-- DBMS: bigquery
CREATE TABLE `isb-cgc-bq.HTAN_versioned.scRNAseq_MSK_Myeloid_SCLC_samples_only_r3`
(
  iObs INT64 OPTIONS(description="Index to cell barcodes"),
  iVar INT64 OPTIONS(description="Index to gene IDs"),
  X_value FLOAT64 OPTIONS(description="Expression value for a given gene and cell"),
  n_genes_by_counts INT64 OPTIONS(description="Number of genes detected in a given cell"),
  log1p_n_genes_by_counts FLOAT64 OPTIONS(description="Log (N+1) on the number of genes"),
  total_counts FLOAT64 OPTIONS(description="Total number of gene expression counts (or UMIs mapped) for a given cell"),
  log1p_total_counts FLOAT64 OPTIONS(description="Log (N+1) on the number of gene expression counts (UMIs mapped) for a given cell"),
  mito_frac FLOAT64 OPTIONS(description="Percent of UMIs mapping to mitochondrial genes"),
  RBP_frac FLOAT64 OPTIONS(description="Percent of UMIs mapping to RNA-binding proteins (RBPs)"),
  batch STRING OPTIONS(description="MSK Sample ID"),
  donor_id STRING OPTIONS(description="Free-text identifier that distinguishes the unique individual that data were derived from"),
  treatment STRING OPTIONS(description="The type of treatment recieved by the patient"),
  procedure STRING OPTIONS(description="The method used in obtaining the tumor specimen, biopsy or resection"),
  author_cell_type STRING OPTIONS(description="Cell phenotype as designated by study authors"),
  cell_type_cluster STRING OPTIONS(description="Cluster labels with cell phenotypes"),
  clusters INT64 OPTIONS(description="Numeric cluster labels applied to each cell"),
  PLCG2_Tumor_Subclone STRING OPTIONS(description="Whether the sample harbors PLCG2 tumor subclone"),
  Mo_M_metacluster STRING OPTIONS(description="Whether the cell is part of a macrophage group."),
  IPF_a1 FLOAT64 OPTIONS(description="Z-score of the gene signature for idiopathic pulmonary fibrosis (IPF) archetype 1"),
  IPF_a2 FLOAT64 OPTIONS(description="Z-score of the gene signature for idiopathic pulmonary fibrosis (IPF) archetype 2"),
  IPF_a3 FLOAT64 OPTIONS(description="Z-score of the gene signature for idiopathic pulmonary fibrosis (IPF) archetype 3"),
  IPF_associated FLOAT64 OPTIONS(description="Z-score of the gene signature for associated idiopathic pulmonary fibrosis (IPF)"),
  IPF_Monocytic FLOAT64 OPTIONS(description="Z-score of the gene signature for monocytic idiopathic pulmonary fibrosis (IPF)"),
  IPF_Fibrotic FLOAT64 OPTIONS(description="Z-score of the gene signature for fibrotic idiopathic pulmonary fibrosis (IPF)"),
  cell_type_ontology_term_id STRING OPTIONS(description="Cell Ontology ID (i.e. CL:0000784)  (REF: https://www.ebi.ac.uk/ols/ontologies/cl)"),
  tissue_ontology_term_id STRING OPTIONS(description="Uber-anatomy ontology ID (REF: https://www.ebi.ac.uk/ols/ontologies/uberon) (ex.UBERON:2001190)"),
  disease_ontology_term_id STRING OPTIONS(description="MONDO disease ontology ID (REF: https://www.ebi.ac.uk/ols/ontologies/mondo) (ex. MONDO:0100426 or PATO:0000461 for 'normal')"),
  assay_ontology_term_id STRING OPTIONS(description="Experimental Factor Ontology ID (REF: https://www.ebi.ac.uk/ols/ontologies/efo)"),
  sex_ontology_term_id STRING OPTIONS(description="Phenotype And Trait Ontology ID, PATO:0000384 for male, PATO:0000383 for female, or unknown if unavailable"),
  self_reported_ethnicity_ontology_term_id STRING OPTIONS(description="If human, the Human Ancestry Ontology ID (i.e. HANCESTRO:0005) (REF: https://www.ebi.ac.uk/ols/ontologies/hancestro); \"multiethnic\" if more than one ethnicity. \"Unknown\" if human and no information, else \"na\" if non-human"),
