a-8dea2842b068.h5ad │
│ 2120.0 │ @KLS$O-?7` │ f32c2c13-bb1a-4ffd-a457-60b64ecfa4cb │ 7296de260dac42b70a8e469d2ea1aac0 │ 7296de260dac42b70a8e469d2ea1aac0 │ │ NULL │ H19.30.002___cerebral cortex___29-year-old human stage___10x 3' v3______normal___TRUE │ 10585 │ cerebral lobes and cortical areas │ 4355 │ 13250.0 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 2 │ 1 │ a98df8d62ba814166c54c3729511a2ad___1.h5ad │ c6e5f05427ee78b65182f93dc5858cf1___1.h5ad │ 10.0 │ 200.0 │ identity_with_max_limit │ true │ Neurons │ Progenitor cells │ HSPC │ NULL │ NULL │ 11475 │ European │ cellxgene_2024/0.4.0 │ @KLS$O-?7` │ f32c2c13-bb1a-4ffd-a457-60b64ecfa4cb │ 7296de260dac42b70a8e469d2ea1aac0 │ neuron │ CL:0000540 │ 10x 3' v3 │ EFO:0009922 │ 29-year-old human stage │ HsapDv:0000123 │ normal │ PATO:0000461 │ H19.30.002 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ cerebral cortex │ UBERON:0000956 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/73ec94b8-e1c8-4de8-966a-8dea2842b068.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/283d65eb-dd53-496d-adb7-7570c7caa443 │ 283d65eb-dd53-496d-adb7-7570c7caa443 │ 73ec94b8-e1c8-4de8-966a-8dea2842b068 │ NULL │ 2022-12-08 │ X │ 2024-06-11 │ 116576 │ 5.1.0 │ tissue │ Dissection: Cerebral cortex (Cx) - Precentral gyrus (PrCG) - Primary motor cortex - M1C │ false │ NULL │ https://cellxgene.cziscience.com/e/f32c2c13-bb1a-4ffd-a457-60b64ecfa4cb.cxg/ │ 116576 │ 59236 │ 1418111189.0 │ H5AD │ 5574.439138416141 │ nucleus │ https://datasets.cellxgene.cziscience.com/73ec94b8-e1c8-4de8-966a-8dea2842b068.h5ad │
│ 2090.0 │ mvD51R>)-9 │ f32c2c13-bb1a-4ffd-a457-60b64ecfa4cb │ 7296de260dac42b70a8e469d2ea1aac0 │ 7296de260dac42b70a8e469d2ea1aac0 │ │ NULL │ H19.30.002___cerebral cortex___29-year-old human stage___10x 3' v3______normal___TRUE │ 10585 │ cerebral lobes and cortical areas │ 3870 │ 8633.0 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 2 │ 1 │ a98df8d62ba814166c54c3729511a2ad___1.h5ad │ c6e5f05427ee78b65182f93dc5858cf1___1.h5ad │ 10.0 │ 200.0 │ identity_with_max_limit │ true │ Neurons │ Progenitor cells │ HSPC │ NULL │ NULL │ 11475 │ European │ cellxgene_2024/0.4.0 │ mvD51R>)-9 │ f32c2c13-bb1a-4ffd-a457-60b64ecfa4cb │ 7296de260dac42b70a8e469d2ea1aac0 │ neuron │ CL:0000540 │ 10x 3' v3 │ EFO:0009922 │ 29-year-old human stage │ HsapDv:0000123 │ normal │ PATO:0000461 │ H19.30.002 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ cerebral cortex │ UBERON:0000956 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/73ec94b8-e1c8-4de8-966a-8dea2842b068.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/283d65eb-dd53-496d-adb7-7570c7caa443 │ 283d65eb-dd53-496d-adb7-7570c7caa443 │ 73ec94b8-e1c8-4de8-966a-8dea2842b068 │ NULL │ 2022-12-08 │ X │ 2024-06-11 │ 116576 │ 5.1.0 │ tissue │ Dissection: Cerebral cortex (Cx) - Precentral gyrus (PrCG) - Primary motor cortex - M1C │ false │ NULL │ https://cellxgene.cziscience.com/e/f32c2c13-bb1a-4ffd-a457-60b64ecfa4cb.cxg/ │ 116576 │ 59236 │ 1418111189.0 │ H5AD │ 5574.439138416141 │ nucleus │ https://datasets.cellxgene.cziscience.com/73ec94b8-e1c8-4de8-966a-8dea2842b068.h5ad │
