-- DBMS: bigquery
CREATE TABLE `isb-cgc-bq.HTAN_versioned.10xvisium_spatialtranscriptomics_scRNAseq_level1_metadata_r5`
(
  UMI_Barcode_Offset STRING OPTIONS(description="Start position of UMI barcode in the sequence. Values: number, 0 for start of read"),
  Reverse_Transcription_Primer STRING OPTIONS(description="An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA"),
  Feature_Reference_Id STRING OPTIONS(description="Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]"),
  Sequencing_Library_Construction_Days_from_Index STRING OPTIONS(description="Number of days between sample for assay was received in lab and day of sequencing library construction [number]. If not applicable please enter 'Not Applicable'"),
  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)"),
  Image_Re_orientation STRING OPTIONS(description="To ensure good fiducial alignment and tissue spots detection, it is important to correct for this shift in orientation."),
  Component STRING OPTIONS(description="Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows."),
  cDNA_Offset STRING OPTIONS(description="Offset in sequence for cDNA read (in bp): number"),
  Run_ID STRING OPTIONS(description="A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow."),
  Permeabilization_Time STRING OPTIONS(description="Fixed and stained tissue sections are permeabilized for different times. Each Capture Area captures polyadenylated mRNA from the attached tissue section. Measure is provided in minutes."),
  DV200 STRING OPTIONS(description="Represents the percentage of RNA fragments that are >200 nucleotides in size. Number"),
  Slide_Version STRING OPTIONS(description="Version of imaging slide used. Slide version is critical for the analysis of the sequencing data as different slides have different capture area layouts."),
  Spatial_Barcode_Offset STRING OPTIONS(description="Offset in sequence for spot barcode read (in bp): number"),
  Slide_ID STRING OPTIONS(description="For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide."),
  Spatial_Library_Construction_Method STRING OPTIONS(description="Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711]"),
  RIN STRING OPTIONS(description="A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products. Number"),
  cDNA_Length STRING OPTIONS(description="Length of cDNA read (in bp): number"),
  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."),
  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"),
  Spatial_Barcode_Length STRING OPTIONS(description="Length of spot barcode read (in bp): number"),
  Filename STRING OPTIONS(description="Name of a file"),
  Spatial_Read2 STRING OPTIONS(description="Read 2 content description"),
  entityId STRING OPTIONS(description="Synapse ID of entity"),
  Protocol_Link STRING OPTIONS(description="Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration,  lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated."),
  End_Bias STRING OPTIONS(description="The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript"),
  Library_Preparation_Days_from_Index STRING OPTIONS(description="Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable'"),
  Capture_Area STRING OPTIONS(description="Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1."),
  Id STRING OPTIONS(description="Unique identifier of entity e.g. a96059eb-81af-4b24-ae50-9242c0d8f819"),
  Read_Indicator STRING OPTIONS(description="Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other"),
  UMI_Barcode_Length STRING OPTIONS(description="Length of UMI barcode read (in bp): number"),
  Spatial_Read1 STRING OPTIONS(description="Read 1 content description"),
  File_Format STRING OPTIONS(description="Format of a file (e.g. txt, csv, fastq, bam, etc.)"),
  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 VISIUM RNA-SEQ LEVEL 1 METADATA R5 VERSIONED",
  description="This table contains the file metadata for first level (i.e. fastq files) 10x Genomics Visium sequencing. Data was extracted from HTAN Synapse projects in April 2024 and corresponds to HTAN Data Release 5.1. More details: see https://data.humantumoratlas.org/standard/spatial_transcriptomics",