  organism_ontology_term_id STRING OPTIONS(description="NCBITaxon ID (REF: https://www.ncbi.nlm.nih.gov/taxonomy) (ex. NCBITaxon:9606 for human, NCBITaxon:10090 for mouse)"),
  is_primary_data BOOL OPTIONS(description="Indicates if the sample is primary or not (True/False)"),
  development_stage_ontology_term_id STRING OPTIONS(description="Human Developmental Stages ID (REF: https://www.ebi.ac.uk/ols/ontologies/hsapdv) or Mouse Developmental Stages ID (REF: https://www.ebi.ac.uk/ols/ontologies/mmusdv) (HsapDv if human, MmusDv if mouse, unknown if information unavailable)"),
  suspension_type STRING OPTIONS(description="Cell, nucleus, or na, as corresponding to sample preparation"),
  HTAN_Biospecimen_ID STRING OPTIONS(description="HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz)"),
  HTAN_Participant_ID STRING OPTIONS(description="HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy )"),
  cell_type STRING OPTIONS(description="The type of cell (i.e. T-cell)"),
  assay STRING OPTIONS(description="An assay based on 10X Genomics. Example : 100x3’ v2"),
  disease STRING OPTIONS(description="Description of disease (example: lung adenocarcinoma) or normal cells"),
  organism STRING OPTIONS(description="The genus and species from which biosamples are derived"),
  sex STRING OPTIONS(description="Phenotypic sex"),
  tissue STRING OPTIONS(description="Derived from UBERON or CL terms that best describes the tissue that the cell was derived from."),
  self_reported_ethnicity STRING OPTIONS(description="Ethnicity of the individual (obtained from HANCESTRO terms for Homo sapiens)"),
  development_stage STRING OPTIONS(description="Human development stage derived from HsapDv term  (Example if data is Homo sapiens, development stage is obtained from Link. HsapDv:0000114 - 20-year-old human stage)"),
  feature_is_filtered BOOL OPTIONS(description="Indicates if the feature (gene) was/should be filtered in analysis"),
  feature_name STRING OPTIONS(description="Gene name from HUGO Human Gene Nomenclature Committee (https://www.genenames.org/)"),
  feature_reference STRING OPTIONS(description="A reference to the feature: NCBI Taxonomy ID"),
  feature_biotype STRING OPTIONS(description="Biological type of feature (e.g. gene)")
)
OPTIONS(
  friendly_name="MSK SCLC MYELOID CELLS SAMPLES ONLY R3 VERSIONED",
  description="Data was derived in April 2023 from an H5AD file (Synapse ID: syn51301557) submitted by the MSK HTAN Center. This dataset is subsetted from the immune dataset and contains both raw gene expression counts and log2(X+1) transformed, median-normalized expression (N=14,072 cells).",
  labels=[("access", "open"), ("reference_genome", "hg38"), ("data_type", "gene_expression"), ("program", "htan"), ("source", "htan-msk"), ("category", "processed_-omics_data"), ("status", "current")]
);

INSERT INTO `isb-cgc-bq.HTAN_versioned.scRNAseq_MSK_Myeloid_SCLC_samples_only_r3` (iObs, iVar, X_value, n_genes_by_counts, log1p_n_genes_by_counts, total_counts, log1p_total_counts, mito_frac, RBP_frac, batch, donor_id, treatment, procedure, author_cell_type, cell_type_cluster, clusters, PLCG2_Tumor_Subclone, Mo_M_metacluster, IPF_a1, IPF_a2, IPF_a3, IPF_associated, IPF_Monocytic, IPF_Fibrotic, cell_type_ontology_term_id, tissue_ontology_term_id, disease_ontology_term_id, assay_ontology_term_id, sex_ontology_term_id, self_reported_ethnicity_ontology_term_id, organism_ontology_term_id, is_primary_data, development_stage_ontology_term_id, suspension_type, HTAN_Biospecimen_ID, HTAN_Participant_ID, cell_type, assay, disease, organism, sex, tissue, self_reported_ethnicity, development_stage, feature_is_filtered, feature_name, feature_reference, feature_biotype) VALUES (1025, 10664, 2.5994911193847656, 1674, 7.423568444259167, 5998.0, 8.699348449707031, 0.009003001265227795, 0.2104034721851349, 'RU1066', 'RU1066', 'Naive', 'Resection', 'pDC', 'pDC_C11', 11, '<0.75%', 'NA', -1.0651310355697183, -0.045768946828185046, -0.40238946976786905, 0.2606606392646032, -1.0651310355697183, -0.40238946976786905, 'CL:0000784', 'UBERON:0002048', 'MONDO:0008433', 'EFO:0009899', 'PATO:0000383', 'HANCESTRO:0005', 'NCBITaxon:9606', False, 'HsapDv:0000168', 'cell', 'HTA8_2003_1', 'HTA8_2003', 'plasmacytoid dendritic cell', '10x 3'' v2', 'small cell lung carcinoma', 'Homo sapiens', 'female', 'lung', 'European', '74-year-old human stage', False, 'MGAT1', 'NCBITaxon:9606', 'gene'), (1025, 5264, 1.819817066192627, 1674, 7.423568444259167, 5998.0, 8.699348449707031, 0.009003001265227795, 0.2104034721851349, 'RU1066', 'RU1066', 'Naive', 'Resection', 'pDC', 'pDC_C11', 11, '<0.75%', 'NA', -1.0651310355697183, -0.045768946828185046, -0.40238946976786905, 0.2606606392646032, -1.0651310355697183, -0.40238946976786905, 'CL:0000784', 'UBERON:0002048', 'MONDO:0008433', 'EFO:0009899', 'PATO:0000383', 'HANCESTRO:0005', 'NCBITaxon:9606', False, 'HsapDv:0000168', 'cell', 'HTA8_2003_1', 'HTA8_2003', 'plasmacytoid dendritic cell', '10x 3'' v2', 'small cell lung carcinoma', 'Homo sapiens', 'female', 'lung', 'European', '74-year-old human stage', False, 'E2F3', 'NCBITaxon:9606', 'gene'), (1025, 6725, 1.819817066192627, 1674, 7.423568444259167, 5998.0, 8.699348449707031, 0.009003001265227795, 0.2104034721851349, 'RU1066', 'RU1066', 'Naive', 'Resection', 'pDC', 'pDC_C11', 11, '<0.75%', 'NA', -1.0651310355697183, -0.045768946828185046, -0.40238946976786905, 0.2606606392646032, -1.0651310355697183, -0.40238946976786905, 'CL:0000784', 'UBERON:0002048', 'MONDO:0008433', 'EFO:0009899', 'PATO:0000383', 'HANCESTRO:0005', 'NCBITaxon:9606', False, 'HsapDv:0000168', 'cell', 'HTA8_2003_1', 'HTA8_2003', 'plasmacytoid dendritic cell', '10x 3'' v2', 'small cell lung carcinoma', 'Homo sapiens', 'female', 'lung', 'European', '74-year-old human stage', False, 'GART', 'NCBITaxon:9606', 'gene'), (1025, 2999, 2.5994911193847656, 1674, 7.423568444259167, 5998.0, 8.699348449707031, 0.009003001265227795, 0.2104034721851349, 'RU1066', 'RU1066', 'Naive', 'Resection', 'pDC', 'pDC_C11', 11, '<0.75%', 'NA', -1.0651310355697183, -0.045768946828185046, -0.40238946976786905, 0.2606606392646032, -1.0651310355697183, -0.40238946976786905, 'CL:0000784', 'UBERON:0002048', 'MONDO:0008433', 'EFO:0009899', 'PATO:0000383', 'HANCESTRO:0005', 'NCBITaxon:9606', False, 'HsapDv:0000168', 'cell', 'HTA8_2003_1', 'HTA8_2003', 'plasmacytoid dendritic cell', '10x 3'' v2', 'small cell lung carcinoma', 'Homo sapiens', 'female', 'lung', 'European', '74-year-old human stage', False, 'CDKN1A', 'NCBITaxon:9606', 'gene'), (1025, 2875, 7.497100353240967, 1674, 7.423568444259167, 5998.0, 8.699348449707031, 0.009003001265227795, 0.2104034721851349, 'RU1066', 'RU1066', 'Naive', 'Resection', 'pDC', 'pDC_C11', 11, '<0.75%', 'NA', -1.0651310355697183, -0.045768946828185046, -0.40238946976786905, 0.2606606392646032, -1.0651310355697183, -0.40238946976786905, 'CL:0000784', 'UBERON:0002048', 'MONDO:0008433', 'EFO:0009899', 'PATO:0000383', 'HANCESTRO:0005', 'NCBITaxon:9606', False, 'HsapDv:0000168', 'cell', 'HTA8_2003_1', 'HTA8_2003', 'plasmacytoid dendritic cell', '10x 3'' v2', 'small cell lung carcinoma', 'Homo sapiens', 'female', 'lung', 'European', '74-year-old human stage', False, 'CD74', 'NCBITaxon:9606', 'gene');