│ 7380.0 │ yqIdKq}KQ0 │ f32c2c13-bb1a-4ffd-a457-60b64ecfa4cb │ 7296de260dac42b70a8e469d2ea1aac0 │ 7296de260dac42b70a8e469d2ea1aac0 │ │ NULL │ H19.30.002___cerebral cortex___29-year-old human stage___10x 3' v3______normal___TRUE │ 10585 │ cerebral lobes and cortical areas │ 5336 │ 16881.0 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 2 │ 1 │ a98df8d62ba814166c54c3729511a2ad___1.h5ad │ c6e5f05427ee78b65182f93dc5858cf1___1.h5ad │ 10.0 │ 200.0 │ identity_with_max_limit │ true │ Neurons │ Myeloid dendritic cells │ HSPC │ NULL │ NULL │ 11475 │ European │ cellxgene_2024/0.4.0 │ yqIdKq}KQ0 │ f32c2c13-bb1a-4ffd-a457-60b64ecfa4cb │ 7296de260dac42b70a8e469d2ea1aac0 │ neuron │ CL:0000540 │ 10x 3' v3 │ EFO:0009922 │ 29-year-old human stage │ HsapDv:0000123 │ normal │ PATO:0000461 │ H19.30.002 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ cerebral cortex │ UBERON:0000956 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/73ec94b8-e1c8-4de8-966a-8dea2842b068.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/283d65eb-dd53-496d-adb7-7570c7caa443 │ 283d65eb-dd53-496d-adb7-7570c7caa443 │ 73ec94b8-e1c8-4de8-966a-8dea2842b068 │ NULL │ 2022-12-08 │ X │ 2024-06-11 │ 116576 │ 5.1.0 │ tissue │ Dissection: Cerebral cortex (Cx) - Precentral gyrus (PrCG) - Primary motor cortex - M1C │ false │ NULL │ https://cellxgene.cziscience.com/e/f32c2c13-bb1a-4ffd-a457-60b64ecfa4cb.cxg/ │ 116576 │ 59236 │ 1418111189.0 │ H5AD │ 5574.439138416141 │ nucleus │ https://datasets.cellxgene.cziscience.com/73ec94b8-e1c8-4de8-966a-8dea2842b068.h5ad │
│ 10477.0 │ 6*!$=L3hVP │ f32c2c13-bb1a-4ffd-a457-60b64ecfa4cb │ 7296de260dac42b70a8e469d2ea1aac0 │ 7296de260dac42b70a8e469d2ea1aac0 │ │ NULL │ H19.30.002___cerebral cortex___29-year-old human stage___10x 3' v3______normal___TRUE │ 10585 │ cerebral lobes and cortical areas │ 5972 │ 19352.0 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 2 │ 1 │ a98df8d62ba814166c54c3729511a2ad___1.h5ad │ c6e5f05427ee78b65182f93dc5858cf1___1.h5ad │ 10.0 │ 200.0 │ identity_with_max_limit │ true │ Neurons │ Plasmacytoid dendritic cells │ HSPC │ NULL │ NULL │ 11475 │ European │ cellxgene_2024/0.4.0 │ 6*!$=L3hVP │ f32c2c13-bb1a-4ffd-a457-60b64ecfa4cb │ 7296de260dac42b70a8e469d2ea1aac0 │ neuron │ CL:0000540 │ 10x 3' v3 │ EFO:0009922 │ 29-year-old human stage │ HsapDv:0000123 │ normal │ PATO:0000461 │ H19.30.002 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ cerebral cortex │ UBERON:0000956 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/73ec94b8-e1c8-4de8-966a-8dea2842b068.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/283d65eb-dd53-496d-adb7-7570c7caa443 │ 283d65eb-dd53-496d-adb7-7570c7caa443 │ 73ec94b8-e1c8-4de8-966a-8dea2842b068 │ NULL │ 2022-12-08 │ X │ 2024-06-11 │ 116576 │ 5.1.0 │ tissue │ Dissection: Cerebral cortex (Cx) - Precentral gyrus (PrCG) - Primary motor cortex - M1C │ false │ NULL │ https://cellxgene.cziscience.com/e/f32c2c13-bb1a-4ffd-a457-60b64ecfa4cb.cxg/ │ 116576 │ 59236 │ 1418111189.0 │ H5AD │ 5574.439138416141 │ nucleus │ https://datasets.cellxgene.cziscience.com/73ec94b8-e1c8-4de8-966a-8dea2842b068.h5ad │
│ 9047.0 │ RzP^sXT4~5 │ f32c2c13-bb1a-4ffd-a457-60b64ecfa4cb │ 7296de260dac42b70a8e469d2ea1aac0 │ 7296de260dac42b70a8e469d2ea1aac0 │ │ NULL │ H19.30.002___cerebral cortex___29-year-old human stage___10x 3' v3______normal___TRUE │ 10585 │ cerebral lobes and cortical areas │ 4753 │ 14704.0 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 2 │ 1 │ a98df8d62ba814166c54c3729511a2ad___1.h5ad │ c6e5f05427ee78b65182f93dc5858cf1___1.h5ad │ 10.0 │ 200.0 │ identity_with_max_limit │ true │ Neurons │ Plasmacytoid dendritic cells │ HSPC │ NULL │ NULL │ 11475 │ European │ cellxgene_2024/0.4.0 │ RzP^sXT4~5 │ f32c2c13-bb1a-4ffd-a457-60b64ecfa4cb │ 7296de260dac42b70a8e469d2ea1aac0 │ neuron │ CL:0000540 │ 10x 3' v3 │ EFO:0009922 │ 29-year-old human stage │ HsapDv:0000123 │ normal │ PATO:0000461 │ H19.30.002 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ cerebral cortex │ UBERON:0000956 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/73ec94b8-e1c8-4de8-966a-8dea2842b068.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/283d65eb-dd53-496d-adb7-7570c7caa443 │ 283d65eb-dd53-496d-adb7-7570c7caa443 │ 73ec94b8-e1c8-4de8-966a-8dea2842b068 │ NULL │ 2022-12-08 │ X │ 2024-06-11 │ 116576 │ 5.1.0 │ tissue │ Dissection: Cerebral cortex (Cx) - Precentral gyrus (PrCG) - Primary motor cortex - M1C │ false │ NULL │ https://cellxgene.cziscience.com/e/f32c2c13-bb1a-4ffd-a457-60b64ecfa4cb.cxg/ │ 116576 │ 59236 │ 1418111189.0 │ H5AD │ 5574.439138416141 │ nucleus │ https://datasets.cellxgene.cziscience.com/73ec94b8-e1c8-4de8-966a-8dea2842b068.h5ad │
