Metadata

Cell line

Information about the cell line or cell culture biomaterial.

View JSON source: cell_linedoneShow required fields only

Properties

Catalog numbercell_line.catalog_numbercopy (string) The supplier catalogue number for the cell line. For example "77650057".
Catalog URLcell_line.catalog_urlcopy (string) The supplier catalogue URL for the cell line. For example "www.phe-culturecollections.org.uk/products/celllines/ipsc/detail.jsp?refId=77650057&collection=ecacc_ipsc".
Percent confluencycell_line.confluencycopy (number) The percent a plate surface is covered by cells. For example "60".
Date establishedcell_line.date_establishedcopy (string) Date when the cell line was established. For example "2017-03-19", "2002/03" or "1995".
Karyotypecell_line.karyotypecopy (string) The karyotype of the cell line. For example "sex chromosome complement of XY" or "del(2) (q11)".
Lot/batch numbercell_line.lot_numbercopy (string) The supplier lot or batch number for the cell line. For example "24.10.14".
Suppliercell_line.suppliercopy (string) The supplier of the cell line. For example "HipSci" or "ATCC".
Cell line typeRequiredcell_line.typecopy (string enum) The type of cell line. Should be one of: "primary", "immortalized", "stem cell", "stem cell-derived", "induced pluripotent" or "synthetic".
Cell line>Cell cycle (cell_cycle_ontology object) The cell cycle phase if the cell line is synchronized growing cells or the phase is known.
Cell cycle ontology IDcell_line.cell_cycle.ontologycopy (string from cell_cycle_ontology) An ontology term identifier in the form prefix:accession. For example "GO:0051321" or "GO:0000080".Graph restriction: Subclasses of GO:0007049, GO:0022403 from obo:hcao or obo:go.
Cell cycle ontology labelcell_line.cell_cycle.ontology_labelcopy (string from cell_cycle_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "meiotic cell cycle" or "mitotic G1 phase".
Cell cycleRequiredcell_line.cell_cycle.textcopy (string from cell_cycle_ontology) The name of a cell cycle of the cells in the specimen. For example "meiotic cell cycle" or "mitotic G1 phase".
Cell line>Cell morphology (cell_morphology object) Features relating to the morphology of the cells.
Cell morphologycell_line.cell_morphology.cell_morphologycopy (string from cell_morphology) General description of the morphology of cells. For example "adherent cells" or "form single layer colonies".
Cell sizecell_line.cell_morphology.cell_sizecopy (string from cell_morphology) Size of cells in Cell size unit. For example "15" or "20-30".
Cell viability methodcell_line.cell_morphology.cell_viability_methodcopy (string from cell_morphology) The method by which cell viability was determined. For example "Fluorescein diacetate hydrolysis" or "ATP test".
Cell viability resultcell_line.cell_morphology.cell_viability_resultcopy (string enum from cell_morphology) Result of the cell viability test. Should be one of: "pass" or "fail".
Percent cell viabilitycell_line.cell_morphology.percent_cell_viabilitycopy (number from cell_morphology) Percent of cells determined to be viable. For example "98.7".
Percent necrotic cellscell_line.cell_morphology.percent_necrosiscopy (number from cell_morphology) Percent of cells identified to be necrotic. For example "10".
Cell line>Cell morphology>Cell size unit (length_unit_ontology object) The unit in which the Cell size is expressed.
Length unit ontology IDcell_line.cell_morphology.cell_size_unit.ontologycopy (string from length_unit_ontology) An ontology term identifier in the form prefix:accession. For example "UO:0000017" or "UO:0000008".Graph restriction: Subclasses of UO:0000001 from obo:efo or obo:uo.
Length unit ontology labelcell_line.cell_morphology.cell_size_unit.ontology_labelcopy (string from length_unit_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "micrometer" or "meter".
Length unitRequiredcell_line.cell_morphology.cell_size_unit.textcopy (string from length_unit_ontology) The name of a length unit being used. For example "micrometer" or "meter".
Cell line>Cell type (cell_type_ontology object) The cell type that the cell line represents.
Cell type ontology IDcell_line.cell_type.ontologycopy (string from cell_type_ontology) An ontology term identifier in the form prefix:accession. For example "CL:1001610" or "CL:0000746".Graph restriction: Subclasses of CL:0000003 from obo:hcao or obo:cl.
Cell type ontology labelcell_line.cell_type.ontology_labelcopy (string from cell_type_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "bone marrow hematopoietic cell" or "cardiac muscle cell".
Cell typeRequiredcell_line.cell_type.textcopy (string from cell_type_ontology) The name of a cell type supplied by a user. For example "bone marrow hematopoietic cell" or "cardiac muscle cell".
Cell line>Disease (disease_ontology object) Short description of any disease association to the cell type.
Disease ontology IDcell_line.disease.ontologycopy (string from disease_ontology) An ontology term identifier in the form prefix:accession. For example "MONDO:0005148" or "PATO:0000461".Graph restriction: Subclasses of MONDO:0000001, PATO:0000461 from obo:mondo or obo:efo including self.
Disease ontology labelcell_line.disease.ontology_labelcopy (string from disease_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "type 2 diabetes mellitus" or "normal".
