Provides access to a copy of the Human Cell Atlas, but with harmonised metdata. This allows for uniform querying across numerous datasets within the Atlas using common fields such as cell type, tissue type, and patient ethnicity. Usage involves first querying the metadata table for cells of interest, and then downloading the corresponding cells into a anndata object.
Project description
cellNexusPy
Importing the package
from cellnexuspy import get_metadata, get_anndata, 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
┌─────────┬────────────────────┬──────────────────────────────────────┬────────────────────────────────────────────────────────┬──────────────────────────────────┬───────────────┬──────────────────┬───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┬──────────┬─────────────────────────────────────┬──────────────────────────────┬────────────────────┬───────────────┬────────────────────────────┬───────────┬──────────────────────┬──────────────────────┬────────────────────┬───────────────┬───────────────────┬──────────────┬────────────┬─────────────────────────┬───────────────────────────────────────────┬───────────────────────────────────────────┬───────────────────┬───────────────────────────┬───────────────────┬─────────┬───────────────────────────────────┬────────────────────────────────┬────────────────────────────┬──────────────────────────┬──────────────────────────┬───────────────────┬───────────────────┬──────────────────────┬────────────────────┬──────────────────────────────────────┬────────────────────────────────────────────────────────┬──────────────────────┬────────────────────────────┬─────────────┬────────────────────────┬──────────────────────────────────────────┬────────────────────────────────────┬────────────────────┬──────────────────────────┬───────────────────────────────────────────────────────────────────────────┬─────────────────┬──────────────┬───────────────────────────┬─────────────────────────┬──────────────────────────────────────────┬─────────┬──────────────────────┬───────────────┬─────────────────────────┬────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┬──────────────────────────────────────┬──────────────────────────────────────┬───────────────────┬──────────────┬───────────────────┬────────────┬────────────────────┬────────────────┬─────────────┬─────────────────────────────────────────────────────────────────────────┬───────────┬────────────────────────────┬──────────────────────────────────────────────────────────────────────────────┬────────────┬───────────────┬───────────────┬──────────┬─────────────────────┬─────────────────┬─────────────────────────────────────────────────────────────────────────────────────┐
│ 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 │
├─────────┼────────────────────┼──────────────────────────────────────┼────────────────────────────────────────────────────────┼──────────────────────────────────┼───────────────┼──────────────────┼───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┼──────────┼─────────────────────────────────────┼──────────────────────────────┼────────────────────┼───────────────┼────────────────────────────┼───────────┼──────────────────────┼──────────────────────┼────────────────────┼───────────────┼───────────────────┼──────────────┼────────────┼─────────────────────────┼───────────────────────────────────────────┼───────────────────────────────────────────┼───────────────────┼───────────────────────────┼───────────────────┼─────────┼───────────────────────────────────┼────────────────────────────────┼────────────────────────────┼──────────────────────────┼──────────────────────────┼───────────────────┼───────────────────┼──────────────────────┼────────────────────┼──────────────────────────────────────┼────────────────────────────────────────────────────────┼──────────────────────┼────────────────────────────┼─────────────┼────────────────────────┼──────────────────────────────────────────┼────────────────────────────────────┼────────────────────┼──────────────────────────┼───────────────────────────────────────────────────────────────────────────┼─────────────────┼──────────────┼───────────────────────────┼─────────────────────────┼──────────────────────────────────────────┼─────────┼──────────────────────┼───────────────┼─────────────────────────┼────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┼──────────────────────────────────────┼──────────────────────────────────────┼───────────────────┼──────────────┼───────────────────┼────────────┼────────────────────┼────────────────┼─────────────┼─────────────────────────────────────────────────────────────────────────┼───────────┼────────────────────────────┼──────────────────────────────────────────────────────────────────────────────┼────────────┼───────────────┼───────────────┼──────────┼─────────────────────┼─────────────────┼─────────────────────────────────────────────────────────────────────────────────────┤
│ 4586.0 │ fuR>bfSG72 │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ d65de8185cc889a2c89adb96104cbcb4___exp4-human-118well. │ d65de8185cc889a2c89adb96104cbcb4 │ │ NULL │ H27432___telencephalon___17th week post-fertilization human stage___sci-RNA-seq______trisomy 18___TRUE │ 119 │ brainstem and cerebellar structures │ 285 │ 25447.21440999952 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ Unknown │ 1 │ 1 │ 4 │ a099a59751e326128c2dd2d0bf0ffaca___1.h5ad │ 10825a9c5f3468936b512ab56aade40b___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Neurons │ Non-switched memory B cells │ Other │ NULL │ NULL │ 6 │ unknown │ cellxgene_2024/0.2.1 │ fuR>bfSG72 │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ d65de8185cc889a2c89adb96104cbcb4___exp4-human-118well. │ glutamatergic neuron │ CL:0000679 │ sci-RNA-seq │ EFO:0010550 │ 17th week post-fertilization human stage │ HsapDv:0000054 │ trisomy 18 │ MONDO:0018071 │ H27432 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ male │ PATO:0000384 │ telencephalon │ UBERON:0001893 │ Publication: https://doi.org/10.1126/science.aba7721 Dataset Version: https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/c114c20f-1ef4-49a5-9c2e-d965787fb90c │ c114c20f-1ef4-49a5-9c2e-d965787fb90c │ 8f6296d0-5b29-4dca-8061-b97147df5fcc │ NULL │ 2021-06-02 │ raw.X │ 2024-06-11 │ 4062980 │ 5.1.0 │ tissue │ Survey of human embryonic development │ false │ NULL │ https://cellxgene.cziscience.com/e/f7c1c579-2dc0-47e2-ba19-8165c5a0e353.cxg/ │ 4062980 │ 46397 │ 20060284412.0 │ H5AD │ 586.3116402246627 │ nucleus │ https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad │
│ 2367.0 │ yyek8Mgo!y │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7a2a38009ef83ef029bb34d4951a079___exp4-human-119well. │ a7a2a38009ef83ef029bb34d4951a079 │ │ NULL │ H27423___telencephalon___16th week post-fertilization human stage___sci-RNA-seq______normal___TRUE │ 112 │ brainstem and cerebellar structures │ 319 │ 155.76816999942093 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 12 │ 5 │ 46 │ 879c4ae3bde35ba36f2e1c8a93cd3041___1.h5ad │ 9b343989f3f7c7bbcdcbb8723ec4899a___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Neurons │ Plasmacytoid dendritic cells │ Other │ NULL │ NULL │ 55 │ unknown │ cellxgene_2024/0.2.1 │ yyek8Mgo!y │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7a2a38009ef83ef029bb34d4951a079___exp4-human-119well. │ glutamatergic neuron │ CL:0000679 │ sci-RNA-seq │ EFO:0010550 │ 16th week post-fertilization human stage │ HsapDv:0000053 │ normal │ PATO:0000461 │ H27423 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ male │ PATO:0000384 │ telencephalon │ UBERON:0001893 │ Publication: https://doi.org/10.1126/science.aba7721 Dataset Version: https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/c114c20f-1ef4-49a5-9c2e-d965787fb90c │ c114c20f-1ef4-49a5-9c2e-d965787fb90c │ 8f6296d0-5b29-4dca-8061-b97147df5fcc │ NULL │ 2021-06-02 │ raw.X │ 2024-06-11 │ 4062980 │ 5.1.0 │ tissue │ Survey of human embryonic development │ false │ NULL │ https://cellxgene.cziscience.com/e/f7c1c579-2dc0-47e2-ba19-8165c5a0e353.cxg/ │ 4062980 │ 46397 │ 20060284412.0 │ H5AD │ 586.3116402246627 │ nucleus │ https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad │
│ 2374.0 │ N$3BCR3tvL │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7a2a38009ef83ef029bb34d4951a079___exp4-human-119well. │ a7a2a38009ef83ef029bb34d4951a079 │ │ NULL │ H27423___telencephalon___16th week post-fertilization human stage___sci-RNA-seq______normal___TRUE │ 112 │ brainstem and cerebellar structures │ 290 │ 90.22862999946665 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 12 │ 5 │ 46 │ 879c4ae3bde35ba36f2e1c8a93cd3041___1.h5ad │ 9b343989f3f7c7bbcdcbb8723ec4899a___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Neurons │ Progenitor cells │ Other │ NULL │ NULL │ 55 │ unknown │ cellxgene_2024/0.2.1 │ N$3BCR3tvL │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7a2a38009ef83ef029bb34d4951a079___exp4-human-119well. │ glutamatergic neuron │ CL:0000679 │ sci-RNA-seq │ EFO:0010550 │ 16th week post-fertilization human stage │ HsapDv:0000053 │ normal │ PATO:0000461 │ H27423 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ male │ PATO:0000384 │ telencephalon │ UBERON:0001893 │ Publication: https://doi.org/10.1126/science.aba7721 Dataset Version: https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/c114c20f-1ef4-49a5-9c2e-d965787fb90c │ c114c20f-1ef4-49a5-9c2e-d965787fb90c │ 8f6296d0-5b29-4dca-8061-b97147df5fcc │ NULL │ 2021-06-02 │ raw.X │ 2024-06-11 │ 4062980 │ 5.1.0 │ tissue │ Survey of human embryonic development │ false │ NULL │ https://cellxgene.cziscience.com/e/f7c1c579-2dc0-47e2-ba19-8165c5a0e353.cxg/ │ 4062980 │ 46397 │ 20060284412.0 │ H5AD │ 586.3116402246627 │ nucleus │ https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad │
│ 2387.0 │ 6R38v9U4Xh │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7a2a38009ef83ef029bb34d4951a079___exp4-human-119well. │ a7a2a38009ef83ef029bb34d4951a079 │ │ NULL │ H27423___telencephalon___16th week post-fertilization human stage___sci-RNA-seq______normal___TRUE │ 112 │ brainstem and cerebellar structures │ 367 │ 174.77107999935834 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 12 │ 5 │ 46 │ 879c4ae3bde35ba36f2e1c8a93cd3041___1.h5ad │ 9b343989f3f7c7bbcdcbb8723ec4899a___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Neurons │ Progenitor cells │ Other │ NULL │ NULL │ 55 │ unknown │ cellxgene_2024/0.2.1 │ 6R38v9U4Xh │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7a2a38009ef83ef029bb34d4951a079___exp4-human-119well. │ glutamatergic neuron │ CL:0000679 │ sci-RNA-seq │ EFO:0010550 │ 16th week post-fertilization human stage │ HsapDv:0000053 │ normal │ PATO:0000461 │ H27423 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ male │ PATO:0000384 │ telencephalon │ UBERON:0001893 │ Publication: https://doi.org/10.1126/science.aba7721 Dataset Version: https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/c114c20f-1ef4-49a5-9c2e-d965787fb90c │ c114c20f-1ef4-49a5-9c2e-d965787fb90c │ 8f6296d0-5b29-4dca-8061-b97147df5fcc │ NULL │ 2021-06-02 │ raw.X │ 2024-06-11 │ 4062980 │ 5.1.0 │ tissue │ Survey of human embryonic development │ false │ NULL │ https://cellxgene.cziscience.com/e/f7c1c579-2dc0-47e2-ba19-8165c5a0e353.cxg/ │ 4062980 │ 46397 │ 20060284412.0 │ H5AD │ 586.3116402246627 │ nucleus │ https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad │
