-- DBMS: bigquery
CREATE TABLE `isb-cgc-bq.HTAN_versioned.scRNAseq_level4_metadata_r3`
(
  Component STRING OPTIONS(description="Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows."),
  Filename STRING OPTIONS(description="Name of a file"),
  File_Format STRING OPTIONS(description="Format of a file (e.g. txt, csv, fastq, bam, etc.)"),
  HTAN_Parent_Data_File_ID STRING OPTIONS(description="HTAN Data File Identifier indicating the file(s) from which these files were derived"),
  HTAN_Data_File_ID STRING OPTIONS(description="Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz)"),
  scRNAseq_Workflow_Type STRING OPTIONS(description="Generic name for the workflow used to analyze a data set."),
  scRNAseq_Workflow_Parameters_Description STRING OPTIONS(description="Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion"),
  Workflow_Version STRING OPTIONS(description="Major version of the workflow (e.g. Cell Ranger v3.1)"),
  Workflow_Link STRING OPTIONS(description="Link to workflow or command. DockStore.org recommended. URL"),
  entityId STRING OPTIONS(description="Synapse ID of entity"),
  HTAN_Center STRING OPTIONS(description="Name of HTAN Center e.g. HTAN HTAPP"),
  Data_Release STRING OPTIONS(description="Inclusion in HTAN Data Release e.g. Release 1.0"),
  Manifest_Version INT64 OPTIONS(description="Latest version of metadata manifest"),
  Uuid STRING OPTIONS(description="Unique identifier of entity e.g. a96059eb-81af-4b24-ae50-9242c0d8f819"),
  File_Size INT64 OPTIONS(description="Size of file (bucket object) in bytes"),
  md5 STRING OPTIONS(description="md5 hash of file"),
  CDS_Release STRING OPTIONS(description="CDS transfer package in which file was included e.g. v22.6.1.seq")
)
OPTIONS(
  friendly_name="HTAN SCRNASEQ LEVEL 4 METADATA R3 VERSIONED",
  description="This table contains the file metadata for the fourth level (t-SNE plot coordinates, etc.) single cell RNA sequencing. Data was extracted from HTAN Synapse projects in April 2023. More details: see https://data.humantumoratlas.org/standard/sequencing",
  labels=[("access", "open"), ("data_type", "file_metadata"), ("program", "htan"), ("source", "htan"), ("status", "current"), ("category", "metadata")]
);

INSERT INTO `isb-cgc-bq.HTAN_versioned.scRNAseq_level4_metadata_r3` (Component, Filename, File_Format, HTAN_Parent_Data_File_ID, HTAN_Data_File_ID, scRNAseq_Workflow_Type, scRNAseq_Workflow_Parameters_Description, Workflow_Version, Workflow_Link, entityId, HTAN_Center, Data_Release, Manifest_Version, Uuid, File_Size, md5, CDS_Release) VALUES ('ScRNA-seqLevel4', 'single_cell_RNAseq_level_4/myeloid.SCLC_samples_only/MAST/myeloid.SCLC_samples_only.c1_vs_moma_adjustFE_treatment_tissue.csv', 'csv', 