{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS8023FPBJ/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS8023FPBJ",
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sample",
"detail": "In vitro system [IGVFSM3098USXZ](/in-vitro-systems/IGVFSM3098USXZ/) has only 1 child sample [IGVFSM3098USXZ](/in-vitro-systems/IGVFSM3098USXZ/) in `parts`. Parent samples are expected to have multiple child samples.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_parent_sample_with_singular_child",
"path": "/in-vitro-systems/IGVFSM3098USXZ/"
},
{
"category": "missing sample",
"detail": "In vitro system [IGVFSM3098USXZ](/in-vitro-systems/IGVFSM3098USXZ/) has only 1 child sample [IGVFSM8941DKFN](/in-vitro-systems/IGVFSM8941DKFN/) in `origin_of`. Parent samples are expected to have multiple child samples.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_parent_sample_with_singular_child",
"path": "/in-vitro-systems/IGVFSM3098USXZ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing files",
"detail": "Auxiliary set [IGVFDS8023FPBJ](/auxiliary-sets/IGVFDS8023FPBJ/) has no `files`. File sets are expected to have files.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_no_files",
"path": "/auxiliary-sets/IGVFDS8023FPBJ/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM3098USXZ](/in-vitro-systems/IGVFSM3098USXZ/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_nucleic_acid_delivery",
"path": "/in-vitro-systems/IGVFSM3098USXZ/"
}
]
},
"award": {
"@id": "/awards/HG012012/",
"component": "data coordination",
"title": "A Data and Administrative Coordinating Center for the Impact of Genomic Variation on Function Consortium"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS7068CPID/",
"accession": "IGVFDS7068CPID",
"file_set_type": "guide library",
"status": "released",
"summary": "guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"control_for": [],
"creation_timestamp": "2023-12-12T22:28:36.882250+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "cell hashing barcode sequencing",
"files": [],
"input_for": [
"/analysis-sets/IGVFDS7216VESH/"
],
"lab": {
"@id": "/labs/j-michael-cherry/",
"title": "J. Michael Cherry, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS0256YYSE/",
"accession": "IGVFDS0256YYSE",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep4-BinD_AmpliconSequencing_idan"
],
"preferred_assay_title": "Variant-EFFECTS",
"status": "in progress"
}
],
"notes": "Testing upgrade. Original file_set_type was oligo-conjugated antibodies. This was replaced to be cell hashing during upgrade. This file_set previously had 1b364e86-e0a2-4f31-a820-cb3018fa5cea submitted as library_construction_platform, but the property library_construction_platform has been now removed.. File_set_type enum cell hashing has been renamed to be cell hashing barcode sequencing.",
"release_timestamp": "2023-12-12T22:28:36.882250+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3098USXZ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3098USXZ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-BinB_idan"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/84486717-53c5-477a-bff0-e686dc38d8a7/",
"modality": "prime editing",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "in progress",
"summary": "THP-1",
"term_name": "THP-1"
}
],
"status": "in progress",
"summary": "Homo sapiens (male) THP-1 cell line modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "12",
"status": "revoked",
"submitted_by": {
"@id": "/users/6bae687f-b77a-46b9-af0e-a02c135cf42e/",
"title": "Meenakshi Kagda"
},
"submitter_comment": "testing upgrade version 5 to 6",
"summary": "cell hashing barcode sequencing for CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "e5937f48-82af-47ca-9d5b-f38b70d3eb3a"
}