│ 2375.0 │ un$JcB@omY │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7a2a38009ef83ef029bb34d4951a079___exp4-human-119well. │ a7a2a38009ef83ef029bb34d4951a079 │ │ NULL │ H27423___telencephalon___16th week post-fertilization human stage___sci-RNA-seq______normal___TRUE │ 112 │ brainstem and cerebellar structures │ 469 │ 101.40374999915366 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 12 │ 5 │ 46 │ 879c4ae3bde35ba36f2e1c8a93cd3041___1.h5ad │ 9b343989f3f7c7bbcdcbb8723ec4899a___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Neurons │ Naive B cells │ Other │ NULL │ NULL │ 55 │ unknown │ cellxgene_2024/0.2.1 │ un$JcB@omY │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7a2a38009ef83ef029bb34d4951a079___exp4-human-119well. │ glutamatergic neuron │ CL:0000679 │ sci-RNA-seq │ EFO:0010550 │ 16th week post-fertilization human stage │ HsapDv:0000053 │ normal │ PATO:0000461 │ H27423 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ male │ PATO:0000384 │ telencephalon │ UBERON:0001893 │ Publication: https://doi.org/10.1126/science.aba7721 Dataset Version: https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/c114c20f-1ef4-49a5-9c2e-d965787fb90c │ c114c20f-1ef4-49a5-9c2e-d965787fb90c │ 8f6296d0-5b29-4dca-8061-b97147df5fcc │ NULL │ 2021-06-02 │ raw.X │ 2024-06-11 │ 4062980 │ 5.1.0 │ tissue │ Survey of human embryonic development │ false │ NULL │ https://cellxgene.cziscience.com/e/f7c1c579-2dc0-47e2-ba19-8165c5a0e353.cxg/ │ 4062980 │ 46397 │ 20060284412.0 │ H5AD │ 586.3116402246627 │ nucleus │ https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad │
│ 2420.0 │ !tkM(o&Ic) │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7a2a38009ef83ef029bb34d4951a079___exp4-human-119well. │ a7a2a38009ef83ef029bb34d4951a079 │ │ NULL │ H27423___telencephalon___16th week post-fertilization human stage___sci-RNA-seq______normal___TRUE │ 112 │ brainstem and cerebellar structures │ 269 │ 566.8388499995344 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 12 │ 5 │ 46 │ 879c4ae3bde35ba36f2e1c8a93cd3041___1.h5ad │ 9b343989f3f7c7bbcdcbb8723ec4899a___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Chondrocytes │ Plasmacytoid dendritic cells │ Other │ NULL │ NULL │ 55 │ unknown │ cellxgene_2024/0.2.1 │ !tkM(o&Ic) │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7a2a38009ef83ef029bb34d4951a079___exp4-human-119well. │ glutamatergic neuron │ CL:0000679 │ sci-RNA-seq │ EFO:0010550 │ 16th week post-fertilization human stage │ HsapDv:0000053 │ normal │ PATO:0000461 │ H27423 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ male │ PATO:0000384 │ telencephalon │ UBERON:0001893 │ Publication: https://doi.org/10.1126/science.aba7721 Dataset Version: https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/c114c20f-1ef4-49a5-9c2e-d965787fb90c │ c114c20f-1ef4-49a5-9c2e-d965787fb90c │ 8f6296d0-5b29-4dca-8061-b97147df5fcc │ NULL │ 2021-06-02 │ raw.X │ 2024-06-11 │ 4062980 │ 5.1.0 │ tissue │ Survey of human embryonic development │ false │ NULL │ https://cellxgene.cziscience.com/e/f7c1c579-2dc0-47e2-ba19-8165c5a0e353.cxg/ │ 4062980 │ 46397 │ 20060284412.0 │ H5AD │ 586.3116402246627 │ nucleus │ https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad │
│ 2389.0 │ QJjg~Xrcmh │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7a2a38009ef83ef029bb34d4951a079___exp4-human-119well. │ a7a2a38009ef83ef029bb34d4951a079 │ │ NULL │ H27423___telencephalon___16th week post-fertilization human stage___sci-RNA-seq______normal___TRUE │ 112 │ brainstem and cerebellar structures │ 439 │ 395.9937799992258 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 12 │ 5 │ 46 │ 879c4ae3bde35ba36f2e1c8a93cd3041___1.h5ad │ 9b343989f3f7c7bbcdcbb8723ec4899a___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Neurons │ Natural killer cells │ Other │ NULL │ NULL │ 55 │ unknown │ cellxgene_2024/0.2.1 │ QJjg~Xrcmh │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7a2a38009ef83ef029bb34d4951a079___exp4-human-119well. │ glutamatergic neuron │ CL:0000679 │ sci-RNA-seq │ EFO:0010550 │ 16th week post-fertilization human stage │ HsapDv:0000053 │ normal │ PATO:0000461 │ H27423 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ male │ PATO:0000384 │ telencephalon │ UBERON:0001893 │ Publication: https://doi.org/10.1126/science.aba7721 Dataset Version: https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/c114c20f-1ef4-49a5-9c2e-d965787fb90c │ c114c20f-1ef4-49a5-9c2e-d965787fb90c │ 8f6296d0-5b29-4dca-8061-b97147df5fcc │ NULL │ 2021-06-02 │ raw.X │ 2024-06-11 │ 4062980 │ 5.1.0 │ tissue │ Survey of human embryonic development │ false │ NULL │ https://cellxgene.cziscience.com/e/f7c1c579-2dc0-47e2-ba19-8165c5a0e353.cxg/ │ 4062980 │ 46397 │ 20060284412.0 │ H5AD │ 586.3116402246627 │ nucleus │ https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad │
│ 6408.0 │ Q+?3zDKBZH │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ fb00a61c604c1fa9e622268d5ac200a4___exp4-human-122well. │ fb00a61c604c1fa9e622268d5ac200a4 │ │ NULL │ H27464___telencephalon___17th week post-fertilization human stage___sci-RNA-seq______normal___TRUE │ 119 │ brainstem and cerebellar structures │ 269 │ 51.996119999868824 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 24 │ 17 │ 95 │ e6cbd0674d0c53922ff9bbcf9b1bfaf2___2.h5ad │ 84d8b1a4a8cd45383a8d8a0ef7082a92___2.h5ad │ 20.0 │ 200.0 │ exp │ true │ Neurons │ Naive CD4 T cells │ HSPC │ NULL │ NULL │ 131 │ unknown │ cellxgene_2024/0.2.1 │ Q+?3zDKBZH │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ fb00a61c604c1fa9e622268d5ac200a4___exp4-human-122well. │ glutamatergic neuron │ CL:0000679 │ sci-RNA-seq │ EFO:0010550 │ 17th week post-fertilization human stage │ HsapDv:0000054 │ normal │ PATO:0000461 │ H27464 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ male │ PATO:0000384 │ telencephalon │ UBERON:0001893 │ Publication: https://doi.org/10.1126/science.aba7721 Dataset Version: https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/c114c20f-1ef4-49a5-9c2e-d965787fb90c │ c114c20f-1ef4-49a5-9c2e-d965787fb90c │ 8f6296d0-5b29-4dca-8061-b97147df5fcc │ NULL │ 2021-06-02 │ raw.X │ 2024-06-11 │ 4062980 │ 5.1.0 │ tissue │ Survey of human embryonic development │ false │ NULL │ https://cellxgene.cziscience.com/e/f7c1c579-2dc0-47e2-ba19-8165c5a0e353.cxg/ │ 4062980 │ 46397 │ 20060284412.0 │ H5AD │ 586.3116402246627 │ nucleus │ https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad │
│ 1721.0 │ um{Xda24Qd │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ fb00a61c604c1fa9e622268d5ac200a4___exp4-human-122well. │ fb00a61c604c1fa9e622268d5ac200a4 │ │ NULL │ H27464___telencephalon___17th week post-fertilization human stage___sci-RNA-seq______normal___TRUE │ 119 │ brainstem and cerebellar structures │ 1291 │ 74.49249999941821 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 24 │ 17 │ 95 │ 4e6bfaad6d76dbb18186e58eefed0aad___1.h5ad │ 84d8b1a4a8cd45383a8d8a0ef7082a92___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Neurons │ Progenitor cells │ HSPC │ NULL │ NULL │ 131 │ unknown │ cellxgene_2024/0.2.1 │ um{Xda24Qd │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ fb00a61c604c1fa9e622268d5ac200a4___exp4-human-122well. │ GABAergic neuron │ CL:0000617 │ sci-RNA-seq │ EFO:0010550 │ 17th week post-fertilization human stage │ HsapDv:0000054 │ normal │ PATO:0000461 │ H27464 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ male │ PATO:0000384 │ telencephalon │ UBERON:0001893 │ Publication: https://doi.org/10.1126/science.aba7721 Dataset Version: https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/c114c20f-1ef4-49a5-9c2e-d965787fb90c │ c114c20f-1ef4-49a5-9c2e-d965787fb90c │ 8f6296d0-5b29-4dca-8061-b97147df5fcc │ NULL │ 2021-06-02 │ raw.X │ 2024-06-11 │ 4062980 │ 5.1.0 │ tissue │ Survey of human embryonic development │ false │ NULL │ https://cellxgene.cziscience.com/e/f7c1c579-2dc0-47e2-ba19-8165c5a0e353.cxg/ │ 4062980 │ 46397 │ 20060284412.0 │ H5AD │ 586.3116402246627 │ nucleus │ https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad │
│ 1729.0 │ VX+asi9z{^ │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ fb00a61c604c1fa9e622268d5ac200a4___exp4-human-122well. │ fb00a61c604c1fa9e622268d5ac200a4 │ │ NULL │ H27464___telencephalon___17th week post-fertilization human stage___sci-RNA-seq______normal___TRUE │ 119 │ brainstem and cerebellar structures │ 200 │ 75.61701999989964 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 24 │ 17 │ 95 │ 4e6bfaad6d76dbb18186e58eefed0aad___1.h5ad │ 84d8b1a4a8cd45383a8d8a0ef7082a92___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Neurons │ Progenitor cells │ HSPC │ NULL │ NULL │ 131 │ unknown │ cellxgene_2024/0.2.1 │ VX+asi9z{^ │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ fb00a61c604c1fa9e622268d5ac200a4___exp4-human-122well. │ GABAergic neuron │ CL:0000617 │ sci-RNA-seq │ EFO:0010550 │ 17th week post-fertilization human stage │ HsapDv:0000054 │ normal │ PATO:0000461 │ H27464 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ male │ PATO:0000384 │ telencephalon │ UBERON:0001893 │ Publication: https://doi.org/10.1126/science.aba7721 Dataset Version: https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/c114c20f-1ef4-49a5-9c2e-d965787fb90c │ c114c20f-1ef4-49a5-9c2e-d965787fb90c │ 8f6296d0-5b29-4dca-8061-b97147df5fcc │ NULL │ 2021-06-02 │ raw.X │ 2024-06-11 │ 4062980 │ 5.1.0 │ tissue │ Survey of human embryonic development │ false │ NULL │ https://cellxgene.cziscience.com/e/f7c1c579-2dc0-47e2-ba19-8165c5a0e353.cxg/ │ 4062980 │ 46397 │ 20060284412.0 │ H5AD │ 586.3116402246627 │ nucleus │ https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ 4074.0 │ *?+vH_WXcP │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 120240563ab864f3cd5dcf65987cb3a2 │ 120240563ab864f3cd5dcf65987cb3a2 │ │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747177I___lung___unknown___10x 3' v2______pulmonary fibrosis___TRUE │ NULL │ respiratory system │ 964 │ 5891.660130000004 │ false │ macrophage │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 11 │ 2 │ 97771b1daba722c24ed6cc9fdb09e34b___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Macrophages │ Intermediate monocytes │ CD14 Mono │ NULL │ NULL │ 3092 │ unknown │ cellxgene_2024/0.2.1 │ *?+vH_WXcP │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 120240563ab864f3cd5dcf65987cb3a2 │ alveolar macrophage │ CL:0000583 │ 10x 3' v2 │ EFO:0009899 │ unknown │ unknown │ pulmonary fibrosis │ MONDO:0002771 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747177I │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ unknown │ unknown │ lung │ UBERON:0002048 │ 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 │
│ 4401.0 │ (AL8BHo#!= │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 120240563ab864f3cd5dcf65987cb3a2 │ 120240563ab864f3cd5dcf65987cb3a2 │ │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747177I___lung___unknown___10x 3' v2______pulmonary fibrosis___TRUE │ NULL │ respiratory system │ 4126 │ 5831.325350000039 │ false │ macrophage │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 11 │ 2 │ 97771b1daba722c24ed6cc9fdb09e34b___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Macrophages │ Classical monocytes │ CD14 Mono │ NULL │ NULL │ 3092 │ unknown │ cellxgene_2024/0.2.1 │ (AL8BHo#!= │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 120240563ab864f3cd5dcf65987cb3a2 │ alveolar macrophage │ CL:0000583 │ 10x 3' v2 │ EFO:0009899 │ unknown │ unknown │ pulmonary fibrosis │ MONDO:0002771 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747177I │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ unknown │ unknown │ lung │ UBERON:0002048 │ 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 │