DiseaseRequiredcell_line.disease.textcopy (string from disease_ontology) The text for the term as the user provides it. For example "type 2 diabetes mellitus" or "normal".
Cell line>Genus species (species_ontology array) The scientific binomial name for the species of the cell line.
Species ontology IDcell_line.genus_species.ontologycopy (string from species_ontology) An ontology term identifier in the form prefix:accession. For example "NCBITaxon:9606" or "NCBITaxon:10090".Graph restriction: Subclasses of OBI:0100026, NCBITaxon:2759 from obo:efo or obo:NCBITaxon.
Species ontology labelcell_line.genus_species.ontology_labelcopy (string from species_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "Homo sapiens" or "Mus musculus".
SpeciesRequiredcell_line.genus_species.textcopy (string from species_ontology) The name of the species to which the organism belongs. For example "Homo sapiens" or "Mus musculus".
Cell line>Growth conditions (growth_conditions object) Features relating to the growth and/or maintenance of the cell lines.
Culture environmentcell_line.growth_conditions.culture_environmentcopy (string from growth_conditions) Cell culture environment in which cells are grown. For example "Adherent cell culture" or "Suspension cell culture".
Drug treatmentcell_line.growth_conditions.drug_treatmentcopy (string from growth_conditions) Description of drugs added to the growth medium. For example "100 ug/mL ampicillin" or "15 ug/mL tetracycline".
Feeder layer typecell_line.growth_conditions.feeder_layer_typecopy (string enum from growth_conditions) Type of feeder layer cells on which biomaterial was grown. Should be one of: "feeder-free", "feeder-dependent, JK1 feeder cells", "feeder-dependent, SNL 76/7 feeder cells", "feeder-dependent, human marrow stromal cells", "feeder-dependent, bovine embryonic fibroblast cells", "feeder-dependent, mouse embryonic fibroblast cells", "feeder-dependent, mouse fibroblast STO cells", "feeder-dependent, mouse bone marrow stromal cells", "feeder-dependent, mouse yolk sac-derived endothelial cells", "feeder-dependent, human foreskin fibroblast cells", "feeder-dependent, human newborn fibroblast cells", "feeder-dependent, human fetal lung fibroblast cells", "feeder-dependent, human uterine endometrial cells", "feeder-dependent, human breast parenchymal cells", "feeder-dependent, human embryonic fibroblast cells", "feeder-dependent, human adipose stromal cells", "feeder-dependent, human amniotic epithelial cells", "feeder-dependent, human placental fibroblast cells", "feeder-dependent, human umbilical cord stromal cells", "feeder-dependent, human fetal muscle cells", "feeder-dependent, human fetal skin cells", "feeder-dependent, human fetal liver stromal cells", "feeder-dependent, human fallopian tubal epithelial cells" or "feeder-dependent, human amniotic mesenchymal cells".
Growth mediumcell_line.growth_conditions.growth_mediumcopy (string from growth_conditions) The solid, liquid, or semi-solid medium used to support growth. For example "human placental cord serum" or "RPMI 1640 + 2mM Glutamine + 10-20% FBS".
Mycoplasma testing methodcell_line.growth_conditions.mycoplasma_testing_methodcopy (string enum from growth_conditions) The method by which the biomaterial was tested for mycoplasma contamination. Should be one of: "Direct DNA stain", "Indirect DNA stain", "Broth and agar culture", "PCR", "Nested PCR", "ELISA", "Autoradiography", "Immunostaining", "Cell-based assay" or "Microbiological assay".
Mycoplasma testing resultscell_line.growth_conditions.mycoplasma_testing_resultscopy (string enum from growth_conditions) Whether the biomaterial passed or failed the mycoplasma test. Should be one of: "pass" or "fail".
Passage numbercell_line.growth_conditions.passage_numbercopy (integer from growth_conditions) The number of passages that the biomaterial has been through. For example "22".
Cell line>Organ modelRequired (organ_ontology object) Organ for which this cell line is a model.
Organ ontology IDcell_line.model_organ.ontologycopy (string from organ_ontology) An ontology term identifier in the form prefix:accession. For example "UBERON:0000948" or "UBERON:0002405".Graph restriction: Subclasses of UBERON:0000465 from obo:hcao or obo:uberon including self.
Organ ontology labelcell_line.model_organ.ontology_labelcopy (string from organ_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "heart" or "immune system".
OrganRequiredcell_line.model_organ.textcopy (string from organ_ontology) The text for the term as the user provides it. For example "heart" or "immune system".
Cell line>Publication (publication object) A publication that cites the cell line creation.
AuthorsRequiredcell_line.publication.authorscopy (array from publication) A list of authors associated with the publication. For example "Doe JD".
Publication DOIcell_line.publication.doicopy (string from publication) The publication digital object identifier (doi) of the publication. For example "10.1016/j.cell.2016.07.054".
Official HCA PublicationRequiredcell_line.publication.official_hca_publicationcopy (boolean from publication) Has the publication been accepted as an official HCA publication, according to the process described in https://www.humancellatlas.org/publications/ ? For example "yes" or "no".
