-- DBMS: bigquery
CREATE TABLE `isb-cgc-bq.HTAN_versioned.imaging_level4_HMS_crc_r3`
(
  CellID INT64 OPTIONS(description="Unique cell identifier in a specific image"),
  DNA_1 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  A488 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  A555 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  A647 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  DNA_2 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  CD3 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  CD11c FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  GranzymeB FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  DNA_3 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  Ki67 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  panCK FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  CD45 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  DNA_4 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  CD11b FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  CD68 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  CD14 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  DNA_5 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  CD163 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  FOXP3 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  CD8a FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  DNA_6 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  CD15 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  CD44 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  PD_L1 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  DNA_7 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  CD4 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  p_TBK1 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  PD_1 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  DNA_8 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  CD57 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  HLA_DR FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  LAG3 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  DNA_9 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  CD20 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  TIM3 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  HLA_A FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  DNA_10 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  CD16 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  pSRC FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  pSTAT1 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  DNA_11 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  CD24 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  Desmin FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  PDPN FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  DNA_12 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  STING FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  pRB FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  pTyr FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  X_centroid FLOAT64 OPTIONS(description="X-position of the centroid calculated as the center of mass of the cell."),
  Y_centroid FLOAT64 OPTIONS(description="Y-position of the centroid calculated as the center of mass of the cell."),
  column_centroid FLOAT64 OPTIONS(description="Column position of the centroid calculated as the center of mass of the cell."),
  row_centroid FLOAT64 OPTIONS(description="Row position of the centroid calculated as the center of mass of the cell."),
  Area INT64 OPTIONS(description="Matlab regionprops function: “Actual number of pixels in the region, returned as a scalar.”"),
  MajorAxisLength FLOAT64 OPTIONS(description="Matlab regionprops function: “Length (in pixels) of the major axis of the ellipse that has the same normalized second central moments as the region, returned as a scalar.”"),
  MinorAxisLength FLOAT64 OPTIONS(description="Matlab regionprops function: “Length (in pixels) of the minor axis of the ellipse that has the same normalized second central moments as the region, returned as a scalar.”"),
  Eccentricity FLOAT64 OPTIONS(description="Matlab regionprops function: “Eccentricity of the ellipse that has the same second-moments as the region, returned as a scalar. The eccentricity is the ratio of the distance between the foci of the ellipse and its major axis length. The value is between 0 and 1. (0 and 1 are degenerate cases. An ellipse whose eccentricity is 0 is actually a circle, while an ellipse whose eccentricity is 1 is a line segment.)”"),
  Solidity FLOAT64 OPTIONS(description="Matlab regionprops function: “Proportion of the pixels in the convex hull that are also in the region, returned as a scalar. Computed as Area/ConvexArea.”"),
  Extent FLOAT64 OPTIONS(description="Matlab regionprops function: “Ratio of pixels in the region to pixels in the total bounding box, returned as a scalar. Computed as the Area divided by the area of the bounding box.”"),
  Orientation FLOAT64 OPTIONS(description="Matlab regionprops function: “Angle between the x-axis and the major axis of the ellipse that has the same second-moments as the region, returned as a scalar. The value is in degrees, ranging from −90 degrees to 90 degrees.”"),
  Source_filename STRING OPTIONS(description="Name of file record was derived from"),
  Source_entityId STRING OPTIONS(description="Synapse ID of source file"),
  HTAN_Center STRING OPTIONS(description="Name of HTAN Center e.g. HTAN HTAPP"),
  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)"),
  HTAN_Biospecimen_ID STRING OPTIONS(description="HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz)"),
  Hoechst1 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  Hoechst2 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  NaKATPase FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  MCM6 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  p53 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  Hoechst3 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  PCNA FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  SMA_1 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  Hoechst4 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  E_Cad FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  SMA_2 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  Vimentin FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  Hoechst5 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  EGFR FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  CDX2 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  Hoechst6 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  pERK FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  H3K27me3 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  H3K27ac FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  Hoechst7 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  beta_Catenin FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  Hoechst8 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  N_Cadherin FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  H2ax FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  ZEB1 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  Hoechst9 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  Nestin FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  CD31 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  Hoechst10 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  S100a FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  GFAP FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  IRF_1 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  Hoechst11 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  pS6_235 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  cPARP FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  p21 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  Hoechst12 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  Unnamed_46 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  KAP1 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  Hoechst13 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  FN3 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  VEGFR2 FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker"),
  NGFR FLOAT64 OPTIONS(description="Mean intensity of pixels for specified marker")
)
OPTIONS(
  friendly_name="HTAN HMS IMAGING LEVEL 4 DATA - COLORECTAL R3 VERSIONED",
  description="This table contains fourth level imaging data for colorectal cancer samples. Data was derived in April 2023 from Imaging Level 4 csv files submitted by the HMS HTAN center. More details: see https://www.cell.com/cell/pdf/S0092-8674(22)01571-9.pdf",
  labels=[("access", "open"), ("data_type", "cell_spatial_characterization"), ("program", "htan"), ("source", "htan-hms"), ("status", "current"), ("category", "processed_-omics_data")]
);

INSERT INTO `isb-cgc-bq.HTAN_versioned.imaging_level4_HMS_crc_r3` (CellID, DNA_1, A488, A555, A647, DNA_2, CD3, CD11c, GranzymeB, DNA_3, Ki67, panCK, CD45, DNA_4, CD11b, CD68, CD14, DNA_5, CD163, FOXP3, CD8a, DNA_6, CD15, CD44, PD_L1, DNA_7, CD4, p_TBK1, PD_1, DNA_8, CD57, HLA_DR, LAG3, DNA_9, CD20, TIM3, HLA_A, DNA_10, CD16, pSRC, pSTAT1, DNA_11, CD24, Desmin, PDPN, DNA_12, STING, pRB, pTyr, X_centroid, Y_centroid, column_centroid, row_centroid, Area, MajorAxisLength, MinorAxisLength, Eccentricity, Solidity, Extent, Orientation, Source_filename, Source_entityId, HTAN_Center, HTAN_Data_File_ID, HTAN_Biospecimen_ID, Hoechst1, Hoechst2, NaKATPase, MCM6, p53, Hoechst3, PCNA, SMA_1, Hoechst4, E_Cad, SMA_2, Vimentin, Hoechst5, EGFR, CDX2, Hoechst6, pERK, H3K27me3, H3K27ac, Hoechst7, beta_Catenin, Hoechst8, N_Cadherin, H2ax, ZEB1, Hoechst9, Nestin, CD31, Hoechst10, S100a, GFAP, IRF_1, Hoechst11, pS6_235, cPARP, p21, Hoechst12, Unnamed_46, KAP1, Hoechst13, FN3, VEGFR2, NGFR) VALUES (1423041, 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