│ 4949.0 │ MUC^Qo$1T8 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 120240563ab864f3cd5dcf65987cb3a2 │ 120240563ab864f3cd5dcf65987cb3a2 │ │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747177I___lung___unknown___10x 3' v2______pulmonary fibrosis___TRUE │ NULL │ respiratory system │ 1604 │ 6520.7126499999895 │ false │ monocytic │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 11 │ 2 │ 97771b1daba722c24ed6cc9fdb09e34b___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Monocytes │ Classical monocytes │ CD14 Mono │ NULL │ NULL │ 42 │ unknown │ cellxgene_2024/0.2.1 │ MUC^Qo$1T8 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 120240563ab864f3cd5dcf65987cb3a2 │ alveolar macrophage │ CL:0000583 │ 10x 3' v2 │ EFO:0009899 │ unknown │ unknown │ pulmonary fibrosis │ MONDO:0002771 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747177I │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ unknown │ unknown │ lung │ UBERON:0002048 │ 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 │
│ 3019.0 │ JZxV3`8xJ^ │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 120240563ab864f3cd5dcf65987cb3a2 │ 120240563ab864f3cd5dcf65987cb3a2 │ │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747177I___lung___unknown___10x 3' v2______pulmonary fibrosis___TRUE │ NULL │ respiratory system │ 3035 │ 5720.999150000003 │ false │ macrophage │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 11 │ 2 │ 97771b1daba722c24ed6cc9fdb09e34b___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Macrophages │ Intermediate monocytes │ CD14 Mono │ NULL │ NULL │ 3092 │ unknown │ cellxgene_2024/0.2.1 │ JZxV3`8xJ^ │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 120240563ab864f3cd5dcf65987cb3a2 │ alveolar macrophage │ CL:0000583 │ 10x 3' v2 │ EFO:0009899 │ unknown │ unknown │ pulmonary fibrosis │ MONDO:0002771 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747177I │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ unknown │ unknown │ lung │ UBERON:0002048 │ 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 │
│ 1505.0 │ <h9A*Wy3M7 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 120240563ab864f3cd5dcf65987cb3a2 │ 120240563ab864f3cd5dcf65987cb3a2 │ │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747177I___lung___unknown___10x 3' v2______pulmonary fibrosis___TRUE │ NULL │ respiratory system │ 3378 │ 5864.594629999974 │ false │ other │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 11 │ 2 │ 5a9e9e73b16c4d4758dbc8c6c9b97dcd___2.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___2.h5ad │ 20.0 │ 200.0 │ exp │ true │ Macrophages │ Intermediate monocytes │ CD14 Mono │ NULL │ NULL │ 1679 │ unknown │ cellxgene_2024/0.2.1 │ <h9A*Wy3M7 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 120240563ab864f3cd5dcf65987cb3a2 │ unknown │ unknown │ 10x 3' v2 │ EFO:0009899 │ unknown │ unknown │ pulmonary fibrosis │ MONDO:0002771 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747177I │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ unknown │ unknown │ lung │ UBERON:0002048 │ 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 │
│ 842.0 │ )ce28WXCfZ │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 120240563ab864f3cd5dcf65987cb3a2 │ 120240563ab864f3cd5dcf65987cb3a2 │ │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747177I___lung___unknown___10x 3' v2______pulmonary fibrosis___TRUE │ NULL │ respiratory system │ 3955 │ 6092.993720000001 │ false │ other │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 11 │ 2 │ 5a9e9e73b16c4d4758dbc8c6c9b97dcd___2.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___2.h5ad │ 20.0 │ 200.0 │ exp │ true │ Macrophages │ Classical monocytes │ CD14 Mono │ NULL │ NULL │ 1679 │ unknown │ cellxgene_2024/0.2.1 │ )ce28WXCfZ │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 120240563ab864f3cd5dcf65987cb3a2 │ unknown │ unknown │ 10x 3' v2 │ EFO:0009899 │ unknown │ unknown │ pulmonary fibrosis │ MONDO:0002771 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747177I │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ unknown │ unknown │ lung │ UBERON:0002048 │ 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 │
│ 3708.0 │ _Wy=Mh2Z-s │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 120240563ab864f3cd5dcf65987cb3a2 │ 120240563ab864f3cd5dcf65987cb3a2 │ │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747177I___lung___unknown___10x 3' v2______pulmonary fibrosis___TRUE │ NULL │ respiratory system │ 3121 │ 5877.761460000002 │ false │ macrophage │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 11 │ 2 │ 97771b1daba722c24ed6cc9fdb09e34b___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Macrophages │ Myeloid dendritic cells │ CD14 Mono │ NULL │ NULL │ 3092 │ unknown │ cellxgene_2024/0.2.1 │ _Wy=Mh2Z-s │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 120240563ab864f3cd5dcf65987cb3a2 │ alveolar macrophage │ CL:0000583 │ 10x 3' v2 │ EFO:0009899 │ unknown │ unknown │ pulmonary fibrosis │ MONDO:0002771 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747177I │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ unknown │ unknown │ lung │ UBERON:0002048 │ 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 │
│ 3926.0 │ z&&NCv<!oD │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 120240563ab864f3cd5dcf65987cb3a2 │ 120240563ab864f3cd5dcf65987cb3a2 │ │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747177I___lung___unknown___10x 3' v2______pulmonary fibrosis___TRUE │ NULL │ respiratory system │ 2153 │ 5026.990319999998 │ false │ macrophage │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 11 │ 2 │ 97771b1daba722c24ed6cc9fdb09e34b___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Macrophages │ Intermediate monocytes │ CD14 Mono │ NULL │ NULL │ 3092 │ unknown │ cellxgene_2024/0.2.1 │ z&&NCv<!oD │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 120240563ab864f3cd5dcf65987cb3a2 │ alveolar macrophage │ CL:0000583 │ 10x 3' v2 │ EFO:0009899 │ unknown │ unknown │ pulmonary fibrosis │ MONDO:0002771 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747177I │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ unknown │ unknown │ lung │ UBERON:0002048 │ 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 │
│ 1182.0 │ 6i4!vU@F5h │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 120240563ab864f3cd5dcf65987cb3a2 │ 120240563ab864f3cd5dcf65987cb3a2 │ │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747177I___lung___unknown___10x 3' v2______pulmonary fibrosis___TRUE │ NULL │ respiratory system │ 1571 │ 4662.853049999993 │ false │ other │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 11 │ 2 │ 5a9e9e73b16c4d4758dbc8c6c9b97dcd___2.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___2.h5ad │ 20.0 │ 200.0 │ exp │ true │ Macrophages │ Myeloid dendritic cells │ CD14 Mono │ NULL │ NULL │ 1679 │ unknown │ cellxgene_2024/0.2.1 │ 6i4!vU@F5h │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 120240563ab864f3cd5dcf65987cb3a2 │ unknown │ unknown │ 10x 3' v2 │ EFO:0009899 │ unknown │ unknown │ pulmonary fibrosis │ MONDO:0002771 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747177I │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ unknown │ unknown │ lung │ UBERON:0002048 │ 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 │
│ 1311.0 │ (CU)nI~@Vu │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 120240563ab864f3cd5dcf65987cb3a2 │ 120240563ab864f3cd5dcf65987cb3a2 │ │ NULL │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747177I___lung___unknown___10x 3' v2______pulmonary fibrosis___TRUE │ NULL │ respiratory system │ 1392 │ 5741.545879999989 │ false │ other │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 11 │ 2 │ 5a9e9e73b16c4d4758dbc8c6c9b97dcd___2.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___2.h5ad │ 20.0 │ 200.0 │ exp │ true │ Macrophages │ Intermediate monocytes │ CD14 Mono │ NULL │ NULL │ 1679 │ unknown │ cellxgene_2024/0.2.1 │ (CU)nI~@Vu │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 120240563ab864f3cd5dcf65987cb3a2 │ unknown │ unknown │ 10x 3' v2 │ EFO:0009899 │ unknown │ unknown │ pulmonary fibrosis │ MONDO:0002771 │ homosapiens_None_2023_None_sikkemalisa_002_d10_1101_2022_03_10_483747177I │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ unknown │ unknown │ lung │ UBERON:0002048 │ 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 │
└─────────┴────────────────────┴──────────────────────────────────────┴────────────────────────────────────────────────────────┴──────────────────────────────────┴───────────────┴──────────────────┴───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┴──────────┴─────────────────────────────────────┴──────────────────────────────┴────────────────────┴───────────────┴────────────────────────────┴───────────┴──────────────────────┴──────────────────────┴────────────────────┴───────────────┴───────────────────┴──────────────┴────────────┴─────────────────────────┴───────────────────────────────────────────┴───────────────────────────────────────────┴───────────────────┴───────────────────────────┴───────────────────┴─────────┴───────────────────────────────────┴────────────────────────────────┴────────────────────────────┴──────────────────────────┴──────────────────────────┴───────────────────┴───────────────────┴──────────────────────┴────────────────────┴──────────────────────────────────────┴────────────────────────────────────────────────────────┴──────────────────────┴────────────────────────────┴─────────────┴────────────────────────┴──────────────────────────────────────────┴────────────────────────────────────┴────────────────────┴──────────────────────────┴───────────────────────────────────────────────────────────────────────────┴─────────────────┴──────────────┴───────────────────────────┴─────────────────────────┴──────────────────────────────────────────┴─────────┴──────────────────────┴───────────────┴─────────────────────────┴────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┴──────────────────────────────────────┴──────────────────────────────────────┴───────────────────┴──────────────┴───────────────────┴────────────┴────────────────────┴────────────────┴─────────────┴─────────────────────────────────────────────────────────────────────────┴───────────┴────────────────────────────┴──────────────────────────────────────────────────────────────────────────────┴────────────┴───────────────┴───────────────┴──────────┴─────────────────────┴─────────────────┴─────────────────────────────────────────────────────────────────────────────────────┘
? 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 │
├─────────────────────────────┼────────────────────────────┼───────┤
│ small intestine │ other │ 431 │
│ ileum │ ilc │ 2319 │
│ ileum │ mast │ 4913 │
│ ileal epithelium │ tgd │ 22 │
│ colonic epithelium │ other │ 387 │
│ colon │ tgd │ 1 │
│ left colon │ monocytic │ 21 │
│ lung │ b memory │ 38011 │
│ lung │ cd4 th1 em │ 15270 │
│ lung │ cdc │ 49477 │
│ · │ · │ · │
│ · │ · │ · │
│ · │ · │ · │
│ heart right ventricle │ cd4 fh em │ 3 │
│ prostate gland │ cd4 naive │ 1 │
│ testis │ granulocyte │ 9 │
│ descending colon │ ilc │ 1 │
│ skin of chest │ cd4 fh em │ 5 │
│ submucosal esophageal gland │ cd4 th1 em │ 1 │
│ skin of abdomen │ cd4 th1/th17 em │ 3 │
│ renal papilla │ cd4 naive │ 1 │
│ sclera │ cd4 th17 em │ 2 │
│ peripheral zone of prostate │ t cd4 │ 1 │
└─────────────────────────────┴────────────────────────────┴───────┘
6413 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 │