│ 11968.0 │ q*gG|#X)ve │ f32c2c13-bb1a-4ffd-a457-60b64ecfa4cb │ 7296de260dac42b70a8e469d2ea1aac0 │ 7296de260dac42b70a8e469d2ea1aac0 │ │ NULL │ H19.30.002___cerebral cortex___29-year-old human stage___10x 3' v3______normal___TRUE │ 10585 │ cerebral lobes and cortical areas │ 4409 │ 11344.0 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 2 │ 1 │ a98df8d62ba814166c54c3729511a2ad___1.h5ad │ c6e5f05427ee78b65182f93dc5858cf1___1.h5ad │ 10.0 │ 200.0 │ identity_with_max_limit │ true │ Neurons │ Plasmacytoid dendritic cells │ HSPC │ NULL │ NULL │ 11475 │ European │ cellxgene_2024/0.4.0 │ q*gG|#X)ve │ f32c2c13-bb1a-4ffd-a457-60b64ecfa4cb │ 7296de260dac42b70a8e469d2ea1aac0 │ neuron │ CL:0000540 │ 10x 3' v3 │ EFO:0009922 │ 29-year-old human stage │ HsapDv:0000123 │ normal │ PATO:0000461 │ H19.30.002 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ European │ HANCESTRO:0005 │ male │ PATO:0000384 │ cerebral cortex │ UBERON:0000956 │ Publication: https://doi.org/10.1126/science.add7046 Dataset Version: https://datasets.cellxgene.cziscience.com/73ec94b8-e1c8-4de8-966a-8dea2842b068.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/283d65eb-dd53-496d-adb7-7570c7caa443 │ 283d65eb-dd53-496d-adb7-7570c7caa443 │ 73ec94b8-e1c8-4de8-966a-8dea2842b068 │ NULL │ 2022-12-08 │ X │ 2024-06-11 │ 116576 │ 5.1.0 │ tissue │ Dissection: Cerebral cortex (Cx) - Precentral gyrus (PrCG) - Primary motor cortex - M1C │ false │ NULL │ https://cellxgene.cziscience.com/e/f32c2c13-bb1a-4ffd-a457-60b64ecfa4cb.cxg/ │ 116576 │ 59236 │ 1418111189.0 │ H5AD │ 5574.439138416141 │ nucleus │ https://datasets.cellxgene.cziscience.com/73ec94b8-e1c8-4de8-966a-8dea2842b068.h5ad │
└─────────┴────────────────────┴──────────────────────────────────────┴──────────────────────────────────┴──────────────────────────────────┴───────────────┴──────────────────┴──────────────────────────────────────────────────────────────────────────────────────────────────────────┴──────────┴───────────────────────────────────┴──────────────────────────────┴────────────────────┴───────────────┴────────────────────────────┴───────────┴──────────────────────┴──────────────────────┴────────────────────┴───────────────┴───────────────────┴──────────────┴────────────┴─────────────────────────┴───────────────────────────────────────────┴───────────────────────────────────────────┴───────────────────┴───────────────────────────┴─────────────────────────┴─────────┴───────────────────────────────────┴────────────────────────────────┴────────────────────────────┴──────────────────────────┴──────────────────────────┴───────────────────┴───────────────────┴──────────────────────┴────────────────────┴──────────────────────────────────────┴──────────────────────────────────┴───────────────────────────────────────────────┴────────────────────────────┴───────────┴────────────────────────┴─────────────────────────┴────────────────────────────────────┴─────────┴──────────────────────────┴───────────────┴─────────────────┴──────────────┴───────────────────────────┴─────────────────────────┴──────────────────────────────────────────┴─────────┴──────────────────────┴─────────────────