  labels=[("access", "open"), ("data_type", "file_metadata"), ("program", "htan"), ("source", "htan"), ("category", "metadata"), ("status", "current")]
);

INSERT INTO `isb-cgc-bq.HTAN_versioned.10xvisium_spatialtranscriptomics_scRNAseq_level1_metadata_r5` (UMI_Barcode_Offset, Reverse_Transcription_Primer, Feature_Reference_Id, Sequencing_Library_Construction_Days_from_Index, HTAN_Data_File_ID, Image_Re_orientation, Component, cDNA_Offset, Run_ID, Permeabilization_Time, DV200, Slide_Version, Spatial_Barcode_Offset, Slide_ID, Spatial_Library_Construction_Method, RIN, cDNA_Length, Sequencing_Platform, HTAN_Parent_Biospecimen_ID, Spatial_Barcode_Length, Filename, Spatial_Read2, entityId, Protocol_Link, End_Bias, Library_Preparation_Days_from_Index, Capture_Area, Id, Read_Indicator, UMI_Barcode_Length, Spatial_Read1, File_Format, HTAN_Center, Manifest_Id, Manifest_Version, File_Size, md5, Data_Release, CDS_Release) VALUES ('0', 'Oligo-dT', NULL, 'Not Applicable', 'HTA12_248_1016', NULL, '10xVisiumSpatialTranscriptomics-RNA-seqLevel1', '0', 'V10L08-060', NULL, NULL, NULL, '0', NULL, '10xV1.0', NULL, '90', 'Illumina NovaSeq 6000', 'HTA12_248_8', '16', 'V10X_level_1_BRCA23/TWCE-HT308B1-S1H1Fc2U1Z1Bs1-HT308B1-S1H1Fc2U1Z1Bs1_1_S1_L004_R1_001.fastq.gz', 'cDNA', 'syn53215820', 'http://dx.doi.org/10.17504/protocols.io.x54v9d3opg3e/v1', '3 Prime', NULL, NULL, '7bcc2902-1c6b-42d3-a72c-b613a1b2d585', 'R1', '12', 'Spatial Barcode and UMI', 'gzip', 'HTAN WUSTL', 'syn53334349', 4, 7167115654, '85752bf0c6569a548645e74b22c535a4', 'Release 5.0', NULL), ('0', 'Oligo-dT', NULL, 'Not Applicable', 'HTA12_248_1018', NULL, '10xVisiumSpatialTranscriptomics-RNA-seqLevel1', '0', 'V10L08-060', NULL, NULL, NULL, '0', NULL, '10xV1.0', NULL, '90', 'Illumina NovaSeq 6000', 'HTA12_248_10', '16', 'V10X_level_1_BRCA23/TWCE-HT308B1-S1H4Fc2U1Z1Bs1-HT308B1-S1H4Fc2U1Z1Bs1_1_S4_L004_R1_001.fastq.gz', 'cDNA', 'syn53215776', 'http://dx.doi.org/10.17504/protocols.io.x54v9d3opg3e/v1', '3 Prime', NULL, NULL, 'a3c614f9-22ce-44c0-a7b7-b870684ce719', 'R1', '12', 'Spatial Barcode and UMI', 'gzip', 'HTAN WUSTL', 'syn53334349', 4, 5813690706, '4342d0a071c1225b9aca4df3114c41fd', 'Release 5.0', NULL), ('0', 'Oligo-dT', NULL, 'Not Applicable', 'HTA12_248_1020', NULL, '10xVisiumSpatialTranscriptomics-RNA-seqLevel1', '0', 'V10L08-060', NULL, NULL, NULL, '0', NULL, '10xV1.0', NULL, '90', 'Illumina NovaSeq 6000', 'HTA12_248_12', '16', 'V10X_level_1_BRCA23/TWCE-HT308B1-S1H5Fc2U1Z1Bs1-HT308B1-S1H5Fc2U1Z1Bs1_1_S5_L003_R1_001.fastq.gz', 'cDNA', 'syn53215888', 'http://dx.doi.org/10.17504/protocols.io.x54v9d3opg3e/v1', '3 Prime', NULL, NULL, '931be189-d9a8-441a-a732-9351ee15f815', 'R1', '12', 'Spatial Barcode and UMI', 'gzip', 'HTAN WUSTL', 'syn53334349', 4, 9522641966, 'b7f224f9f7c7b5300f566e2ebeb3ba09', 'Release 5.0', NULL), ('0', 'Oligo-dT', NULL, 'Not Applicable', 'HTA12_248_1017', NULL, '10xVisiumSpatialTranscriptomics-RNA-seqLevel1', '0', 'V10L08-060', NULL, NULL, NULL, '0', NULL, '10xV1.0', NULL, '90', 'Illumina NovaSeq 6000', 'HTA12_248_8', '16', 'V10X_level_1_BRCA23/TWCE-HT308B1-S1H1Fc2U1Z1Bs1-HT308B1-S1H1Fc2U1Z1Bs1_1_S1_L004_R2_001.fastq.gz', 'cDNA', 'syn53216155', 'http://dx.doi.org/10.17504/protocols.io.x54v9d3opg3e/v1', '3 Prime', NULL, NULL, 'e06b64ee-c3e1-4e15-89c3-b8615e57a026', 'R2', '12', 'Spatial Barcode and UMI', 'gzip', 'HTAN WUSTL', 'syn53334349', 4, 21528692196, '7fb754eff7b7f1a6df8ab14a04cfa5a8', 'Release 5.0', NULL), ('0', 'Oligo-dT', NULL, 'Not Applicable', 'HTA12_248_1019', NULL, '10xVisiumSpatialTranscriptomics-RNA-seqLevel1', '0', 'V10L08-060', NULL, NULL, NULL, '0', NULL, '10xV1.0', NULL, '90', 'Illumina NovaSeq 6000', 'HTA12_248_10', '16', 'V10X_level_1_BRCA23/TWCE-HT308B1-S1H4Fc2U1Z1Bs1-HT308B1-S1H4Fc2U1Z1Bs1_1_S4_L004_R2_001.fastq.gz', 'cDNA', 'syn53216061', 'http://dx.doi.org/10.17504/protocols.io.x54v9d3opg3e/v1', '3 Prime', NULL, NULL, '929a0157-5c64-40bf-a22e-85c53cae284f', 'R2', '12', 'Spatial Barcode and UMI', 'gzip', 'HTAN WUSTL', 'syn53334349', 4, 18658644973, 'b8739441089c9317be08030ed6814332', 'Release 5.0', NULL);