├─────────┼────────────────────┼──────────────────────────────────────┼──────────────────────────────────────────────────┼──────────────────────────────────┼───────────────┼──────────────────┼──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┼──────────┼─────────────────────────────────────┼──────────────────────────────┼───────────────────┼───────────────┼────────────────────────────┼───────────┼──────────────────────┼──────────────────────┼────────────────────┼───────────────┼───────────────────┼──────────────┼────────────┼─────────────────────────┼───────────────────────────────────────────┼───────────────────────────────────────────┼───────────────────┼───────────────────────────┼───────────────────┼─────────┼───────────────────────────────────┼────────────────────────────────┼────────────────────────────┼──────────────────────────┼──────────────────────────┼───────────────────┼───────────────────┼──────────────────────┼────────────────────┼──────────────────────────────────────┼──────────────────────────────────────────────────┼─────────────────────────────────┼────────────────────────────┼───────────┼────────────────────────┼─────────────────────────┼────────────────────────────────────┼─────────┼──────────────────────────┼───────────────────────────────────────────────────────────────────────────┼─────────────────┼──────────────┼───────────────────────────┼─────────────────────────┼──────────────────────────────────────────┼─────────┼──────────────────────┼─────────────────┼─────────────────────────┼────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┼──────────────────────────────────────┼──────────────────────────────────────┼───────────────────┼──────────────┼───────────────────┼────────────┼────────────────────┼────────────────┼─────────────┼─────────────────────────────────────────────────────────────────────────┼───────────┼────────────────────────────┼──────────────────────────────────────────────────────────────────────────────┼────────────┼───────────────┼───────────────┼──────────┼─────────────────────┼─────────────────┼─────────────────────────────────────────────────────────────────────────────────────┤
│ 83.0 │ rqPaQiAr79 │ edc8d3fe-153c-4e3d-8be0-2108d30f8d70 │ 16af564bc3cbc7ae6ac41cebefa08f2e │ 16af564bc3cbc7ae6ac41cebefa08f2e │ │ NULL │ AN9___nasal cavity___human adult stage___10x 5' v1______normal___TRUE │ 14600 │ nasal, oral, and pharyngeal regions │ 3659 │ 8930.822090000003 │ false │ secretory │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ 07043d1851ce115fd54efa0c8472c1ce___1.h5ad │ ffc7a76b3cbedaa608e5935f55291dd2___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Epithelial cells │ Classical monocytes │ CD4 TCM │ 1.0 │ FALSE │ 1180 │ African │ cellxgene_2024/0.2.1 │ rqPaQiAr79 │ edc8d3fe-153c-4e3d-8be0-2108d30f8d70 │ 16af564bc3cbc7ae6ac41cebefa08f2e │ tracheal goblet cell │ CL:1000329 │ 10x 5' v1 │ EFO:0011025 │ human adult stage │ HsapDv:0000087 │ normal │ PATO:0000461 │ AN9 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ nasal cavity │ UBERON:0001707 │ Publication: https://doi.org/10.1038/s41586-021-04345-x Dataset Version: https://datasets.cellxgene.cziscience.com/69be948c-03f4-46e8-896e-530c79080808.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/03f821b4-87be-4ff4-b65a-b5fc00061da7 │ 03f821b4-87be-4ff4-b65a-b5fc00061da7 │ 69be948c-03f4-46e8-896e-530c79080808 │ X_umap │ 2022-03-24 │ raw.X │ 2024-06-11 │ 236977 │ 5.1.0 │ tissue │ Airway │ false │ NULL │ https://cellxgene.cziscience.com/e/edc8d3fe-153c-4e3d-8be0-2108d30f8d70.cxg/ │ 236977 │ 33145 │ 3612172554.0 │ H5AD │ 2078.208851491917 │ cell │ https://datasets.cellxgene.cziscience.com/69be948c-03f4-46e8-896e-530c79080808.h5ad │
│ 3.0 │ D6K<>x_iX3 │ edc8d3fe-153c-4e3d-8be0-2108d30f8d70 │ 16af564bc3cbc7ae6ac41cebefa08f2e │ 16af564bc3cbc7ae6ac41cebefa08f2e │ │ NULL │ AN9___nasal cavity___human adult stage___10x 5' v1______normal___TRUE │ 14600 │ nasal, oral, and pharyngeal regions │ 2844 │ 8194.458260000003 │ false │ mast │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ 7b72cf7b4f0e9fe2c5e412ea2d971da1___1.h5ad │ ffc7a76b3cbedaa608e5935f55291dd2___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ MEP │ Low-density basophils │ CD4 TCM │ 1.0 │ FALSE │ 4 │ African │ cellxgene_2024/0.2.1 │ D6K<>x_iX3 │ edc8d3fe-153c-4e3d-8be0-2108d30f8d70 │ 16af564bc3cbc7ae6ac41cebefa08f2e │ mast cell │ CL:0000097 │ 10x 5' v1 │ EFO:0011025 │ human adult stage │ HsapDv:0000087 │ normal │ PATO:0000461 │ AN9 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ nasal cavity │ UBERON:0001707 │ Publication: https://doi.org/10.1038/s41586-021-04345-x Dataset Version: https://datasets.cellxgene.cziscience.com/69be948c-03f4-46e8-896e-530c79080808.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/03f821b4-87be-4ff4-b65a-b5fc00061da7 │ 03f821b4-87be-4ff4-b65a-b5fc00061da7 │ 69be948c-03f4-46e8-896e-530c79080808 │ X_umap │ 2022-03-24 │ raw.X │ 2024-06-11 │ 236977 │ 5.1.0 │ tissue │ Airway │ false │ NULL │ https://cellxgene.cziscience.com/e/edc8d3fe-153c-4e3d-8be0-2108d30f8d70.cxg/ │ 236977 │ 33145 │ 3612172554.0 │ H5AD │ 2078.208851491917 │ cell │ https://datasets.cellxgene.cziscience.com/69be948c-03f4-46e8-896e-530c79080808.h5ad │
│ 445.0 │ l61uIvGC5D │ edc8d3fe-153c-4e3d-8be0-2108d30f8d70 │ 16af564bc3cbc7ae6ac41cebefa08f2e │ 16af564bc3cbc7ae6ac41cebefa08f2e │ │ NULL │ AN9___nasal cavity___human adult stage___10x 5' v1______normal___TRUE │ 14600 │ nasal, oral, and pharyngeal regions │ 2801 │ 8067.58465 │ false │ secretory │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ 07043d1851ce115fd54efa0c8472c1ce___1.h5ad │ ffc7a76b3cbedaa608e5935f55291dd2___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Epithelial cells │ Non classical monocytes │ CD4 TCM │ 1.0 │ FALSE │ 1180 │ African │ cellxgene_2024/0.2.1 │ l61uIvGC5D │ edc8d3fe-153c-4e3d-8be0-2108d30f8d70 │ 16af564bc3cbc7ae6ac41cebefa08f2e │ tracheal goblet cell │ CL:1000329 │ 10x 5' v1 │ EFO:0011025 │ human adult stage │ HsapDv:0000087 │ normal │ PATO:0000461 │ AN9 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ nasal cavity │ UBERON:0001707 │ Publication: https://doi.org/10.1038/s41586-021-04345-x Dataset Version: https://datasets.cellxgene.cziscience.com/69be948c-03f4-46e8-896e-530c79080808.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/03f821b4-87be-4ff4-b65a-b5fc00061da7 │ 03f821b4-87be-4ff4-b65a-b5fc00061da7 │ 69be948c-03f4-46e8-896e-530c79080808 │ X_umap │ 2022-03-24 │ raw.X │ 2024-06-11 │ 236977 │ 5.1.0 │ tissue │ Airway │ false │ NULL │ https://cellxgene.cziscience.com/e/edc8d3fe-153c-4e3d-8be0-2108d30f8d70.cxg/ │ 236977 │ 33145 │ 3612172554.0 │ H5AD │ 2078.208851491917 │ cell │ https://datasets.cellxgene.cziscience.com/69be948c-03f4-46e8-896e-530c79080808.h5ad │
│ 473.0 │ G^mTo&@hZj │ edc8d3fe-153c-4e3d-8be0-2108d30f8d70 │ 16af564bc3cbc7ae6ac41cebefa08f2e │ 16af564bc3cbc7ae6ac41cebefa08f2e │ │ NULL │ AN9___nasal cavity___human adult stage___10x 5' v1______normal___TRUE │ 14600 │ nasal, oral, and pharyngeal regions │ 3151 │ 8901.910449999998 │ false │ secretory │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ 07043d1851ce115fd54efa0c8472c1ce___1.h5ad │ ffc7a76b3cbedaa608e5935f55291dd2___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Epithelial cells │ Myeloid dendritic cells │ CD4 TCM │ 1.0 │ FALSE │ 1180 │ African │ cellxgene_2024/0.2.1 │ G^mTo&@hZj │ edc8d3fe-153c-4e3d-8be0-2108d30f8d70 │ 16af564bc3cbc7ae6ac41cebefa08f2e │ tracheal goblet cell │ CL:1000329 │ 10x 5' v1 │ EFO:0011025 │ human adult stage │ HsapDv:0000087 │ normal │ PATO:0000461 │ AN9 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ nasal cavity │ UBERON:0001707 │ Publication: https://doi.org/10.1038/s41586-021-04345-x Dataset Version: https://datasets.cellxgene.cziscience.com/69be948c-03f4-46e8-896e-530c79080808.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/03f821b4-87be-4ff4-b65a-b5fc00061da7 │ 03f821b4-87be-4ff4-b65a-b5fc00061da7 │ 69be948c-03f4-46e8-896e-530c79080808 │ X_umap │ 2022-03-24 │ raw.X │ 2024-06-11 │ 236977 │ 5.1.0 │ tissue │ Airway │ false │ NULL │ https://cellxgene.cziscience.com/e/edc8d3fe-153c-4e3d-8be0-2108d30f8d70.cxg/ │ 236977 │ 33145 │ 3612172554.0 │ H5AD │ 2078.208851491917 │ cell │ https://datasets.cellxgene.cziscience.com/69be948c-03f4-46e8-896e-530c79080808.h5ad │
│ 506.0 │ Is{bN@|~A~ │ edc8d3fe-153c-4e3d-8be0-2108d30f8d70 │ 16af564bc3cbc7ae6ac41cebefa08f2e │ 16af564bc3cbc7ae6ac41cebefa08f2e │ │ NULL │ AN9___nasal cavity___human adult stage___10x 5' v1______normal___TRUE │ 14600 │ nasal, oral, and pharyngeal regions │ 4149 │ 8826.95317 │ false │ epithelial │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ 8e746462b4d9619928369bfd17ebf504___1.h5ad │ ffc7a76b3cbedaa608e5935f55291dd2___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Epithelial cells │ Intermediate monocytes │ CD4 TCM │ 1.0 │ FALSE │ 138 │ African │ cellxgene_2024/0.2.1 │ Is{bN@|~A~ │ edc8d3fe-153c-4e3d-8be0-2108d30f8d70 │ 16af564bc3cbc7ae6ac41cebefa08f2e │ ciliated cell │ CL:0000064 │ 10x 5' v1 │ EFO:0011025 │ human adult stage │ HsapDv:0000087 │ normal │ PATO:0000461 │ AN9 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ nasal cavity │ UBERON:0001707 │ Publication: https://doi.org/10.1038/s41586-021-04345-x Dataset Version: https://datasets.cellxgene.cziscience.com/69be948c-03f4-46e8-896e-530c79080808.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/03f821b4-87be-4ff4-b65a-b5fc00061da7 │ 03f821b4-87be-4ff4-b65a-b5fc00061da7 │ 69be948c-03f4-46e8-896e-530c79080808 │ X_umap │ 2022-03-24 │ raw.X │ 2024-06-11 │ 236977 │ 5.1.0 │ tissue │ Airway │ false │ NULL │ https://cellxgene.cziscience.com/e/edc8d3fe-153c-4e3d-8be0-2108d30f8d70.cxg/ │ 236977 │ 33145 │ 3612172554.0 │ H5AD │ 2078.208851491917 │ cell │ https://datasets.cellxgene.cziscience.com/69be948c-03f4-46e8-896e-530c79080808.h5ad │
│ 694.0 │ f3kmm-coD# │ edc8d3fe-153c-4e3d-8be0-2108d30f8d70 │ 16af564bc3cbc7ae6ac41cebefa08f2e │ 16af564bc3cbc7ae6ac41cebefa08f2e │ │ NULL │ AN9___nasal cavity___human adult stage___10x 5' v1______normal___TRUE │ 14600 │ nasal, oral, and pharyngeal regions │ 878 │ 8863.955789999998 │ false │ secretory │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ 07043d1851ce115fd54efa0c8472c1ce___1.h5ad │ ffc7a76b3cbedaa608e5935f55291dd2___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Epithelial cells │ Intermediate monocytes │ CD4 TCM │ 1.0 │ FALSE │ 1180 │ African │ cellxgene_2024/0.2.1 │ f3kmm-coD# │ edc8d3fe-153c-4e3d-8be0-2108d30f8d70 │ 16af564bc3cbc7ae6ac41cebefa08f2e │ tracheal goblet cell │ CL:1000329 │ 10x 5' v1 │ EFO:0011025 │ human adult stage │ HsapDv:0000087 │ normal │ PATO:0000461 │ AN9 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ nasal cavity │ UBERON:0001707 │ Publication: https://doi.org/10.1038/s41586-021-04345-x Dataset Version: https://datasets.cellxgene.cziscience.com/69be948c-03f4-46e8-896e-530c79080808.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/03f821b4-87be-4ff4-b65a-b5fc00061da7 │ 03f821b4-87be-4ff4-b65a-b5fc00061da7 │ 69be948c-03f4-46e8-896e-530c79080808 │ X_umap │ 2022-03-24 │ raw.X │ 2024-06-11 │ 236977 │ 5.1.0 │ tissue │ Airway │ false │ NULL │ https://cellxgene.cziscience.com/e/edc8d3fe-153c-4e3d-8be0-2108d30f8d70.cxg/ │ 236977 │ 33145 │ 3612172554.0 │ H5AD │ 2078.208851491917 │ cell │ https://datasets.cellxgene.cziscience.com/69be948c-03f4-46e8-896e-530c79080808.h5ad │