┴─────────────────────────┴────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┴──────────────────────────────────────┴──────────────────────────────────────┴───────────────────┴──────────────┴───────────────────┴────────────┴────────────────────┴────────────────┴─────────────┴─────────────────────────────────────────────────────────────────────────────────────────┴───────────┴────────────────────────────┴──────────────────────────────────────────────────────────────────────────────┴────────────┴───────────────┴──────────────┴──────────┴─────────────────────┴─────────────────┴─────────────────────────────────────────────────────────────────────────────────────┘
? rows (>9999 rows, 20 shown) 79 columns
Query raw counts
Once you have filtered your query accordingly, you can pass it into get_anndata() to obtain an AnnData object:
adata = table.filter("""
self_reported_ethnicity == 'African American' AND
assay == '10x 3'' v3' AND
tissue == 'breast' AND
cell_type == 'T cell'
""").get_anndata(assays = "counts")
adata
Downloading https://object-store.rc.nectar.org.au/v1/AUTH_06d6e008e3e642da99d806ba3ea629c5/cellNexus-anndata/cellxgene_2024/0.4.0/counts/25abd48f5a79cc3a0e0bd05856c1b38c___1.h5ad to /home/juan/.cache/cellNexusPy/cellxgene_2024/0.4.0/single_cell/counts/25abd48f5a79cc3a0e0bd05856c1b38c___1.h5ad
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Downloading https://object-store.rc.nectar.org.au/v1/AUTH_06d6e008e3e642da99d806ba3ea629c5/cellNexus-anndata/cellxgene_2024/0.4.0/counts/1207f64fe9042392bf6cd4f12b44cae1___1.h5ad to /home/juan/.cache/cellNexusPy/cellxgene_2024/0.4.0/single_cell/counts/1207f64fe9042392bf6cd4f12b44cae1___1.h5ad
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Downloading https://object-store.rc.nectar.org.au/v1/AUTH_06d6e008e3e642da99d806ba3ea629c5/cellNexus-anndata/cellxgene_2024/0.4.0/counts/4f58dca4a0382ba2be314b7d2a90c00d___1.h5ad to /home/juan/.cache/cellNexusPy/cellxgene_2024/0.4.0/single_cell/counts/4f58dca4a0382ba2be314b7d2a90c00d___1.h5ad
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Downloading https://object-store.rc.nectar.org.au/v1/AUTH_06d6e008e3e642da99d806ba3ea629c5/cellNexus-anndata/cellxgene_2024/0.4.0/counts/4628066dbf02df9c67eabcfb6d42d139___1.h5ad to /home/juan/.cache/cellNexusPy/cellxgene_2024/0.4.0/single_cell/counts/4628066dbf02df9c67eabcfb6d42d139___1.h5ad
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Downloading https://object-store.rc.nectar.org.au/v1/AUTH_06d6e008e3e642da99d806ba3ea629c5/cellNexus-anndata/cellxgene_2024/0.4.0/counts/9e7e0780c4e91a6a5420c2ba42714ad3___1.h5ad to /home/juan/.cache/cellNexusPy/cellxgene_2024/0.4.0/single_cell/counts/9e7e0780c4e91a6a5420c2ba42714ad3___1.h5ad
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View of AnnData object with n_obs × n_vars = 2924 × 33145
obs: 'cell_id', 'observation_joinid', 'dataset_id', 'sample_id', 'sample_', 'experiment___', 'run_from_cell_id', 'sample_heuristic', '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', 'sample_chunk', 'cell_chunk', 'sample_pseudobulk_chunk', 'file_id_cellNexus_single_cell', 'file_id_cellNexus_pseudobulk', 'count_upper_bound', 'nfeature_expressed_thresh', 'inverse_transform', 'alive', 'cell_annotation_blueprint_singler', 'cell_annotation_monaco_singler', 'cell_annotation_azimuth_l2', 'ethnicity_flagging_score', 'low_confidence_ethnicity', '.aggregated_cells', 'imputed_ethnicity', 'atlas_id', 'observation_joinid_1', 'dataset_id_1', 'sample_id_1', 'cell_type', 'cell_type_ontology_term_id', 'assay', 'assay_ontology_term_id', 'development_stage', 'development_stage_ontology_term_id', 'disease', 