-- DBMS: bigquery
CREATE TABLE `isb-cgc-bq.HTAN_versioned.scRNAseq_VUMC_HTAN_DIS_EPI_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="ABS = absorptive cells, TUF = tuft cells, EE = enteroendocrine cells, ASC = adenoma specific cells, TAC = transient amplifying cells, CT = crypt top cells, GOB = goblet cells, SSC= serrated specific cells, STM = stem cells"),
  Tissue_Subtype STRING OPTIONS(description="TA = tubular adenoma, HP = hyperplastic polyp, TVA = tubulovillus adenoma, SSL = sessile serrated lesion, UNC = unclassified, NL = normal"),
  Tissue_Type STRING OPTIONS(description="AD = conventional adenoma, SER = serrated polyp, UNC = unclassified, NL = normal"),
  Gene_Name STRING OPTIONS(description="Measured gene")
)
OPTIONS(
  friendly_name="HTAN HG38 SCRNASEQ GENE EXPRESSION DISCOVERY COHORT EPITHELIAL R2 VERSIONED",
  description="Data was derived in April 2022 from an H5AD file (Synapse ID: syn27056097) submitted by the Vanderbilt HTAN Center. This data set contains raw gene expression counts from 62 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 the epithelial cells derived from the discsovery (DIS) cohort, 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_DIS_EPI_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 (28085, 8423, 31.0, 'GAGAAAGACCTTCGCTGG-45', 'HTA11_5363_200000101113111', 'HTA11_5363_2000001011', 'CT', 'SSL', 'SER', 'EEF1A1'), (38856, 8423, 15.0, 'CTTTCTTTATGGAAAT-60', 'HTA11_2992_200000101113111', 'HTA11_2992_2000001011', 'CT', 'HP', 'SER', 'EEF1A1'), (28085, 3160, 2.0, 'GAGAAAGACCTTCGCTGG-45', 'HTA11_5363_200000101113111', 'HTA11_5363_2000001011', 'CT', 'SSL', 'SER', 'ATP5B'), (39073, 4832, 2.0, 'TGATATTGCCTTTCACATA-60', 'HTA11_2992_200000101113111', 'HTA11_2992_2000001011', 'CT', 'HP', 'SER', 'CDC42'), (39043, 30074, 2.0, 'AGTCAAAGAGAATTCGT-60', 'HTA11_2992_200000101113111', 'HTA11_2992_2000001011', 'CT', 'HP', 'SER', 'SF1');