│ 1121.0 │ rJPqb5E*@O │ edc8d3fe-153c-4e3d-8be0-2108d30f8d70 │ 16af564bc3cbc7ae6ac41cebefa08f2e │ 16af564bc3cbc7ae6ac41cebefa08f2e │ │ NULL │ AN9___nasal cavity___human adult stage___10x 5' v1______normal___TRUE │ 14600 │ nasal, oral, and pharyngeal regions │ 526 │ 8323.492890000001 │ false │ secretory │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ 07043d1851ce115fd54efa0c8472c1ce___1.h5ad │ ffc7a76b3cbedaa608e5935f55291dd2___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Epithelial cells │ Intermediate monocytes │ CD4 TCM │ 1.0 │ FALSE │ 1180 │ African │ cellxgene_2024/0.2.1 │ rJPqb5E*@O │ edc8d3fe-153c-4e3d-8be0-2108d30f8d70 │ 16af564bc3cbc7ae6ac41cebefa08f2e │ tracheal goblet cell │ CL:1000329 │ 10x 5' v1 │ EFO:0011025 │ human adult stage │ HsapDv:0000087 │ normal │ PATO:0000461 │ AN9 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ nasal cavity │ UBERON:0001707 │ Publication: https://doi.org/10.1038/s41586-021-04345-x Dataset Version: https://datasets.cellxgene.cziscience.com/69be948c-03f4-46e8-896e-530c79080808.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/03f821b4-87be-4ff4-b65a-b5fc00061da7 │ 03f821b4-87be-4ff4-b65a-b5fc00061da7 │ 69be948c-03f4-46e8-896e-530c79080808 │ X_umap │ 2022-03-24 │ raw.X │ 2024-06-11 │ 236977 │ 5.1.0 │ tissue │ Airway │ false │ NULL │ https://cellxgene.cziscience.com/e/edc8d3fe-153c-4e3d-8be0-2108d30f8d70.cxg/ │ 236977 │ 33145 │ 3612172554.0 │ H5AD │ 2078.208851491917 │ cell │ https://datasets.cellxgene.cziscience.com/69be948c-03f4-46e8-896e-530c79080808.h5ad │
│ 1665.0 │ 0c*l8dHood │ edc8d3fe-153c-4e3d-8be0-2108d30f8d70 │ 16af564bc3cbc7ae6ac41cebefa08f2e │ 16af564bc3cbc7ae6ac41cebefa08f2e │ │ NULL │ AN9___nasal cavity___human adult stage___10x 5' v1______normal___TRUE │ 14600 │ nasal, oral, and pharyngeal regions │ 949 │ 8375.536209999997 │ false │ secretory │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ 07043d1851ce115fd54efa0c8472c1ce___1.h5ad │ ffc7a76b3cbedaa608e5935f55291dd2___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Epithelial cells │ Myeloid dendritic cells │ CD4 TCM │ 1.0 │ FALSE │ 1180 │ African │ cellxgene_2024/0.2.1 │ 0c*l8dHood │ edc8d3fe-153c-4e3d-8be0-2108d30f8d70 │ 16af564bc3cbc7ae6ac41cebefa08f2e │ tracheal goblet cell │ CL:1000329 │ 10x 5' v1 │ EFO:0011025 │ human adult stage │ HsapDv:0000087 │ normal │ PATO:0000461 │ AN9 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ nasal cavity │ UBERON:0001707 │ Publication: https://doi.org/10.1038/s41586-021-04345-x Dataset Version: https://datasets.cellxgene.cziscience.com/69be948c-03f4-46e8-896e-530c79080808.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/03f821b4-87be-4ff4-b65a-b5fc00061da7 │ 03f821b4-87be-4ff4-b65a-b5fc00061da7 │ 69be948c-03f4-46e8-896e-530c79080808 │ X_umap │ 2022-03-24 │ raw.X │ 2024-06-11 │ 236977 │ 5.1.0 │ tissue │ Airway │ false │ NULL │ https://cellxgene.cziscience.com/e/edc8d3fe-153c-4e3d-8be0-2108d30f8d70.cxg/ │ 236977 │ 33145 │ 3612172554.0 │ H5AD │ 2078.208851491917 │ cell │ https://datasets.cellxgene.cziscience.com/69be948c-03f4-46e8-896e-530c79080808.h5ad │
│ 1679.0 │ RhL})tU$F; │ edc8d3fe-153c-4e3d-8be0-2108d30f8d70 │ 16af564bc3cbc7ae6ac41cebefa08f2e │ 16af564bc3cbc7ae6ac41cebefa08f2e │ │ NULL │ AN9___nasal cavity___human adult stage___10x 5' v1______normal___TRUE │ 14600 │ nasal, oral, and pharyngeal regions │ 774 │ 8447.617640000002 │ false │ secretory │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ 07043d1851ce115fd54efa0c8472c1ce___1.h5ad │ ffc7a76b3cbedaa608e5935f55291dd2___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Epithelial cells │ Intermediate monocytes │ CD4 TCM │ 1.0 │ FALSE │ 1180 │ African │ cellxgene_2024/0.2.1 │ RhL})tU$F; │ edc8d3fe-153c-4e3d-8be0-2108d30f8d70 │ 16af564bc3cbc7ae6ac41cebefa08f2e │ tracheal goblet cell │ CL:1000329 │ 10x 5' v1 │ EFO:0011025 │ human adult stage │ HsapDv:0000087 │ normal │ PATO:0000461 │ AN9 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ nasal cavity │ UBERON:0001707 │ Publication: https://doi.org/10.1038/s41586-021-04345-x Dataset Version: https://datasets.cellxgene.cziscience.com/69be948c-03f4-46e8-896e-530c79080808.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/03f821b4-87be-4ff4-b65a-b5fc00061da7 │ 03f821b4-87be-4ff4-b65a-b5fc00061da7 │ 69be948c-03f4-46e8-896e-530c79080808 │ X_umap │ 2022-03-24 │ raw.X │ 2024-06-11 │ 236977 │ 5.1.0 │ tissue │ Airway │ false │ NULL │ https://cellxgene.cziscience.com/e/edc8d3fe-153c-4e3d-8be0-2108d30f8d70.cxg/ │ 236977 │ 33145 │ 3612172554.0 │ H5AD │ 2078.208851491917 │ cell │ https://datasets.cellxgene.cziscience.com/69be948c-03f4-46e8-896e-530c79080808.h5ad │
│ 1836.0 │ WJt7EvvK>{ │ edc8d3fe-153c-4e3d-8be0-2108d30f8d70 │ 16af564bc3cbc7ae6ac41cebefa08f2e │ 16af564bc3cbc7ae6ac41cebefa08f2e │ │ NULL │ AN9___nasal cavity___human adult stage___10x 5' v1______normal___TRUE │ 14600 │ nasal, oral, and pharyngeal regions │ 941 │ 8425.191350000003 │ false │ secretory │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 1 │ 1 │ 07043d1851ce115fd54efa0c8472c1ce___1.h5ad │ ffc7a76b3cbedaa608e5935f55291dd2___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Epithelial cells │ Progenitor cells │ CD4 TCM │ 1.0 │ FALSE │ 1180 │ African │ cellxgene_2024/0.2.1 │ WJt7EvvK>{ │ edc8d3fe-153c-4e3d-8be0-2108d30f8d70 │ 16af564bc3cbc7ae6ac41cebefa08f2e │ tracheal goblet cell │ CL:1000329 │ 10x 5' v1 │ EFO:0011025 │ human adult stage │ HsapDv:0000087 │ normal │ PATO:0000461 │ AN9 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ African │ HANCESTRO:0010 │ female │ PATO:0000383 │ nasal cavity │ UBERON:0001707 │ Publication: https://doi.org/10.1038/s41586-021-04345-x Dataset Version: https://datasets.cellxgene.cziscience.com/69be948c-03f4-46e8-896e-530c79080808.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/03f821b4-87be-4ff4-b65a-b5fc00061da7 │ 03f821b4-87be-4ff4-b65a-b5fc00061da7 │ 69be948c-03f4-46e8-896e-530c79080808 │ X_umap │ 2022-03-24 │ raw.X │ 2024-06-11 │ 236977 │ 5.1.0 │ tissue │ Airway │ false │ NULL │ https://cellxgene.cziscience.com/e/edc8d3fe-153c-4e3d-8be0-2108d30f8d70.cxg/ │ 236977 │ 33145 │ 3612172554.0 │ H5AD │ 2078.208851491917 │ cell │ https://datasets.cellxgene.cziscience.com/69be948c-03f4-46e8-896e-530c79080808.h5ad │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ 3499.0 │ 1A#K<{>yh9 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP92_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 │ 1544 │ 7643.678419999992 │ false │ pneumocyte │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 11 │ 2 │ 36c0492b8230a9b6f6eb278301c33835___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Adipocytes │ Myeloid dendritic cells │ HSPC │ 1.0 │ FALSE │ 1545 │ African │ cellxgene_2024/0.2.1 │ 1A#K<{>yh9 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP92_1_duong │ type II pneumocyte │ CL:0002063 │ 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 │
│ 3972.0 │ Den2ABCfz@ │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP92_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 │ 2369 │ 7632.894089999999 │ false │ pneumocyte │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 11 │ 2 │ 36c0492b8230a9b6f6eb278301c33835___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Adipocytes │ Myeloid dendritic cells │ HSPC │ 1.0 │ FALSE │ 1545 │ African │ cellxgene_2024/0.2.1 │ Den2ABCfz@ │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP92_1_duong │ type II pneumocyte │ CL:0002063 │ 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 │
│ 8133.0 │ c2U#Lm77c# │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP92_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 │ 408 │ 7601.078429999996 │ false │ other │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 11 │ 2 │ 5a9e9e73b16c4d4758dbc8c6c9b97dcd___2.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___2.h5ad │ 20.0 │ 200.0 │ exp │ true │ Neutrophils │ Low-density neutrophils │ HSPC │ 1.0 │ FALSE │ 1224 │ African │ cellxgene_2024/0.2.1 │ c2U#Lm77c# │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP92_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 │
│ 7768.0 │ flQPBhbrE_ │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP92_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 │ 2702 │ 7662.14396999999 │ false │ other │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 11 │ 2 │ 5a9e9e73b16c4d4758dbc8c6c9b97dcd___2.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___2.h5ad │ 20.0 │ 200.0 │ exp │ true │ Chondrocytes │ Myeloid dendritic cells │ HSPC │ 1.0 │ FALSE │ 1224 │ African │ cellxgene_2024/0.2.1 │ flQPBhbrE_ │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP92_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 │
│ 7074.0 │ *da&D_0dSn │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP92_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 │ 7387.439840000009 │ false │ other │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 11 │ 2 │ 5a9e9e73b16c4d4758dbc8c6c9b97dcd___2.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___2.h5ad │ 20.0 │ 200.0 │ exp │ true │ CD4+ T-cells │ MAIT cells │ HSPC │ 1.0 │ FALSE │ 1224 │ African │ cellxgene_2024/0.2.1 │ *da&D_0dSn │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP92_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 │
│ 3182.0 │ KjXg8B6K=9 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP92_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 │ 1737 │ 7645.434180000008 │ false │ pneumocyte │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 11 │ 2 │ 36c0492b8230a9b6f6eb278301c33835___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Epithelial cells │ Myeloid dendritic cells │ HSPC │ 1.0 │ FALSE │ 1545 │ African │ cellxgene_2024/0.2.1 │ KjXg8B6K=9 │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP92_1_duong │ type II pneumocyte │ CL:0002063 │ 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 │
│ 3180.0 │ El8R5*NiUp │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP92_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 │ 1436 │ 7598.521849999997 │ false │ endothelial │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 11 │ 2 │ 7f6bcf24b66d17e83fade402534a6a4d___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Adipocytes │ Intermediate monocytes │ HSPC │ 1.0 │ FALSE │ 1642 │ African │ cellxgene_2024/0.2.1 │ El8R5*NiUp │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP92_1_duong │ capillary endothelial cell │ CL:0002144 │ 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 │
│ 2370.0 │ #+v+^)h%k& │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP92_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 │ 1911 │ 7594.092110000013 │ false │ endothelial │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 11 │ 2 │ 7f6bcf24b66d17e83fade402534a6a4d___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Adipocytes │ Progenitor cells │ HSPC │ 1.0 │ FALSE │ 1642 │ African │ cellxgene_2024/0.2.1 │ #+v+^)h%k& │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP92_1_duong │ capillary endothelial cell │ CL:0002144 │ 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 │
│ 3617.0 │ i+nUd@nTze │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP92_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 │ 1551 │ 7382.60421 │ false │ cd8 tcm │ true │ 0 │ 0 │ false │ false │ singlet │ 1 │ 11 │ 2 │ 89eaf5ae0c927acd47bd4cb19d5a8f71___1.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ CD8+ Tcm │ Non-Vd2 gd T cells │ HSPC │ 1.0 │ FALSE │ 12 │ African │ cellxgene_2024/0.2.1 │ i+nUd@nTze │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP92_1_duong │ CD8-positive, alpha-beta T cell │ CL:0000625 │ 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 │
│ 7985.0 │ RH!?+Ir_9z │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP92_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 │ 2152 │ 7625.652039999982 │ false │ other │ false │ 0 │ 0 │ false │ false │ singlet │ 1 │ 11 │ 2 │ 5a9e9e73b16c4d4758dbc8c6c9b97dcd___2.h5ad │ c25a6ea6b00d263d6cbb2d06a542a2c7___2.h5ad │ 20.0 │ 200.0 │ exp │ true │ Monocytes │ Classical monocytes │ HSPC │ 1.0 │ FALSE │ 1224 │ African │ cellxgene_2024/0.2.1 │ RH!?+Ir_9z │ 9f222629-9e39-47d0-b83f-e08d610c7479 │ 9c8fa5a8d2ae37179b579a0217670512___LAP92_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 │