'disease_ontology_term_id', 'donor_id', 'is_primary_data', 'organism', 'organism_ontology_term_id', 'self_reported_ethnicity', 'self_reported_ethnicity_ontology_term_id', 'sex', 'sex_ontology_term_id', 'tissue', 'tissue_ontology_term_id', 'citation', 'collection_id', 'dataset_version_id', 'default_embedding', 'published_at', 'raw_data_location', 'revised_at', 'primary_cell_count', 'schema_version', 'tissue_type', 'title', 'tombstone', 'x_approximate_distribution', 'explorer_url', 'cell_count', 'feature_count', 'filesize', 'filetype', 'mean_genes_per_cell', 'suspension_type', 'url'
layers: 'counts'
Query counts scaled per million
You can query counts scaled per million. This is helpful if just few genes are of interest:
adata = table.filter("""
self_reported_ethnicity == 'African American' AND
assay == '10x 3'' v3' AND
tissue == 'breast' AND
cell_type == 'T cell'
""").get_anndata(assays = 'cpm')
adata
Downloading https://object-store.rc.nectar.org.au/v1/AUTH_06d6e008e3e642da99d806ba3ea629c5/cellNexus-anndata/cellxgene_2024/0.4.0/cpm/4f58dca4a0382ba2be314b7d2a90c00d___1.h5ad to /home/juan/.cache/cellNexusPy/cellxgene_2024/0.4.0/single_cell/cpm/4f58dca4a0382ba2be314b7d2a90c00d___1.h5ad
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View of AnnData object with n_obs × n_vars = 2924 × 33145
obs: 'cell_id', 'observation_joinid', 'dataset_id', 'sample_id', 'sample_', 'experiment___', 'run_from_cell_id', 'sample_heuristic', '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', 'sample_chunk', 'cell_chunk', 'sample_pseudobulk_chunk', 'file_id_cellNexus_single_cell', 'file_id_cellNexus_pseudobulk', 'count_upper_bound', 'nfeature_expressed_thresh', 'inverse_transform', 'alive', 'cell_annotation_blueprint_singler', 'cell_annotation_monaco_singler', 'cell_annotation_azimuth_l2', 'ethnicity_flagging_score', 'low_confidence_ethnicity', '.aggregated_cells', 'imputed_ethnicity', 'atlas_id', 'observation_joinid_1', 'dataset_id_1', 'sample_id_1', 'cell_type', 'cell_type_ontology_term_id', 'assay', 'assay_ontology_term_id', 'development_stage', 'development_stage_ontology_term_id', 'disease', 'disease_ontology_term_id', 'donor_id', 'is_primary_data', 'organism', 'organism_ontology_term_id', 'self_reported_ethnicity', 'self_reported_ethnicity_ontology_term_id', 'sex', 'sex_ontology_term_id', 'tissue', 'tissue_ontology_term_id', 'citation', 'collection_id', 'dataset_version_id', 'default_embedding', 'published_at', 'raw_data_location', 'revised_at', 'primary_cell_count', 'schema_version', 'tissue_type', 'title', 'tombstone', 'x_approximate_distribution', 'explorer_url', 'cell_count', 'feature_count', 'filesize', 'filetype', 'mean_genes_per_cell', 'suspension_type', 'url'
layers: 'cpm'
Query SCT normalized counts
You can query counts normalized using SCT (Single-Cell Transform):
adata = table.filter("""
self_reported_ethnicity == 'African American' AND
assay == '10x 3'' v3' AND
tissue == 'breast' AND
cell_type == 'T cell'
""").get_anndata(assays = 'sct')
adata
Downloading https://object-store.rc.nectar.org.au/v1/AUTH_06d6e008e3e642da99d806ba3ea629c5/cellNexus-anndata/cellxgene_2024/0.4.0/sct/4628066dbf02df9c67eabcfb6d42d139___1.h5ad to /home/juan/.cache/cellNexusPy/cellxgene_2024/0.4.0/single_cell/sct/4628066dbf02df9c67eabcfb6d42d139___1.h5ad
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/home/juan/miniconda3/envs/cellnexuspy/lib/python3.14/site-packages/anndata/_core/anndata.py:740: UserWarning:
AnnData expects .obs.index to contain strings, but got values like:
[0, 1, 2, 3, 4]
Inferred to be: integer
value_idx = self._prep_dim_index(value.index, attr)
