-- DBMS: bigquery
CREATE TABLE `isb-cgc-bq.HTAN_versioned.bulkMethylationseq_level1_metadata_r4`
(
  entityId STRING OPTIONS(description="Synapse ID of entity"),
  Bisulfite_Conversion STRING OPTIONS(description="Name of the kit used in bisulfite conversion."),
  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)"),
  Nucleic_Acid_Source STRING OPTIONS(description="The source of the input nucleic molecule"),
  Id STRING OPTIONS(description="Unique identifier of entity e.g. a96059eb-81af-4b24-ae50-9242c0d8f819"),
  Total_DNA_Input STRING OPTIONS(description="Overall number of reads for a given sample in digits (microgram, nanogram)."),
  Sequencing_Platform STRING OPTIONS(description="A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument."),
  Bulk_Methylation_Assay_Type STRING OPTIONS(description="Assay types normally determine genomic coverage"),
  HTAN_Parent_Biospecimen_ID STRING OPTIONS(description="HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated"),
  Component STRING OPTIONS(description="Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows."),
  Replicate_Type STRING OPTIONS(description="A common term for all files belonging to the same sample. We suggest using a stable sample accession from a biosample archive like BioSamples."),
  File_Format STRING OPTIONS(description="Format of a file (e.g. txt, csv, fastq, bam, etc.)"),
  Filename STRING OPTIONS(description="Name of a file"),
  HTAN_Center STRING OPTIONS(description="Name of HTAN Center e.g. HTAN HTAPP"),
  Manifest_Id STRING OPTIONS(description="Synapse ID of manifest containing file annotation"),
  Manifest_Version INT64 OPTIONS(description="Latest version of metadata manifest"),
  File_Size INT64 OPTIONS(description="Size of file (bucket object) in bytes"),
  md5 STRING OPTIONS(description="md5 hash of file"),
  Data_Release STRING OPTIONS(description="Inclusion in HTAN Data Release e.g. Release 1.0"),
  CDS_Release STRING OPTIONS(description="CDS transfer package in which file was included e.g. v22.6.1.seq")
)
OPTIONS(
  friendly_name="HTAN BULKMETHYLATION SEQ LEVEL 1 METADATA R4 VERSIONED",
  description="This table contains the file metadata for the first level Bulk Methyl sequencing. Data was extracted from HTAN Synapse projects in October 2023. More details: see https://data.humantumoratlas.org/standard/sequencing",
  labels=[("access", "open"), ("data_type", "file_metadata"), ("program", "htan"), ("source", "htan"), ("category", "metadata"), ("status", "current")]
);

INSERT INTO `isb-cgc-bq.HTAN_versioned.bulkMethylationseq_level1_metadata_r4` (entityId, Bisulfite_Conversion, HTAN_Data_File_ID, Nucleic_Acid_Source, Id, Total_DNA_Input, Sequencing_Platform, Bulk_Methylation_Assay_Type, HTAN_Parent_Biospecimen_ID, Component, Replicate_Type, File_Format, Filename, HTAN_Center, Manifest_Id, Manifest_Version, File_Size, md5, Data_Release, CDS_Release) VALUES ('syn45135795', 'NEBNext Enzymatic Methyl-seq Kit', 'HTA10_01_43208332606526216901477335450321', 'Bulk Whole Cell', 'c68b50d7-417e-46b0-a6ed-00e492247858', NULL, 'Ultima Genomics UG100', 'Whole genome', 'HTA10_01_004', 'BulkMethylation-seqLevel1', 'Not Applicable', 'fastq', 'bulk_methyl_seq_level_1/A001_C004_120648.fq.gz', 'HTAN Stanford', 'syn51718142', 4, 85384456129, 'e32a8ddc6065c6cb69014773dfef03c1', 'Release 4.0', NULL), ('syn45136011', 'NEBNext Enzymatic Methyl-seq Kit', 'HTA10_01_31241678407000619453059401802613', 'Bulk Whole Cell', 'd8a770f1-ac5e-4bd5-811f-cf5125ab72ac', NULL, 'Ultima Genomics UG100', 'Whole genome', 'HTA10_01_004', 'BulkMethylation-seqLevel1', 'Not Applicable', 'fastq', 'bulk_methyl_seq_level_1/A001_C004_120655.fq.gz', 'HTAN Stanford', 'syn51718142', 4, 77772434012, 'd1ceb678ea7a006194530f94a18a2613', 'Release 4.0', NULL), ('syn45137935', 'NEBNext Enzymatic Methyl-seq Kit', 'HTA10_01_46294077943108131591650144554192', 'Bulk Whole Cell', '8d0a3213-d7bc-4929-89ae-8e13cb5d32b7', NULL, 'Ultima Genomics UG100', 'Whole genome', 'HTA10_01_005', 'BulkMethylation-seqLevel1', 'Not Applicable', 'fastq', 'bulk_methyl_seq_level_1/A001_C005_120648.fq.gz', 'HTAN Stanford', 'syn51718142', 4, 68983195386, '46c94077943b081dbf9b6f0beeffe19c', 'Release 4.0', NULL), ('syn45138173', 'NEBNext Enzymatic Methyl-seq Kit', 'HTA10_01_54114060048152634471554202053055', 'Bulk Whole Cell', '5f6d6067-fe33-4988-a140-c0074206d98c', NULL, 'Ultima Genomics UG100', 'Whole genome', 'HTA10_01_005', 'BulkMethylation-seqLevel1', 'Not Applicable', 'fastq', 'bulk_methyl_seq_level_1/A001_C005_120655.fq.gz', 'HTAN Stanford', 'syn51718142', 4, 60541623943, 'f41be06aa481f26dee7bf5eca205da55', 'Release 4.0', NULL), ('syn45138938', 'NEBNext Enzymatic Methyl-seq Kit', 'HTA10_01_87763024572233951479832245018290', 'Bulk Whole Cell', '488bb6b6-d6a6-460f-8704-dfe3da21d251', NULL, 'Ultima Genomics UG100', 'Whole genome', 'HTA10_01_007', 'BulkMethylation-seqLevel1', 'Not Applicable', 'fastq', 'bulk_methyl_seq_level_1/A001_C007_120648.fq.gz', 'HTAN Stanford', 'syn51718142', 4, 68720236239, '877630c4572c3d9fbe798dc2ef0b8290', 'Release 4.0', NULL);