└─────────┴────────────────────┴──────────────────────────────────────┴──────────────────────────────────────────────────┴──────────────────────────────────┴───────────────┴──────────────────┴──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┴──────────┴─────────────────────────────────────┴──────────────────────────────┴───────────────────┴───────────────┴────────────────────────────┴───────────┴──────────────────────┴──────────────────────┴────────────────────┴───────────────┴───────────────────┴──────────────┴────────────┴─────────────────────────┴───────────────────────────────────────────┴───────────────────────────────────────────┴───────────────────┴───────────────────────────┴───────────────────┴─────────┴───────────────────────────────────┴────────────────────────────────┴────────────────────────────┴──────────────────────────┴──────────────────────────┴───────────────────┴───────────────────┴──────────────────────┴────────────────────┴──────────────────────────────────────┴──────────────────────────────────────────────────┴─────────────────────────────────┴────────────────────────────┴───────────┴────────────────────────┴─────────────────────────┴────────────────────────────────────┴─────────┴──────────────────────────┴───────────────────────────────────────────────────────────────────────────┴─────────────────┴──────────────┴───────────────────────────┴─────────────────────────┴──────────────────────────────────────────┴─────────┴──────────────────────┴─────────────────┴─────────────────────────┴────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┴──────────────────────────────────────┴──────────────────────────────────────┴───────────────────┴──────────────┴───────────────────┴────────────┴────────────────────┴────────────────┴─────────────┴─────────────────────────────────────────────────────────────────────────┴───────────┴────────────────────────────┴──────────────────────────────────────────────────────────────────────────────┴────────────┴───────────────┴───────────────┴──────────┴─────────────────────┴─────────────────┴─────────────────────────────────────────────────────────────────────────────────────┘
? 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 │
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│ 4586.0 │ fuR>bfSG72 │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ d65de8185cc889a2c89adb96104cbcb4___exp4-human-118well. │ d65de8185cc889a2c89adb96104cbcb4 │ │ NULL │ H27432___telencephalon___17th week post-fertilization human stage___sci-RNA-seq______trisomy 18___TRUE │ 119 │ brainstem and cerebellar structures │ 285 │ 25447.21440999952 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ Unknown │ 1 │ 1 │ 4 │ a099a59751e326128c2dd2d0bf0ffaca___1.h5ad │ 10825a9c5f3468936b512ab56aade40b___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Neurons │ Non-switched memory B cells │ Other │ NULL │ NULL │ 6 │ unknown │ cellxgene_2024/0.2.1 │ fuR>bfSG72 │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ d65de8185cc889a2c89adb96104cbcb4___exp4-human-118well. │ glutamatergic neuron │ CL:0000679 │ sci-RNA-seq │ EFO:0010550 │ 17th week post-fertilization human stage │ HsapDv:0000054 │ trisomy 18 │ MONDO:0018071 │ H27432 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ male │ PATO:0000384 │ telencephalon │ UBERON:0001893 │ Publication: https://doi.org/10.1126/science.aba7721 Dataset Version: https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/c114c20f-1ef4-49a5-9c2e-d965787fb90c │ c114c20f-1ef4-49a5-9c2e-d965787fb90c │ 8f6296d0-5b29-4dca-8061-b97147df5fcc │ NULL │ 2021-06-02 │ raw.X │ 2024-06-11 │ 4062980 │ 5.1.0 │ tissue │ Survey of human embryonic development │ false │ NULL │ https://cellxgene.cziscience.com/e/f7c1c579-2dc0-47e2-ba19-8165c5a0e353.cxg/ │ 4062980 │ 46397 │ 20060284412.0 │ H5AD │ 586.3116402246627 │ nucleus │ https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad │
│ 2367.0 │ yyek8Mgo!y │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7a2a38009ef83ef029bb34d4951a079___exp4-human-119well. │ a7a2a38009ef83ef029bb34d4951a079 │ │ NULL │ H27423___telencephalon___16th week post-fertilization human stage___sci-RNA-seq______normal___TRUE │ 112 │ brainstem and cerebellar structures │ 319 │ 155.76816999942093 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 12 │ 5 │ 46 │ 879c4ae3bde35ba36f2e1c8a93cd3041___1.h5ad │ 9b343989f3f7c7bbcdcbb8723ec4899a___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Neurons │ Plasmacytoid dendritic cells │ Other │ NULL │ NULL │ 55 │ unknown │ cellxgene_2024/0.2.1 │ yyek8Mgo!y │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7a2a38009ef83ef029bb34d4951a079___exp4-human-119well. │ glutamatergic neuron │ CL:0000679 │ sci-RNA-seq │ EFO:0010550 │ 16th week post-fertilization human stage │ HsapDv:0000053 │ normal │ PATO:0000461 │ H27423 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ male │ PATO:0000384 │ telencephalon │ UBERON:0001893 │ Publication: https://doi.org/10.1126/science.aba7721 Dataset Version: https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/c114c20f-1ef4-49a5-9c2e-d965787fb90c │ c114c20f-1ef4-49a5-9c2e-d965787fb90c │ 8f6296d0-5b29-4dca-8061-b97147df5fcc │ NULL │ 2021-06-02 │ raw.X │ 2024-06-11 │ 4062980 │ 5.1.0 │ tissue │ Survey of human embryonic development │ false │ NULL │ https://cellxgene.cziscience.com/e/f7c1c579-2dc0-47e2-ba19-8165c5a0e353.cxg/ │ 4062980 │ 46397 │ 20060284412.0 │ H5AD │ 586.3116402246627 │ nucleus │ https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad │
│ 2374.0 │ N$3BCR3tvL │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7a2a38009ef83ef029bb34d4951a079___exp4-human-119well. │ a7a2a38009ef83ef029bb34d4951a079 │ │ NULL │ H27423___telencephalon___16th week post-fertilization human stage___sci-RNA-seq______normal___TRUE │ 112 │ brainstem and cerebellar structures │ 290 │ 90.22862999946665 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 12 │ 5 │ 46 │ 879c4ae3bde35ba36f2e1c8a93cd3041___1.h5ad │ 9b343989f3f7c7bbcdcbb8723ec4899a___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Neurons │ Progenitor cells │ Other │ NULL │ NULL │ 55 │ unknown │ cellxgene_2024/0.2.1 │ N$3BCR3tvL │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7a2a38009ef83ef029bb34d4951a079___exp4-human-119well. │ glutamatergic neuron │ CL:0000679 │ sci-RNA-seq │ EFO:0010550 │ 16th week post-fertilization human stage │ HsapDv:0000053 │ normal │ PATO:0000461 │ H27423 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ male │ PATO:0000384 │ telencephalon │ UBERON:0001893 │ Publication: https://doi.org/10.1126/science.aba7721 Dataset Version: https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/c114c20f-1ef4-49a5-9c2e-d965787fb90c │ c114c20f-1ef4-49a5-9c2e-d965787fb90c │ 8f6296d0-5b29-4dca-8061-b97147df5fcc │ NULL │ 2021-06-02 │ raw.X │ 2024-06-11 │ 4062980 │ 5.1.0 │ tissue │ Survey of human embryonic development │ false │ NULL │ https://cellxgene.cziscience.com/e/f7c1c579-2dc0-47e2-ba19-8165c5a0e353.cxg/ │ 4062980 │ 46397 │ 20060284412.0 │ H5AD │ 586.3116402246627 │ nucleus │ https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad │
│ 2387.0 │ 6R38v9U4Xh │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7a2a38009ef83ef029bb34d4951a079___exp4-human-119well. │ a7a2a38009ef83ef029bb34d4951a079 │ │ NULL │ H27423___telencephalon___16th week post-fertilization human stage___sci-RNA-seq______normal___TRUE │ 112 │ brainstem and cerebellar structures │ 367 │ 174.77107999935834 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 12 │ 5 │ 46 │ 879c4ae3bde35ba36f2e1c8a93cd3041___1.h5ad │ 9b343989f3f7c7bbcdcbb8723ec4899a___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Neurons │ Progenitor cells │ Other │ NULL │ NULL │ 55 │ unknown │ cellxgene_2024/0.2.1 │ 6R38v9U4Xh │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7a2a38009ef83ef029bb34d4951a079___exp4-human-119well. │ glutamatergic neuron │ CL:0000679 │ sci-RNA-seq │ EFO:0010550 │ 16th week post-fertilization human stage │ HsapDv:0000053 │ normal │ PATO:0000461 │ H27423 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ male │ PATO:0000384 │ telencephalon │ UBERON:0001893 │ Publication: https://doi.org/10.1126/science.aba7721 Dataset Version: https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/c114c20f-1ef4-49a5-9c2e-d965787fb90c │ c114c20f-1ef4-49a5-9c2e-d965787fb90c │ 8f6296d0-5b29-4dca-8061-b97147df5fcc │ NULL │ 2021-06-02 │ raw.X │ 2024-06-11 │ 4062980 │ 5.1.0 │ tissue │ Survey of human embryonic development │ false │ NULL │ https://cellxgene.cziscience.com/e/f7c1c579-2dc0-47e2-ba19-8165c5a0e353.cxg/ │ 4062980 │ 46397 │ 20060284412.0 │ H5AD │ 586.3116402246627 │ nucleus │ https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad │
│ 2375.0 │ un$JcB@omY │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7a2a38009ef83ef029bb34d4951a079___exp4-human-119well. │ a7a2a38009ef83ef029bb34d4951a079 │ │ NULL │ H27423___telencephalon___16th week post-fertilization human stage___sci-RNA-seq______normal___TRUE │ 112 │ brainstem and cerebellar structures │ 469 │ 101.40374999915366 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 12 │ 5 │ 46 │ 879c4ae3bde35ba36f2e1c8a93cd3041___1.h5ad │ 9b343989f3f7c7bbcdcbb8723ec4899a___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Neurons │ Naive B cells │ Other │ NULL │ NULL │ 55 │ unknown │ cellxgene_2024/0.2.1 │ un$JcB@omY │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7a2a38009ef83ef029bb34d4951a079___exp4-human-119well. │ glutamatergic neuron │ CL:0000679 │ sci-RNA-seq │ EFO:0010550 │ 16th week post-fertilization human stage │ HsapDv:0000053 │ normal │ PATO:0000461 │ H27423 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ male │ PATO:0000384 │ telencephalon │ UBERON:0001893 │ Publication: https://doi.org/10.1126/science.aba7721 Dataset Version: https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/c114c20f-1ef4-49a5-9c2e-d965787fb90c │ c114c20f-1ef4-49a5-9c2e-d965787fb90c │ 8f6296d0-5b29-4dca-8061-b97147df5fcc │ NULL │ 2021-06-02 │ raw.X │ 2024-06-11 │ 4062980 │ 5.1.0 │ tissue │ Survey of human embryonic development │ false │ NULL │ https://cellxgene.cziscience.com/e/f7c1c579-2dc0-47e2-ba19-8165c5a0e353.cxg/ │ 4062980 │ 46397 │ 20060284412.0 │ H5AD │ 586.3116402246627 │ nucleus │ https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad │
│ 2420.0 │ !tkM(o&Ic) │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7a2a38009ef83ef029bb34d4951a079___exp4-human-119well. │ a7a2a38009ef83ef029bb34d4951a079 │ │ NULL │ H27423___telencephalon___16th week post-fertilization human stage___sci-RNA-seq______normal___TRUE │ 112 │ brainstem and cerebellar structures │ 269 │ 566.8388499995344 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 12 │ 5 │ 46 │ 879c4ae3bde35ba36f2e1c8a93cd3041___1.h5ad │ 9b343989f3f7c7bbcdcbb8723ec4899a___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Chondrocytes │ Plasmacytoid dendritic cells │ Other │ NULL │ NULL │ 55 │ unknown │ cellxgene_2024/0.2.1 │ !tkM(o&Ic) │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7a2a38009ef83ef029bb34d4951a079___exp4-human-119well. │ glutamatergic neuron │ CL:0000679 │ sci-RNA-seq │ EFO:0010550 │ 16th week post-fertilization human stage │ HsapDv:0000053 │ normal │ PATO:0000461 │ H27423 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ male │ PATO:0000384 │ telencephalon │ UBERON:0001893 │ Publication: https://doi.org/10.1126/science.aba7721 Dataset Version: https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/c114c20f-1ef4-49a5-9c2e-d965787fb90c │ c114c20f-1ef4-49a5-9c2e-d965787fb90c │ 8f6296d0-5b29-4dca-8061-b97147df5fcc │ NULL │ 2021-06-02 │ raw.X │ 2024-06-11 │ 4062980 │ 5.1.0 │ tissue │ Survey of human embryonic development │ false │ NULL │ https://cellxgene.cziscience.com/e/f7c1c579-2dc0-47e2-ba19-8165c5a0e353.cxg/ │ 4062980 │ 46397 │ 20060284412.0 │ H5AD │ 586.3116402246627 │ nucleus │ https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad │
│ 2389.0 │ QJjg~Xrcmh │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7a2a38009ef83ef029bb34d4951a079___exp4-human-119well. │ a7a2a38009ef83ef029bb34d4951a079 │ │ NULL │ H27423___telencephalon___16th week post-fertilization human stage___sci-RNA-seq______normal___TRUE │ 112 │ brainstem and cerebellar structures │ 439 │ 395.9937799992258 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 12 │ 5 │ 46 │ 879c4ae3bde35ba36f2e1c8a93cd3041___1.h5ad │ 9b343989f3f7c7bbcdcbb8723ec4899a___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Neurons │ Natural killer cells │ Other │ NULL │ NULL │ 55 │ unknown │ cellxgene_2024/0.2.1 │ QJjg~Xrcmh │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7a2a38009ef83ef029bb34d4951a079___exp4-human-119well. │ glutamatergic neuron │ CL:0000679 │ sci-RNA-seq │ EFO:0010550 │ 16th week post-fertilization human stage │ HsapDv:0000053 │ normal │ PATO:0000461 │ H27423 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ male │ PATO:0000384 │ telencephalon │ UBERON:0001893 │ Publication: https://doi.org/10.1126/science.aba7721 Dataset Version: https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/c114c20f-1ef4-49a5-9c2e-d965787fb90c │ c114c20f-1ef4-49a5-9c2e-d965787fb90c │ 8f6296d0-5b29-4dca-8061-b97147df5fcc │ NULL │ 2021-06-02 │ raw.X │ 2024-06-11 │ 4062980 │ 5.1.0 │ tissue │ Survey of human embryonic development │ false │ NULL │ https://cellxgene.cziscience.com/e/f7c1c579-2dc0-47e2-ba19-8165c5a0e353.cxg/ │ 4062980 │ 46397 │ 20060284412.0 │ H5AD │ 586.3116402246627 │ nucleus │ https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad │
│ 6408.0 │ Q+?3zDKBZH │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ fb00a61c604c1fa9e622268d5ac200a4___exp4-human-122well. │ fb00a61c604c1fa9e622268d5ac200a4 │ │ NULL │ H27464___telencephalon___17th week post-fertilization human stage___sci-RNA-seq______normal___TRUE │ 119 │ brainstem and cerebellar structures │ 269 │ 51.996119999868824 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 24 │ 17 │ 95 │ e6cbd0674d0c53922ff9bbcf9b1bfaf2___2.h5ad │ 84d8b1a4a8cd45383a8d8a0ef7082a92___2.h5ad │ 20.0 │ 200.0 │ exp │ true │ Neurons │ Naive CD4 T cells │ HSPC │ NULL │ NULL │ 131 │ unknown │ cellxgene_2024/0.2.1 │ Q+?3zDKBZH │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ fb00a61c604c1fa9e622268d5ac200a4___exp4-human-122well. │ glutamatergic neuron │ CL:0000679 │ sci-RNA-seq │ EFO:0010550 │ 17th week post-fertilization human stage │ HsapDv:0000054 │ normal │ PATO:0000461 │ H27464 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ male │ PATO:0000384 │ telencephalon │ UBERON:0001893 │ Publication: https://doi.org/10.1126/science.aba7721 Dataset Version: https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/c114c20f-1ef4-49a5-9c2e-d965787fb90c │ c114c20f-1ef4-49a5-9c2e-d965787fb90c │ 8f6296d0-5b29-4dca-8061-b97147df5fcc │ NULL │ 2021-06-02 │ raw.X │ 2024-06-11 │ 4062980 │ 5.1.0 │ tissue │ Survey of human embryonic development │ false │ NULL │ https://cellxgene.cziscience.com/e/f7c1c579-2dc0-47e2-ba19-8165c5a0e353.cxg/ │ 4062980 │ 46397 │ 20060284412.0 │ H5AD │ 586.3116402246627 │ nucleus │ https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad │
│ 1721.0 │ um{Xda24Qd │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ fb00a61c604c1fa9e622268d5ac200a4___exp4-human-122well. │ fb00a61c604c1fa9e622268d5ac200a4 │ │ NULL │ H27464___telencephalon___17th week post-fertilization human stage___sci-RNA-seq______normal___TRUE │ 119 │ brainstem and cerebellar structures │ 1291 │ 74.49249999941821 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 24 │ 17 │ 95 │ 4e6bfaad6d76dbb18186e58eefed0aad___1.h5ad │ 84d8b1a4a8cd45383a8d8a0ef7082a92___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Neurons │ Progenitor cells │ HSPC │ NULL │ NULL │ 131 │ unknown │ cellxgene_2024/0.2.1 │ um{Xda24Qd │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ fb00a61c604c1fa9e622268d5ac200a4___exp4-human-122well. │ GABAergic neuron │ CL:0000617 │ sci-RNA-seq │ EFO:0010550 │ 17th week post-fertilization human stage │ HsapDv:0000054 │ normal │ PATO:0000461 │ H27464 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ male │ PATO:0000384 │ telencephalon │ UBERON:0001893 │ Publication: https://doi.org/10.1126/science.aba7721 Dataset Version: https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/c114c20f-1ef4-49a5-9c2e-d965787fb90c │ c114c20f-1ef4-49a5-9c2e-d965787fb90c │ 8f6296d0-5b29-4dca-8061-b97147df5fcc │ NULL │ 2021-06-02 │ raw.X │ 2024-06-11 │ 4062980 │ 5.1.0 │ tissue │ Survey of human embryonic development │ false │ NULL │ https://cellxgene.cziscience.com/e/f7c1c579-2dc0-47e2-ba19-8165c5a0e353.cxg/ │ 4062980 │ 46397 │ 20060284412.0 │ H5AD │ 586.3116402246627 │ nucleus │ https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad │
│ 1729.0 │ VX+asi9z{^ │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ fb00a61c604c1fa9e622268d5ac200a4___exp4-human-122well. │ fb00a61c604c1fa9e622268d5ac200a4 │ │ NULL │ H27464___telencephalon___17th week post-fertilization human stage___sci-RNA-seq______normal___TRUE │ 119 │ brainstem and cerebellar structures │ 200 │ 75.61701999989964 │ false │ neuron │ false │ 0 │ 0 │ false │ false │ singlet │ 24 │ 17 │ 95 │ 4e6bfaad6d76dbb18186e58eefed0aad___1.h5ad │ 84d8b1a4a8cd45383a8d8a0ef7082a92___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Neurons │ Progenitor cells │ HSPC │ NULL │ NULL │ 131 │ unknown │ cellxgene_2024/0.2.1 │ VX+asi9z{^ │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ fb00a61c604c1fa9e622268d5ac200a4___exp4-human-122well. │ GABAergic neuron │ CL:0000617 │ sci-RNA-seq │ EFO:0010550 │ 17th week post-fertilization human stage │ HsapDv:0000054 │ normal │ PATO:0000461 │ H27464 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ male │ PATO:0000384 │ telencephalon │ UBERON:0001893 │ Publication: https://doi.org/10.1126/science.aba7721 Dataset Version: https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/c114c20f-1ef4-49a5-9c2e-d965787fb90c │ c114c20f-1ef4-49a5-9c2e-d965787fb90c │ 8f6296d0-5b29-4dca-8061-b97147df5fcc │ NULL │ 2021-06-02 │ raw.X │ 2024-06-11 │ 4062980 │ 5.1.0 │ tissue │ Survey of human embryonic development │ false │ NULL │ https://cellxgene.cziscience.com/e/f7c1c579-2dc0-47e2-ba19-8165c5a0e353.cxg/ │ 4062980 │ 46397 │ 20060284412.0 │ H5AD │ 586.3116402246627 │ nucleus │ https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │ · │
│ 18214.0 │ (7O)EXtvQI │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7c93f16d6c068e7a76d1d81d56e1ad6 │ a7c93f16d6c068e7a76d1d81d56e1ad6 │ │ NULL │ H27799___intestine___10th week post-fertilization human stage___sci-RNA-seq______normal___TRUE │ 70 │ digestive system (general) │ 208 │ 26.30222999999296 │ false │ stromal │ false │ 0 │ 0 │ false │ false │ singlet │ 31 │ 40 │ 121 │ ef7a75c574b22cfb0c0d9428cce1252f___1.h5ad │ 8d21e56974824befdfa4f35f52300f8e___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Chondrocytes │ Progenitor cells │ HSPC │ NULL │ NULL │ 3473 │ unknown │ cellxgene_2024/0.2.1 │ (7O)EXtvQI │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7c93f16d6c068e7a76d1d81d56e1ad6 │ stromal cell │ CL:0000499 │ sci-RNA-seq │ EFO:0010550 │ 10th week post-fertilization human stage │ HsapDv:0000047 │ normal │ PATO:0000461 │ H27799 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ female │ PATO:0000383 │ intestine │ UBERON:0000160 │ Publication: https://doi.org/10.1126/science.aba7721 Dataset Version: https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/c114c20f-1ef4-49a5-9c2e-d965787fb90c │ c114c20f-1ef4-49a5-9c2e-d965787fb90c │ 8f6296d0-5b29-4dca-8061-b97147df5fcc │ NULL │ 2021-06-02 │ raw.X │ 2024-06-11 │ 4062980 │ 5.1.0 │ tissue │ Survey of human embryonic development │ false │ NULL │ https://cellxgene.cziscience.com/e/f7c1c579-2dc0-47e2-ba19-8165c5a0e353.cxg/ │ 4062980 │ 46397 │ 20060284412.0 │ H5AD │ 586.3116402246627 │ cell │ https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad │
│ 4068.0 │ T0kbYpS61$ │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7c93f16d6c068e7a76d1d81d56e1ad6 │ a7c93f16d6c068e7a76d1d81d56e1ad6 │ │ NULL │ H27799___intestine___10th week post-fertilization human stage___sci-RNA-seq______normal___TRUE │ 70 │ digestive system (general) │ 398 │ 38.93762999998762 │ false │ epithelial │ false │ 0 │ 0 │ false │ false │ singlet │ 31 │ 40 │ 121 │ 56efd85f64db1ad082afc5f9a7bfa0b0___1.h5ad │ 8d21e56974824befdfa4f35f52300f8e___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Epithelial cells │ Progenitor cells │ HSPC │ NULL │ NULL │ 3954 │ unknown │ cellxgene_2024/0.2.1 │ T0kbYpS61$ │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7c93f16d6c068e7a76d1d81d56e1ad6 │ intestinal epithelial cell │ CL:0002563 │ sci-RNA-seq │ EFO:0010550 │ 10th week post-fertilization human stage │ HsapDv:0000047 │ normal │ PATO:0000461 │ H27799 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ female │ PATO:0000383 │ intestine │ UBERON:0000160 │ Publication: https://doi.org/10.1126/science.aba7721 Dataset Version: https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/c114c20f-1ef4-49a5-9c2e-d965787fb90c │ c114c20f-1ef4-49a5-9c2e-d965787fb90c │ 8f6296d0-5b29-4dca-8061-b97147df5fcc │ NULL │ 2021-06-02 │ raw.X │ 2024-06-11 │ 4062980 │ 5.1.0 │ tissue │ Survey of human embryonic development │ false │ NULL │ https://cellxgene.cziscience.com/e/f7c1c579-2dc0-47e2-ba19-8165c5a0e353.cxg/ │ 4062980 │ 46397 │ 20060284412.0 │ H5AD │ 586.3116402246627 │ cell │ https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad │
│ 4076.0 │ K*EdKIM%Qh │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7c93f16d6c068e7a76d1d81d56e1ad6 │ a7c93f16d6c068e7a76d1d81d56e1ad6 │ │ NULL │ H27799___intestine___10th week post-fertilization human stage___sci-RNA-seq______normal___TRUE │ 70 │ digestive system (general) │ 308 │ 29.197289999993245 │ false │ epithelial │ false │ 0 │ 0 │ false │ false │ singlet │ 31 │ 40 │ 121 │ 56efd85f64db1ad082afc5f9a7bfa0b0___1.h5ad │ 8d21e56974824befdfa4f35f52300f8e___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Mesangial cells │ Progenitor cells │ HSPC │ NULL │ NULL │ 3954 │ unknown │ cellxgene_2024/0.2.1 │ K*EdKIM%Qh │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7c93f16d6c068e7a76d1d81d56e1ad6 │ intestinal epithelial cell │ CL:0002563 │ sci-RNA-seq │ EFO:0010550 │ 10th week post-fertilization human stage │ HsapDv:0000047 │ normal │ PATO:0000461 │ H27799 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ female │ PATO:0000383 │ intestine │ UBERON:0000160 │ Publication: https://doi.org/10.1126/science.aba7721 Dataset Version: https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/c114c20f-1ef4-49a5-9c2e-d965787fb90c │ c114c20f-1ef4-49a5-9c2e-d965787fb90c │ 8f6296d0-5b29-4dca-8061-b97147df5fcc │ NULL │ 2021-06-02 │ raw.X │ 2024-06-11 │ 4062980 │ 5.1.0 │ tissue │ Survey of human embryonic development │ false │ NULL │ https://cellxgene.cziscience.com/e/f7c1c579-2dc0-47e2-ba19-8165c5a0e353.cxg/ │ 4062980 │ 46397 │ 20060284412.0 │ H5AD │ 586.3116402246627 │ cell │ https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad │
│ 769.0 │ ZF{@~k}to; │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7c93f16d6c068e7a76d1d81d56e1ad6 │ a7c93f16d6c068e7a76d1d81d56e1ad6 │ │ NULL │ H27799___intestine___10th week post-fertilization human stage___sci-RNA-seq______normal___TRUE │ 70 │ digestive system (general) │ 237 │ 18.56666999999561 │ false │ glial │ false │ 0 │ 0 │ false │ false │ singlet │ 31 │ 40 │ 121 │ c30bf959aa8c769b3c25e61c9c362538___1.h5ad │ 8d21e56974824befdfa4f35f52300f8e___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Neurons │ Progenitor cells │ HSPC │ NULL │ NULL │ 731 │ unknown │ cellxgene_2024/0.2.1 │ ZF{@~k}to; │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7c93f16d6c068e7a76d1d81d56e1ad6 │ glial cell │ CL:0000125 │ sci-RNA-seq │ EFO:0010550 │ 10th week post-fertilization human stage │ HsapDv:0000047 │ normal │ PATO:0000461 │ H27799 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ female │ PATO:0000383 │ intestine │ UBERON:0000160 │ Publication: https://doi.org/10.1126/science.aba7721 Dataset Version: https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/c114c20f-1ef4-49a5-9c2e-d965787fb90c │ c114c20f-1ef4-49a5-9c2e-d965787fb90c │ 8f6296d0-5b29-4dca-8061-b97147df5fcc │ NULL │ 2021-06-02 │ raw.X │ 2024-06-11 │ 4062980 │ 5.1.0 │ tissue │ Survey of human embryonic development │ false │ NULL │ https://cellxgene.cziscience.com/e/f7c1c579-2dc0-47e2-ba19-8165c5a0e353.cxg/ │ 4062980 │ 46397 │ 20060284412.0 │ H5AD │ 586.3116402246627 │ cell │ https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad │
│ 18250.0 │ !7l)UmkY}; │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7c93f16d6c068e7a76d1d81d56e1ad6 │ a7c93f16d6c068e7a76d1d81d56e1ad6 │ │ NULL │ H27799___intestine___10th week post-fertilization human stage___sci-RNA-seq______normal___TRUE │ 70 │ digestive system (general) │ 233 │ 22.311899999996967 │ false │ stromal │ false │ 0 │ 0 │ false │ false │ singlet │ 31 │ 40 │ 121 │ ef7a75c574b22cfb0c0d9428cce1252f___1.h5ad │ 8d21e56974824befdfa4f35f52300f8e___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Pericytes │ Progenitor cells │ HSPC │ NULL │ NULL │ 3473 │ unknown │ cellxgene_2024/0.2.1 │ !7l)UmkY}; │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7c93f16d6c068e7a76d1d81d56e1ad6 │ stromal cell │ CL:0000499 │ sci-RNA-seq │ EFO:0010550 │ 10th week post-fertilization human stage │ HsapDv:0000047 │ normal │ PATO:0000461 │ H27799 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ female │ PATO:0000383 │ intestine │ UBERON:0000160 │ Publication: https://doi.org/10.1126/science.aba7721 Dataset Version: https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/c114c20f-1ef4-49a5-9c2e-d965787fb90c │ c114c20f-1ef4-49a5-9c2e-d965787fb90c │ 8f6296d0-5b29-4dca-8061-b97147df5fcc │ NULL │ 2021-06-02 │ raw.X │ 2024-06-11 │ 4062980 │ 5.1.0 │ tissue │ Survey of human embryonic development │ false │ NULL │ https://cellxgene.cziscience.com/e/f7c1c579-2dc0-47e2-ba19-8165c5a0e353.cxg/ │ 4062980 │ 46397 │ 20060284412.0 │ H5AD │ 586.3116402246627 │ cell │ https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad │
│ 18248.0 │ #(eC&rsEO7 │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7c93f16d6c068e7a76d1d81d56e1ad6 │ a7c93f16d6c068e7a76d1d81d56e1ad6 │ │ NULL │ H27799___intestine___10th week post-fertilization human stage___sci-RNA-seq______normal___TRUE │ 70 │ digestive system (general) │ 433 │ 36.48708999999235 │ false │ stromal │ false │ 0 │ 0 │ false │ false │ singlet │ 31 │ 40 │ 121 │ ef7a75c574b22cfb0c0d9428cce1252f___1.h5ad │ 8d21e56974824befdfa4f35f52300f8e___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Chondrocytes │ Natural killer cells │ HSPC │ NULL │ NULL │ 3473 │ unknown │ cellxgene_2024/0.2.1 │ #(eC&rsEO7 │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7c93f16d6c068e7a76d1d81d56e1ad6 │ stromal cell │ CL:0000499 │ sci-RNA-seq │ EFO:0010550 │ 10th week post-fertilization human stage │ HsapDv:0000047 │ normal │ PATO:0000461 │ H27799 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ female │ PATO:0000383 │ intestine │ UBERON:0000160 │ Publication: https://doi.org/10.1126/science.aba7721 Dataset Version: https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/c114c20f-1ef4-49a5-9c2e-d965787fb90c │ c114c20f-1ef4-49a5-9c2e-d965787fb90c │ 8f6296d0-5b29-4dca-8061-b97147df5fcc │ NULL │ 2021-06-02 │ raw.X │ 2024-06-11 │ 4062980 │ 5.1.0 │ tissue │ Survey of human embryonic development │ false │ NULL │ https://cellxgene.cziscience.com/e/f7c1c579-2dc0-47e2-ba19-8165c5a0e353.cxg/ │ 4062980 │ 46397 │ 20060284412.0 │ H5AD │ 586.3116402246627 │ cell │ https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad │
│ 18234.0 │ _GyPxPu;k$ │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7c93f16d6c068e7a76d1d81d56e1ad6 │ a7c93f16d6c068e7a76d1d81d56e1ad6 │ │ NULL │ H27799___intestine___10th week post-fertilization human stage___sci-RNA-seq______normal___TRUE │ 70 │ digestive system (general) │ 258 │ 23.67109999999184 │ false │ stromal │ false │ 0 │ 0 │ false │ false │ singlet │ 31 │ 40 │ 121 │ ef7a75c574b22cfb0c0d9428cce1252f___1.h5ad │ 8d21e56974824befdfa4f35f52300f8e___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Smooth muscle │ Plasmacytoid dendritic cells │ HSPC │ NULL │ NULL │ 3473 │ unknown │ cellxgene_2024/0.2.1 │ _GyPxPu;k$ │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7c93f16d6c068e7a76d1d81d56e1ad6 │ stromal cell │ CL:0000499 │ sci-RNA-seq │ EFO:0010550 │ 10th week post-fertilization human stage │ HsapDv:0000047 │ normal │ PATO:0000461 │ H27799 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ female │ PATO:0000383 │ intestine │ UBERON:0000160 │ Publication: https://doi.org/10.1126/science.aba7721 Dataset Version: https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/c114c20f-1ef4-49a5-9c2e-d965787fb90c │ c114c20f-1ef4-49a5-9c2e-d965787fb90c │ 8f6296d0-5b29-4dca-8061-b97147df5fcc │ NULL │ 2021-06-02 │ raw.X │ 2024-06-11 │ 4062980 │ 5.1.0 │ tissue │ Survey of human embryonic development │ false │ NULL │ https://cellxgene.cziscience.com/e/f7c1c579-2dc0-47e2-ba19-8165c5a0e353.cxg/ │ 4062980 │ 46397 │ 20060284412.0 │ H5AD │ 586.3116402246627 │ cell │ https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad │
│ 1490.0 │ qtpG8eL!lg │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7c93f16d6c068e7a76d1d81d56e1ad6 │ a7c93f16d6c068e7a76d1d81d56e1ad6 │ │ NULL │ H27799___intestine___10th week post-fertilization human stage___sci-RNA-seq______normal___TRUE │ 70 │ digestive system (general) │ 422 │ 40.88365999998996 │ false │ immune │ false │ 0 │ 0 │ false │ false │ singlet │ 31 │ 40 │ 121 │ e3b48138101cce8d3a4a5081d9af8949___1.h5ad │ 8d21e56974824befdfa4f35f52300f8e___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Monocytes │ Intermediate monocytes │ HSPC │ NULL │ NULL │ 683 │ unknown │ cellxgene_2024/0.2.1 │ qtpG8eL!lg │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7c93f16d6c068e7a76d1d81d56e1ad6 │ myeloid cell │ CL:0000763 │ sci-RNA-seq │ EFO:0010550 │ 10th week post-fertilization human stage │ HsapDv:0000047 │ normal │ PATO:0000461 │ H27799 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ female │ PATO:0000383 │ intestine │ UBERON:0000160 │ Publication: https://doi.org/10.1126/science.aba7721 Dataset Version: https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/c114c20f-1ef4-49a5-9c2e-d965787fb90c │ c114c20f-1ef4-49a5-9c2e-d965787fb90c │ 8f6296d0-5b29-4dca-8061-b97147df5fcc │ NULL │ 2021-06-02 │ raw.X │ 2024-06-11 │ 4062980 │ 5.1.0 │ tissue │ Survey of human embryonic development │ false │ NULL │ https://cellxgene.cziscience.com/e/f7c1c579-2dc0-47e2-ba19-8165c5a0e353.cxg/ │ 4062980 │ 46397 │ 20060284412.0 │ H5AD │ 586.3116402246627 │ cell │ https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad │
│ 1497.0 │ DiH2(N`$gB │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7c93f16d6c068e7a76d1d81d56e1ad6 │ a7c93f16d6c068e7a76d1d81d56e1ad6 │ │ NULL │ H27799___intestine___10th week post-fertilization human stage___sci-RNA-seq______normal___TRUE │ 70 │ digestive system (general) │ 298 │ 33.19808999999486 │ false │ immune │ false │ 0 │ 0 │ false │ false │ singlet │ 31 │ 40 │ 121 │ e3b48138101cce8d3a4a5081d9af8949___1.h5ad │ 8d21e56974824befdfa4f35f52300f8e___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Macrophages │ Intermediate monocytes │ HSPC │ NULL │ NULL │ 683 │ unknown │ cellxgene_2024/0.2.1 │ DiH2(N`$gB │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7c93f16d6c068e7a76d1d81d56e1ad6 │ myeloid cell │ CL:0000763 │ sci-RNA-seq │ EFO:0010550 │ 10th week post-fertilization human stage │ HsapDv:0000047 │ normal │ PATO:0000461 │ H27799 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ female │ PATO:0000383 │ intestine │ UBERON:0000160 │ Publication: https://doi.org/10.1126/science.aba7721 Dataset Version: https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/c114c20f-1ef4-49a5-9c2e-d965787fb90c │ c114c20f-1ef4-49a5-9c2e-d965787fb90c │ 8f6296d0-5b29-4dca-8061-b97147df5fcc │ NULL │ 2021-06-02 │ raw.X │ 2024-06-11 │ 4062980 │ 5.1.0 │ tissue │ Survey of human embryonic development │ false │ NULL │ https://cellxgene.cziscience.com/e/f7c1c579-2dc0-47e2-ba19-8165c5a0e353.cxg/ │ 4062980 │ 46397 │ 20060284412.0 │ H5AD │ 586.3116402246627 │ cell │ https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad │
│ 18240.0 │ b4P&2wkQkL │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7c93f16d6c068e7a76d1d81d56e1ad6 │ a7c93f16d6c068e7a76d1d81d56e1ad6 │ │ NULL │ H27799___intestine___10th week post-fertilization human stage___sci-RNA-seq______normal___TRUE │ 70 │ digestive system (general) │ 248 │ 22.637160000000677 │ false │ stromal │ false │ 0 │ 0 │ false │ false │ singlet │ 31 │ 40 │ 121 │ ef7a75c574b22cfb0c0d9428cce1252f___1.h5ad │ 8d21e56974824befdfa4f35f52300f8e___1.h5ad │ 20.0 │ 200.0 │ exp │ true │ Pericytes │ Intermediate monocytes │ HSPC │ NULL │ NULL │ 3473 │ unknown │ cellxgene_2024/0.2.1 │ b4P&2wkQkL │ f7c1c579-2dc0-47e2-ba19-8165c5a0e353 │ a7c93f16d6c068e7a76d1d81d56e1ad6 │ stromal cell │ CL:0000499 │ sci-RNA-seq │ EFO:0010550 │ 10th week post-fertilization human stage │ HsapDv:0000047 │ normal │ PATO:0000461 │ H27799 │ TRUE │ Homo sapiens │ NCBITaxon:9606 │ unknown │ unknown │ female │ PATO:0000383 │ intestine │ UBERON:0000160 │ Publication: https://doi.org/10.1126/science.aba7721 Dataset Version: https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/c114c20f-1ef4-49a5-9c2e-d965787fb90c │ c114c20f-1ef4-49a5-9c2e-d965787fb90c │ 8f6296d0-5b29-4dca-8061-b97147df5fcc │ NULL │ 2021-06-02 │ raw.X │ 2024-06-11 │ 4062980 │ 5.1.0 │ tissue │ Survey of human embryonic development │ false │ NULL │ https://cellxgene.cziscience.com/e/f7c1c579-2dc0-47e2-ba19-8165c5a0e353.cxg/ │ 4062980 │ 46397 │ 20060284412.0 │ H5AD │ 586.3116402246627 │ cell │ https://datasets.cellxgene.cziscience.com/8f6296d0-5b29-4dca-8061-b97147df5fcc.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
View of AnnData object with n_obs × n_vars = 2908 × 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
View of AnnData object with n_obs × n_vars = 2908 × 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
View of AnnData object with n_obs × n_vars = 2908 × 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
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 0x70a46b7b9730>,
┌───────────┬─────────┬─────────┬───────────┬────────────────────────┬─────────┬─────────────────────┬─────────────────────────┬──────────────┬────────────────────┬────────────────┬───────────────────────┬────────────────────┬──────────────────────────────────┬───────────────────┬─────────────────────┐
│ 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.
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