Downloading https://object-store.rc.nectar.org.au/v1/AUTH_06d6e008e3e642da99d806ba3ea629c5/cellNexus-anndata/cellxgene_2024/0.4.0/sct/25abd48f5a79cc3a0e0bd05856c1b38c___1.h5ad to /home/juan/.cache/cellNexusPy/cellxgene_2024/0.4.0/single_cell/sct/25abd48f5a79cc3a0e0bd05856c1b38c___1.h5ad
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/home/juan/miniconda3/envs/cellnexuspy/lib/python3.14/site-packages/anndata/_core/anndata.py:740: UserWarning:
AnnData expects .obs.index to contain strings, but got values like:
[0, 1, 2, 3, 4]
Inferred to be: integer
value_idx = self._prep_dim_index(value.index, attr)
Downloading https://object-store.rc.nectar.org.au/v1/AUTH_06d6e008e3e642da99d806ba3ea629c5/cellNexus-anndata/cellxgene_2024/0.4.0/sct/dee2434b0eac086c39cfd4b6e2a8ced8___1.h5ad to /home/juan/.cache/cellNexusPy/cellxgene_2024/0.4.0/single_cell/sct/dee2434b0eac086c39cfd4b6e2a8ced8___1.h5ad
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/home/juan/miniconda3/envs/cellnexuspy/lib/python3.14/site-packages/anndata/_core/anndata.py:740: UserWarning:
AnnData expects .obs.index to contain strings, but got values like:
[0, 1, 2, 3, 4]
Inferred to be: integer
value_idx = self._prep_dim_index(value.index, attr)
Downloading https://object-store.rc.nectar.org.au/v1/AUTH_06d6e008e3e642da99d806ba3ea629c5/cellNexus-anndata/cellxgene_2024/0.4.0/sct/2aad1b31e2f3469b90409a420580a751___1.h5ad to /home/juan/.cache/cellNexusPy/cellxgene_2024/0.4.0/single_cell/sct/2aad1b31e2f3469b90409a420580a751___1.h5ad
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View of AnnData object with n_obs × n_vars = 1244 × 33145
obs: 'cell_id', 'observation_joinid', 'dataset_id', 'sample_id', 'sample_', 'experiment___', 'run_from_cell_id', 'sample_heuristic', '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', 'sample_chunk', 'cell_chunk', 'sample_pseudobulk_chunk', 'file_id_cellNexus_single_cell', 'file_id_cellNexus_pseudobulk', 'count_upper_bound', 'nfeature_expressed_thresh', 'inverse_transform', 'alive', 'cell_annotation_blueprint_singler', 'cell_annotation_monaco_singler', 'cell_annotation_azimuth_l2', 'ethnicity_flagging_score', 'low_confidence_ethnicity', '.aggregated_cells', 'imputed_ethnicity', 'atlas_id', 'observation_joinid_1', 'dataset_id_1', 'sample_id_1', 'cell_type', 'cell_type_ontology_term_id', 'assay', 'assay_ontology_term_id', 'development_stage', 'development_stage_ontology_term_id', 'disease', 'disease_ontology_term_id', 'donor_id', 'is_primary_data', 'organism', 'organism_ontology_term_id', 'self_reported_ethnicity', 'self_reported_ethnicity_ontology_term_id', 'sex', 'sex_ontology_term_id', 'tissue', 'tissue_ontology_term_id', 'citation', 'collection_id', 'dataset_version_id', 'default_embedding', 'published_at', 'raw_data_location', 'revised_at', 'primary_cell_count', 'schema_version', 'tissue_type', 'title', 'tombstone', 'x_approximate_distribution', 'explorer_url', 'cell_count', 'feature_count', 'filesize', 'filetype', 'mean_genes_per_cell', 'suspension_type', 'url'
layers: 'sct'
Query pseudobulk
cellNexusPy metadata allows to work with pseudobulk data:
adata = table.filter("""
assay == '10x 5'' v1' AND
tissue == 'lung' AND
cell_type == 'classical monocyte'
""").get_pseudobulk()
adata
Downloading https://object-store.rc.nectar.org.au/v1/AUTH_06d6e008e3e642da99d806ba3ea629c5/cellNexus-anndata/cellxgene_2024/0.4.0/pseudobulk/counts/25d99bbda1b544585f6ff0fa05353b97___1.h5ad to /home/juan/.cache/cellNexusPy/cellxgene_2024/0.4.0/pseudobulk/counts/25d99bbda1b544585f6ff0fa05353b97___1.h5ad
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View of AnnData object with n_obs × n_vars = 139 × 15888