Publication PMIDcell_line.publication.pmidcopy (integer from publication) The PubMed ID of the publication. For example "27565351".
Publication titleRequiredcell_line.publication.titlecopy (string from publication) The title of the publication. For example "Study of single cells in the human body.".
Publication URLcell_line.publication.urlcopy (string from publication) A URL for the publication. For example "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5667944/".
Cell line>Timecourse (timecourse object) Information relating to a timecourse associated with this cell line.
Timecourse relevancecell_line.timecourse.relevancecopy (string from timecourse) Relevance of the Timecourse value/unit to the experiment. For example "Collection after tumor cells injected into the mammary gland" or "Time tissue underwent liberase digestion".
Timecourse valueRequiredcell_line.timecourse.valuecopy (string from timecourse) The numerical value in Timecourse unit associated with a time interval used in the experiment. For example "2" or "5.5-10.5".
Cell line>Timecourse>Timecourse unitRequired (time_unit_ontology object) The unit in which the Timecourse value is expressed.
Time unit ontology IDcell_line.timecourse.unit.ontologycopy (string from time_unit_ontology) An ontology term identifier in the form prefix:accession. For example "UO:0000010" or "UO:0000034".Graph restriction: Subclasses of UO:0000003, UO:0000149 from obo:efo or obo:uo.
Time unit ontology labelcell_line.timecourse.unit.ontology_labelcopy (string from time_unit_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "second" or "week".
Time unitRequiredcell_line.timecourse.unit.textcopy (string from time_unit_ontology) The name of a time unit being used. For example "second" or "week".
Cell line>Tissue (organ_part_ontology object) The tissue that the cell line was derived from.
Organ part ontology IDcell_line.tissue.ontologycopy (string from organ_part_ontology) An ontology term identifier in the form prefix:accession. For example "UBERON:0002371" or "UBERON:0000006".Graph restriction: Subclasses of UBERON:0000465 from obo:hcao or obo:uberon including self.
Organ part ontology labelcell_line.tissue.ontology_labelcopy (string from organ_part_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "bone marrow" or "islet of Langerhans".
Organ partRequiredcell_line.tissue.textcopy (string from organ_part_ontology) The text for the term as the user provides it. For example "bone marrow" or "islet of Langerhans".
Cell line>Biomaterial coreRequired (biomaterial_core object) Core biomaterial-level information.
HDBR accessioncell_line.biomaterial_core.HDBR_accessioncopy (string from biomaterial_core) A Human Developmental Biology Resource (HDBR) sample accession. For example "34526" or "14758, 2, liver".
Biomaterial descriptioncell_line.biomaterial_core.biomaterial_descriptioncopy (string from biomaterial_core) A general description of the biomaterial.
Biomaterial IDRequiredcell_line.biomaterial_core.biomaterial_idcopy (string from biomaterial_core) A unique ID for the biomaterial.
Biomaterial namecell_line.biomaterial_core.biomaterial_namecopy (string from biomaterial_core) A short, descriptive name for the biomaterial that need not be unique.
BioSamples accessioncell_line.biomaterial_core.biosamples_accessioncopy (string from biomaterial_core) A BioSamples accession. For example "SAMN00000000".
Genotypecell_line.biomaterial_core.genotypecopy (string from biomaterial_core) Genotype of the biomaterial. For example "DRB1 0401 protective allele" or "HLA-B*3901 allele".
INSDC sample accessioncell_line.biomaterial_core.insdc_sample_accessioncopy (string from biomaterial_core) An International Nucleotide Sequence Database Collaboration (INSDC) sample accession. For example "SRS0000000".
NCBI taxon IDRequiredcell_line.biomaterial_core.ncbi_taxon_idcopy (array from biomaterial_core) A taxonomy ID (taxonID) from NCBI. For example "9606".
Supplementary filescell_line.biomaterial_core.supplementary_filescopy (array from biomaterial_core) A list of filenames of biomaterial-level supplementary files. For example "sample_site_image.jpg".
Cell line>provenance (provenance object) Provenance information provided by the system.
Accessioncell_line.provenance.accessioncopy (string from provenance) A unique accession for this entity, provided by the broker.
Document IDRequiredcell_line.provenance.document_idcopy (string from provenance) Identifier for document.
Schema major versioncell_line.provenance.schema_major_versioncopy (integer from provenance) The major version number of the schema. For example "4" or "10".
Schema minor versioncell_line.provenance.schema_minor_versioncopy (integer from provenance) The minor version number of the schema. For example "6" or "15".
Submission dateRequiredcell_line.provenance.submission_datecopy (string from provenance) When project was first submitted to database.
Submitter IDcell_line.provenance.submitter_idcopy (string from provenance) ID of individual who first submitted project.
Update datecell_line.provenance.update_datecopy (string from provenance) When project was last updated.
Updater IDcell_line.provenance.updater_idcopy (string from provenance) ID of individual who last updated project.