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Experimental Overview And Metadata

Experimental data from Allen Cell Types Database is associated with the "Mouse Cell Types" and "Human Cell Types" Products.  Each cell is represented as Specimen object. Each cell Specimen is associated with an anatomical Structure and CellSomaLocation record containing the coordinate of the cell in the Common Coordinate Framework and a normalized depth between pia (value of 0) and white matter (value of 1) surfaces.  Each cell Specimen is also associated with two SpecimenTags describing the “dendrite type” All data used in the web application is available in the ApiCellTypesSpecimenDetail table.  Data includes structure, cortical layer, dendrite type (spiny, aspiny, sparsely spiny) and the “apical dendrite” , n/a), apical dendrite status (intact, truncated, n/a).  Human specimens are tagged with Conditions that indicate any donor disease conditions (tumor, epilepsy, , and others.   Mouse-specific records include the transgenic line name and reporter status.  Mouse-specific records include disease condition (epilepsy, tumor, none) and years of seizure history, if applicable.

See whitepapers for detailed experimental and annotation information.

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Examples:

  • All cells in the "Mouse Cell Types" Productdatabase

    No Format
    http://api.brain-map.org/api/v2/data/query.xml?criteria=
    model::SpecimenApiCellTypesSpecimenDetail
    ,rma::criteria,[is_cell_specimen$eq'true'],products[name$eq'Mouse Cell Types']
    ,rma::include,structure,donor(transgenic_lines),specimen_tags,cell_soma_locations
    ,rma::options[num_rows$eqall]
    
  • All cells tagged with 'dendrite type - spiny'

    No Format
    http://api.brain-map.org/api/v2/data/query.xml?criteria=
    model::SpecimenApiCellTypesSpecimenDetail
    ,rma::criteria,[istag_cell_specimen$eq'true'],products[name$eq'Mouse Cell Types']
    ,rma::include,
    structure,donor(transgenic_lines),specimen_tags[name$eq'dendrite type - spiny'],cell_soma_locations_dendrite_type$eq'spiny']
    ,rma::options[num_rows$eqall]
    
  • All cells annotated to be in layer 4

    No Format
    http://api.brain-map.org/api/v2/data/query.xml?criteria=
    model::SpecimenApiCellTypesSpecimenDetail
    ,rma::criteria,[isstructure_cell_specimen$eq'true'],products[name$eq'Mouse Cell Types']
    ,rma::include,structure[name$il'*layer 4*'],donor(transgenic_lines),specimen_tags,cell_soma_locationslayer$eq'4']
    ,rma::options[num_rows$eqall]
    
  • All human cells

    No Format
    http://api.brain-map.org/api/v2/data/query.xml?criteria=
    model::SpecimenApiCellTypesSpecimenDetail
    ,rma::criteria,[isdonor_cell_specimen$eqspecies$il'truehomo sapiens']
    ,products[name$eq'Human Cell Types']
    rma::options[num_rows$eqall]
  • All human cells with disease condition 'epilepsy'

    No Format
    http://api.brain-map.org/api/v2/data/query.xml?criteria=
    model::ApiCellTypesSpecimenDetail
    ,rma::includecriteria,structure,[donor(transgenic_lines,conditions),specimen_tags,cell_soma_locations_disease_state$il'epilepsy']
    ,rma::options[num_rows$eqall]



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