obs: 'dataset_id', 'sample_id', 'sample_', 'experiment___', 'run_from_cell_id', 'sample_heuristic', 'age_days', 'tissue_groups', 'cell_type_unified_ensemble', 'sample_chunk', 'cell_chunk', 'sample_pseudobulk_chunk', 'file_id_cellNexus_pseudobulk', 'count_upper_bound', 'nfeature_expressed_thresh', 'inverse_transform', 'ethnicity_flagging_score', 'low_confidence_ethnicity', '.aggregated_cells', 'imputed_ethnicity', 'atlas_id', 'observation_joinid_1', 'dataset_id_1', 'sample_id_1', 'assay', 'assay_ontology_term_id', 'development_stage', 'development_stage_ontology_term_id', 'disease', 'disease_ontology_term_id', 'donor_id', 'is_primary_data', 'organism', 'organism_ontology_term_id', 'self_reported_ethnicity', 'self_reported_ethnicity_ontology_term_id', 'sex', 'sex_ontology_term_id', 'tissue', 'tissue_ontology_term_id', 'citation', 'collection_id', 'dataset_version_id', 'default_embedding', 'published_at', 'raw_data_location', 'revised_at', 'primary_cell_count', 'schema_version', 'tissue_type', 'title', 'tombstone', 'x_approximate_distribution', 'explorer_url', 'cell_count', 'feature_count', 'filesize', 'filetype', 'mean_genes_per_cell', 'suspension_type', 'url'
layers: 'counts'
Download cell communication metadata
Cell communication metadata was generated based on post-QC cells per sample using CellChat v2 method. It uses our harmonised cell type annotation (cell_type_unified_ensemble) to infer the communication. It captures inferred communication at both the ligand–receptor pair level and the signalling pathway level.
- interaction_count: The number of inferred interactions between each pair of cell groups.
- interaction_weight: The aggregated communication strength between each pair of cell groups.
For definitions of additional annotations, please refer to the CellChat v2 documentation: https://github.com/jinworks/CellChat.
For demonstration purpose, read cell communication metadata from a demo file here. Users do not need to specify parquet_url argument in this case.
get_cell_communication_strength(parquet_url = get_metadata_url("cellNexus_lr_signaling_pathway_strength_DEMO.parquet"))
(<_duckdb.DuckDBPyConnection at 0x763a55adb230>,
┌───────────┬─────────┬─────────┬───────────┬────────────────────────┬─────────┬─────────────────────┬─────────────────────────┬──────────────┬────────────────────┬────────────────┬───────────────────────┬────────────────────┬──────────────────────────────────┬───────────────────┬─────────────────────┐
│ source │ target │ ligand │ receptor │ lr_prob │ lr_pval │ interaction_name │ interaction_name_2 │ pathway_name │ annotation │ evidence │ pathway_prob │ pathway_pval │ sample_id │ interaction_count │ interaction_weight │
│ varchar │ varchar │ varchar │ varchar │ double │ double │ varchar │ varchar │ varchar │ varchar │ varchar │ double │ double │ varchar │ double │ double │
├───────────┼─────────┼─────────┼───────────┼────────────────────────┼─────────┼─────────────────────┼─────────────────────────┼──────────────┼────────────────────┼────────────────┼───────────────────────┼────────────────────┼──────────────────────────────────┼───────────────────┼─────────────────────┤
│ b │ b │ TGFB1 │ TGFbR1_R2 │ 0.00011572297912110056 │ 1.0 │ TGFB1_TGFBR1_TGFBR2 │ TGFB1 - (TGFBR1+TGFBR2) │ TGFb │ Secreted Signaling │ KEGG: hsa04350 │ 0.0004201449591179544 │ 1.0 │ b290d7ef52f83156391e1827e60e5466 │ 24.0 │ 0.6718443772855172 │
│ b memory │ b │ TGFB1 │ TGFbR1_R2 │ 0.0008647641397195719 │ 1.0 │ TGFB1_TGFBR1_TGFBR2 │ TGFB1 - (TGFBR1+TGFBR2) │ TGFb │ Secreted Signaling │ KEGG: hsa04350 │ 0.001845932371036158 │ 1.0 │ b290d7ef52f83156391e1827e60e5466 │ 27.0 │ 0.6520273348503719 │