'HTA8_1001_310001,HTA8_1001_310002,HTA8_1001_310003,HTA8_1001_310004,HTA8_1002_310001,HTA8_1002_310002,HTA8_1002_310003,HTA8_1002_310004,HTA8_1003_310001,HTA8_1003_310002,HTA8_1003_310003,HTA8_1003_310004,HTA8_1004_310001,HTA8_1004_310002,HTA8_1004_310003,HTA8_1004_310004,HTA8_1005_310001,HTA8_1005_310002,HTA8_1005_310003,HTA8_1005_310004,HTA8_1005_320001,HTA8_1005_320002,HTA8_1005_320003,HTA8_1005_320004,HTA8_1006_310001,HTA8_1006_310002,HTA8_1006_310003,HTA8_1006_310004,HTA8_1007_310001,HTA8_1007_310002,HTA8_1007_310003,HTA8_1007_310004,HTA8_1008_310001,HTA8_1008_310002,HTA8_1008_310003,HTA8_1008_310004,HTA8_1009_310001,HTA8_1009_310002,HTA8_1009_310003,HTA8_1009_310004,HTA8_1009_320001,HTA8_1009_320002,HTA8_1009_320003,HTA8_1009_320004,HTA8_1009_330001,HTA8_1009_330002,HTA8_1009_330003,HTA8_1009_330004,HTA8_1010_310001,HTA8_1010_310002,HTA8_1010_310003,HTA8_1010_310004,HTA8_1011_310001,HTA8_1011_310002,HTA8_1011_310003,HTA8_1011_310004,HTA8_1012_310001,HTA8_1012_310002,HTA8_1012_310003,HTA8_1012_310004,HTA8_1013_310001,HTA8_1013_310002,HTA8_1013_310003,HTA8_1013_310004,HTA8_1014_310001,HTA8_1014_310002,HTA8_1014_310003,HTA8_1014_310004,HTA8_1015_310001,HTA8_1015_310002,HTA8_1015_310003,HTA8_1015_310004,HTA8_1016_310001,HTA8_1016_310002,HTA8_1016_310003,HTA8_1016_310004,HTA8_1017_310001,HTA8_1017_310002,HTA8_1017_310003,HTA8_1017_310004,HTA8_1018_310001,HTA8_1018_310002,HTA8_1018_310003,HTA8_1018_310004,HTA8_1019_310001,HTA8_1019_310002,HTA8_1019_310003,HTA8_1019_310004,HTA8_1020_310001,HTA8_1020_310002,HTA8_1020_310003,HTA8_1020_310004,HTA8_1021_310001,HTA8_1021_310002,HTA8_1021_310003,HTA8_1021_310004,HTA8_1022_310001,HTA8_1022_310002,HTA8_1022_310003,HTA8_1022_310004,HTA8_1023_310001,HTA8_1023_310002,HTA8_1023_310003,HTA8_1023_310004,HTA8_1024_310001,HTA8_1024_310002,HTA8_1024_310003,HTA8_1024_310004,HTA8_1025_310001,HTA8_1025_310002,HTA8_1025_310003,HTA8_1025_310004,HTA8_1026_310001,HTA8_1026_310002,HTA8_1026_310003,HTA8_1026_310004,HTA8_1027_310001,HTA8_1027_310002,HTA8_1027_310003,HTA8_1027_310004,HTA8_2001_310001,HTA8_2001_310002,HTA8_2001_310003,HTA8_2001_310004,HTA8_2002_310001,HTA8_2002_310002,HTA8_2002_310003,HTA8_2002_310004,HTA8_2003_310001,HTA8_2003_310002,HTA8_2003_310003,HTA8_2003_310004,HTA8_2004_310001,HTA8_2004_310002,HTA8_2004_310003,HTA8_2004_310004,HTA8_2005_310001,HTA8_2005_310002,HTA8_2005_310003,HTA8_2005_310004,HTA8_2005_320001,HTA8_2005_320002,HTA8_2005_320003,HTA8_2005_320004,HTA8_2005_330001,HTA8_2005_330002,HTA8_2005_330003,HTA8_2005_330004,HTA8_2006_310001,HTA8_2006_310002,HTA8_2006_310003,HTA8_2006_310004,HTA8_2007_310001,HTA8_2007_310002,HTA8_2007_310003,HTA8_2007_310004,HTA8_2007_320001,HTA8_2007_320002,HTA8_2007_320003,HTA8_2007_320004,HTA8_2008_310001,HTA8_2008_310002,HTA8_2008_310003,HTA8_2008_310004,HTA8_2009_310001,HTA8_2009_310002,HTA8_2009_310003,HTA8_2009_310004,HTA8_2010_310001,HTA8_2010_310002,HTA8_2010_310003,HTA8_2010_310004,HTA8_2010_320001,HTA8_2010_320002,HTA8_2010_320003,HTA8_2010_320004,HTA8_2011_310001,HTA8_2011_310002,HTA8_2011_310003,HTA8_2011_310004,HTA8_2012_310001,HTA8_2012_310002,HTA8_2012_310003,HTA8_2012_310004,HTA8_2013_310001,HTA8_2013_310002,HTA8_2013_310003,HTA8_2013_310004,HTA8_2014_310001,HTA8_2014_310002,HTA8_2014_310003,HTA8_2014_310004,HTA8_2015_310001,HTA8_2015_310002,HTA8_2015_310003,HTA8_2015_310004,HTA8_2016_310001,HTA8_2016_310002,HTA8_2016_310003,HTA8_2016_310004,HTA8_2017_310001,HTA8_2017_310002,HTA8_2017_310003,HTA8_2017_310004,HTA8_2018_310001,HTA8_2018_310002,HTA8_2018_310003,HTA8_2018_310004,HTA8_2019_310001,HTA8_2019_310002,HTA8_2019_310003,HTA8_2019_310004,HTA8_3001_310001,HTA8_3001_310002,HTA8_3001_310003,HTA8_3001_310004,HTA8_3002_310001,HTA8_3002_310002,HTA8_3002_310003,HTA8_3002_310004,HTA8_3003_310001,HTA8_3003_310002,HTA8_3003_310003,HTA8_3003_310004,HTA8_3004_310001,HTA8_3004_310002,HTA8_3004_310003,HTA8_3004_310004', 'HTA8_4_100051', 'Other', 'DEGs cluster 1 vs MoMf in SCLC myeloid dataset', 'MAST', 'https://github.com/RGLab/MAST', 'syn23626836', 'HTAN MSK', 'Release 1.0', 1, 'adf3cb65-7fb7-477f-9030-1d2aa8d20633', 1700430, 'ca9620cf683e51b3545fe5a202a91cd0', NULL), ('ScRNA-seqLevel4', 'single_cell_RNAseq_level_4/myeloid.SCLC_samples_only/MAST/myeloid.SCLC_samples_only.momaA_vs_momaB_adjustFE_treatment_tissue.csv', 'csv', 'HTA8_1001_310001,HTA8_1001_310002,HTA8_1001_310003,HTA8_1001_310004,HTA8_1002_310001,HTA8_1002_310002,HTA8_1002_310003,HTA8_1002_310004,HTA8_1003_310001,HTA8_1003_310002,HTA8_1003_310003,HTA8_1003_310004,HTA8_1004_310001,HTA8_1004_310002,HTA8_1004_310003,HTA8_1004_310004,HTA8_1005_310001,HTA8_1005_310002,HTA8_1005_310003,HTA8_1005_310004,HTA8_1005_320001,HTA8_1005_320002,HTA8_1005_320003,HTA8_1005_320004,HTA8_1006_310001,HTA8_1006_310002,HTA8_1006_310003,HTA8_1006_310004,HTA8_1007_310001,HTA8_1007_310002,HTA8_1007_310003,HTA8_1007_310004,HTA8_1008_310001,HTA8_1008_310002,HTA8_1008_310003,HTA8_1008_310004,HTA8_1009_310001,HTA8_1009_310002,HTA8_1009_310003,HTA8_1009_310004,HTA8_1009_320001,HTA8_1009_320002,HTA8_1009_320003,HTA8_1009_320004,HTA8_1009_330001,HTA8_1009_330002,HTA8_1009_330003,HTA8_1009_330004,HTA8_1010_310001,HTA8_1010_310002,HTA8_1010_310003,HTA8_1010_310004,HTA8_1011_310001,HTA8_1011_310002,HTA8_1011_310003,HTA8_1011_310004,HTA8_1012_310001,HTA8_1012_310002,HTA8_1012_310003,HTA8_1012_310004,HTA8_1013_310001,HTA8_1013_310002,HTA8_1013_310003,HTA8_1013_310004,HTA8_1014_310001,HTA8_1014_310002,HTA8_1014_310003,HTA8_1014_310004,HTA8_1015_310001,HTA8_1015_310002,HTA8_1015_310003,HTA8_1015_310004,HTA8_1016_310001,HTA8_1016_310002,HTA8_1016_310003,HTA8_1016_310004,HTA8_1017_310001,HTA8_1017_310002,HTA8_1017_310003,HTA8_1017_310004,HTA8_1018_310001,HTA8_1018_310002,HTA8_1018_310003,HTA8_1018_310004,HTA8_1019_310001,HTA8_1019_310002,HTA8_1019_310003,HTA8_1019_310004,HTA8_1020_310