{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1953KIOT/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1953KIOT",
"aliases": [
"lea-starita:F9-DMS-Heavy-chain-antibody-Tile2-Replicate1-Bin3-FileSet_idan",
"igvf:my-alias"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003659/",
"assay_slims": [
"CRISPR screens"
],
"status": "released",
"term_name": "in vitro CRISPR screen assay"
},
"audit": {
"ERROR": [
{
"category": "inconsistent preferred assay title",
"detail": "Measurement set [IGVFDS1953KIOT](/measurement-sets/IGVFDS1953KIOT/) has `assay_term` in vitro CRISPR screen assay, but `preferred_assay_title` VAMP-seq. Measurement sets are expected to specify an appropriate preferred assay title for its respective assay term.",
"level": 60,
"level_name": "ERROR",
"name": "audit_preferred_assay_title",
"path": "/measurement-sets/IGVFDS1953KIOT/"
}
],
"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/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS1953KIOT](/measurement-sets/IGVFDS1953KIOT/) has in progress subobject in vitro system [IGVFSM3098USXZ](/in-vitro-systems/IGVFSM3098USXZ/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS1953KIOT/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing files",
"detail": "Measurement set [IGVFDS1953KIOT](/measurement-sets/IGVFDS1953KIOT/) has no `files`. File sets are expected to have files.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_no_files",
"path": "/measurement-sets/IGVFDS1953KIOT/"
},
{
"category": "missing construct library set",
"detail": "Measurement set [IGVFDS1953KIOT](/measurement-sets/IGVFDS1953KIOT/) has no `construct_library_sets` of type expression vector library linked in its `samples`. VAMP-seq measurement sets are expected to link to a construct library set of the type expression vector library in its samples.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_construct_library_set",
"path": "/measurement-sets/IGVFDS1953KIOT/"
},
{
"category": "missing protocol",
"detail": "Measurement set [IGVFDS1953KIOT](/measurement-sets/IGVFDS1953KIOT/) has no `protocols`. Measurement sets are expected to specify the experimental protocol utilized for conducting the assay on protocols.io.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_unspecified_protocol",
"path": "/measurement-sets/IGVFDS1953KIOT/"
}
],
"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/HG011969/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/65fd52d5-dc5d-457d-9563-a301f7a15ecc/",
"title": "Lea Starita"
},
"title": "The Center for Actionable Variant Analysis; measuring variant function at scale"
},
"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": "2024-03-29T00:30:42.387579+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [],
"input_for": [
"/analysis-sets/IGVFDS7736VVSH/"
],
"lab": {
"@id": "/labs/doug-fowler/",
"title": "Doug Fowler, UW"
},
"notes": "This file_set previously had fcd3ad7e-baa4-4f99-b779-f104501a8df7 submitted as library_construction_platform, but the property library_construction_platform has been now removed.",
"preferred_assay_title": "VAMP-seq",
"release_timestamp": "2024-03-22T23:04:37.145369+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": "26",
"status": "released",
"submitted_by": {
"@id": "/users/98fb23d3-0d79-4c3d-981d-01539e6589f1/",
"title": "Idan Gabdank"
},
"summary": "CRISPR prime editing VAMP-seq integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "ff3751eb-8590-4c56-ab5d-5b00960f510a"
}