│ b naive │ b │ TGFB1 │ TGFbR1_R2 │ 0.0006964938883689721 │ 0.99 │ TGFB1_TGFBR1_TGFBR2 │ TGFB1 - (TGFBR1+TGFBR2) │ TGFb │ Secreted Signaling │ KEGG: hsa04350 │ 0.0014559020673046948 │ 0.9944444444444445 │ b290d7ef52f83156391e1827e60e5466 │ 19.0 │ 0.7177834557225372 │
│ cd14 mono │ b │ TGFB1 │ TGFbR1_R2 │ 0.0024049907871326443 │ 0.81 │ TGFB1_TGFBR1_TGFBR2 │ TGFB1 - (TGFBR1+TGFBR2) │ TGFb │ Secreted Signaling │ KEGG: hsa04350 │ 0.004716764702589936 │ 0.9244444444444444 │ b290d7ef52f83156391e1827e60e5466 │ 46.0 │ 0.5737335068227721 │
│ cd4 naive │ b │ TGFB1 │ TGFbR1_R2 │ 0.0009571851813537339 │ 1.0 │ TGFB1_TGFBR1_TGFBR2 │ TGFB1 - (TGFBR1+TGFBR2) │ TGFb │ Secreted Signaling │ KEGG: hsa04350 │ 0.0020071802827783644 │ 0.9977777777777778 │ b290d7ef52f83156391e1827e60e5466 │ 21.0 │ 0.33115603633814017 │
│ cd4 tem │ b │ TGFB1 │ TGFbR1_R2 │ 0.0024169229493851787 │ 0.76 │ TGFB1_TGFBR1_TGFBR2 │ TGFB1 - (TGFBR1+TGFBR2) │ TGFb │ Secreted Signaling │ KEGG: hsa04350 │ 0.0046745766723373895 │ 0.7966666666666666 │ b290d7ef52f83156391e1827e60e5466 │ 23.0 │ 0.3335206917229981 │
└───────────┴─────────┴─────────┴───────────┴────────────────────────┴─────────┴─────────────────────┴─────────────────────────┴──────────────┴────────────────────┴────────────────┴───────────────────────┴────────────────────┴──────────────────────────────────┴───────────────────┴─────────────────────┘)
Extract only a subset of genes
We can query a subset of genes. Notice how the result only has nvars = 1:
adata = table.filter("""
self_reported_ethnicity == 'African American' AND
assay == '10x 3'' v3' AND
tissue == 'breast' AND
cell_type == 'T cell'
""").get_anndata(assays = "cpm", features = ['ENSG00000134644'])
adata
View of AnnData object with n_obs × n_vars = 2908 × 1
obs: 'cell_id', 'observation_joinid', 'dataset_id', 'sample_id', 'sample_', 'experiment___', 'run_from_cell_id', 'sample_heuristic', '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', 'sample_chunk', 'cell_chunk', 'sample_pseudobulk_chunk', 'file_id_cellNexus_single_cell', 'file_id_cellNexus_pseudobulk', 'count_upper_bound', 'nfeature_expressed_thresh', 'inverse_transform', 'alive', 'cell_annotation_blueprint_singler', 'cell_annotation_monaco_singler', 'cell_annotation_azimuth_l2', 'ethnicity_flagging_score', 'low_confidence_ethnicity', '.aggregated_cells', 'imputed_ethnicity', 'atlas_id', 'observation_joinid_1', 'dataset_id_1', 'sample_id_1', 'cell_type', 'cell_type_ontology_term_id', 'assay', 'assay_ontology_term_id', 'development_stage', 'development_stage_ontology_term_id', 'disease', 'disease_ontology_term_id', 'donor_id', 'is_primary_data', 'organism', 'organism_ontology_term_id', 'self_reported_ethnicity', 'self_reported_ethnicity_ontology_term_id', 'sex', 'sex_ontology_term_id', 'tissue', 'tissue_ontology_term_id', 'citation', 'collection_id', 'dataset_version_id', 'default_embedding', 'published_at', 'raw_data_location', 'revised_at', 'primary_cell_count', 'schema_version', 'tissue_type', 'title', 'tombstone', 'x_approximate_distribution', 'explorer_url', 'cell_count', 'feature_count', 'filesize', 'filetype', 'mean_genes_per_cell', 'suspension_type', 'url'
layers: 'cpm'
Visualizing gene expression
Taking advantage of the AnnData object, we can use scanpy library to visualize gene expression gfor a groups of interest:
adata = table.filter("""
cell_type_unified_ensemble = 'cd14 mono'
""").get_anndata(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)
# convert all remaining object columns to str
for col in adata.obs.select_dtypes(include="object").columns:
adata.obs[col] = adata.obs[col].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.