001,HTA8_1020_310002,HTA8_1020_310003,HTA8_1020_310004,HTA8_1021_310001,HTA8_1021_310002,HTA8_1021_310003,HTA8_1021_310004,HTA8_1022_310001,HTA8_1022_310002,HTA8_1022_310003,HTA8_1022_310004,HTA8_1023_310001,HTA8_1023_310002,HTA8_1023_310003,HTA8_1023_310004,HTA8_1024_310001,HTA8_1024_310002,HTA8_1024_310003,HTA8_1024_310004,HTA8_1025_310001,HTA8_1025_310002,HTA8_1025_310003,HTA8_1025_310004,HTA8_1026_310001,HTA8_1026_310002,HTA8_1026_310003,HTA8_1026_310004,HTA8_1027_310001,HTA8_1027_310002,HTA8_1027_310003,HTA8_1027_310004,HTA8_2001_310001,HTA8_2001_310002,HTA8_2001_310003,HTA8_2001_310004,HTA8_2002_310001,HTA8_2002_310002,HTA8_2002_310003,HTA8_2002_310004,HTA8_2003_310001,HTA8_2003_310002,HTA8_2003_310003,HTA8_2003_310004,HTA8_2004_310001,HTA8_2004_310002,HTA8_2004_310003,HTA8_2004_310004,HTA8_2005_310001,HTA8_2005_310002,HTA8_2005_310003,HTA8_2005_310004,HTA8_2005_320001,HTA8_2005_320002,HTA8_2005_320003,HTA8_2005_320004,HTA8_2005_330001,HTA8_2005_330002,HTA8_2005_330003,HTA8_2005_330004,HTA8_2006_310001,HTA8_2006_310002,HTA8_2006_310003,HTA8_2006_310004,HTA8_2007_310001,HTA8_2007_310002,HTA8_2007_310003,HTA8_2007_310004,HTA8_2007_320001,HTA8_2007_320002,HTA8_2007_320003,HTA8_2007_320004,HTA8_2008_310001,HTA8_2008_310002,HTA8_2008_310003,HTA8_2008_310004,HTA8_2009_310001,HTA8_2009_310002,HTA8_2009_310003,HTA8_2009_310004,HTA8_2010_310001,HTA8_2010_310002,HTA8_2010_310003,HTA8_2010_310004,HTA8_2010_320001,HTA8_2010_320002,HTA8_2010_320003,HTA8_2010_320004,HTA8_2011_310001,HTA8_2011_310002,HTA8_2011_310003,HTA8_2011_310004,HTA8_2012_310001,HTA8_2012_310002,HTA8_2012_310003,HTA8_2012_310004,HTA8_2013_310001,HTA8_2013_310002,HTA8_2013_310003,HTA8_2013_310004,HTA8_2014_310001,HTA8_2014_310002,HTA8_2014_310003,HTA8_2014_310004,HTA8_2015_310001,HTA8_2015_310002,HTA8_2015_310003,HTA8_2015_310004,HTA8_2016_310001,HTA8_2016_310002,HTA8_2016_310003,HTA8_2016_310004,HTA8_2017_310001,HTA8_2017_310002,HTA8_2017_310003,HTA8_2017_310004,HTA8_2018_310001,HTA8_2018_310002,HTA8_2018_310003,HTA8_2018_310004,HTA8_2019_310001,HTA8_2019_310002,HTA8_2019_310003,HTA8_2019_310004,HTA8_3001_310001,HTA8_3001_310002,HTA8_3001_310003,HTA8_3001_310004,HTA8_3002_310001,HTA8_3002_310002,HTA8_3002_310003,HTA8_3002_310004,HTA8_3003_310001,HTA8_3003_310002,HTA8_3003_310003,HTA8_3003_310004,HTA8_3004_310001,HTA8_3004_310002,HTA8_3004_310003,HTA8_3004_310004', 'HTA8_4_100052', 'Other', 'DEGs MoMf-A vs MoMf-B in SCLC myeloid dataset', 'MAST', 'https://github.com/RGLab/MAST', 'syn23626835', 'HTAN MSK', 'Release 1.0', 1, '34340473-2295-4235-b0ed-4c8e6665bbfe', 1659996, '7c1ee7003ed014330d87c89e2064a2ec', NULL), ('ScRNA-seqLevel4', 'single_cell_RNAseq_level_4/SCLC/MAST/MAST.individual/PleuralEffusion/MAST.clusters_phenographLV/clusters_phenographLV.0.filtered.csv', 'csv', 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