-- DBMS: bigquery
CREATE TABLE `isb-cgc-bq.HTAN_versioned.scRNAseq_VUMC_HTAN_VAL_DIS_NONEPI_V2_r2`
(
  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."),
  Cell_Barcode_Number STRING OPTIONS(description="Barcodes used for each droplet that contains the cell in the sequencing process"),
  HTAN_Parent_Data_File_ID STRING OPTIONS(description="HTAN Data File Identifier indicating the file(s) from which these files were derived"),
  HTAN_Biospecimen_ID STRING OPTIONS(description="HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz)"),
  Cell_Type STRING OPTIONS(description="B = B cell, T = T cell, END = endothelial, FIB = fibroblast, MAS = mast cell, MYE = myeloid, PLA = plasma"),
  Tissue_Subtype STRING OPTIONS(description="TA = tubular adenoma, HP = hyperplastic polyp, TVA = tubulovillus adenoma, SSL = sessile serrated lesion, NL = normal, MSI-H =microsatellite instability high CRC, MSS = microsatellite stable CRC"),
  Tissue_Type STRING OPTIONS(description="AD = conventional adenoma, SER = serrated polyp, NL = normal, MSI-H =microsatellite instability high CRC, MSS = microsatellite stable CRC"),
  Gene_Name STRING OPTIONS(description="Measured gene")
)
OPTIONS(
  friendly_name="HTAN HG38 SCRNASEQ GENE EXPRESSION CUMULATIVE NON-EPITHELIAL R2 VERSIONED",
  description="Data was derived in April 2022 from an H5AD file (Synapse ID:  syn27056098) submitted by the Vanderbilt HTAN Center. This data set contains raw gene expression counts from 128 patient samples. Data was generated using the InDrop V2 chemistry (see https://doi.org/10.1186/s12864-020-06843-0 ) and was processed using a DropEst-based pipeline (see https://doi.org/10.1016/j.xpro.2021.100450 ), where reads were mapped to HG38, followed by processing with scanpy and aformentioned pipeline to filter cells. Low-dimensional embeddings are derived from a regulon space, generated using SCENIC. This dataset contains all non-epithelial cells derived from both the discovery (DIS) and validation (VAL) cohorts, as described in https://doi.org/10.1016/j.cell.2021.11.031.",
  labels=[("access", "open"), ("reference_genome", "hg38"), ("data_type", "gene_expression"), ("program", "htan"), ("source", "htan-vumc"), ("category", "processed_-omics_data"), ("status", "current")]
);

INSERT INTO `isb-cgc-bq.HTAN_versioned.scRNAseq_VUMC_HTAN_VAL_DIS_NONEPI_V2_r2` (iObs, iVar, X_value, Cell_Barcode_Number, HTAN_Parent_Data_File_ID, HTAN_Biospecimen_ID, Cell_Type, Tissue_Subtype, Tissue_Type, Gene_Name) VALUES (2827, 15691, 2.0, 'ATGCTCCGTTTGGATCG-54', 'HTA11_6310_200000202113111', 'HTA11_6310_2000002021', 'B', 'NL', 'NL', 'PCNP'), (6875, 27125, 2.0, 'TGCGTATCAGCTACGG-16-5607', 'HTA11_8099_200000201113111', 'HTA11_8099_2000002011', 'B', 'NL', 'NL', 'TBC1D5'), (5768, 28591, 2.0, 'TGACGTAGAAGCTACTTGT-4-5607', 'HTA11_10167_200000202113111', 'HTA11_10167_2000002021', 'B', 'NL', 'NL', 'UBC'), (3238, 4200, 2.0, 'TGAGTCCATGTATCCCACG-54', 'HTA11_6310_200000202113111', 'HTA11_6310_2000002021', 'B', 'NL', 'NL', 'CCSER1'), (2796, 26484, 13.0, 'TGACGTATCGGCGCTCTCA-54', 'HTA11_6310_200000202113111', 'HTA11_6310_2000002021', 'B', 'NL', 'NL', 'SPICE1');