{
"@context": "/terms/",
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"FileSet",
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],
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],
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"term_name": "in vitro CRISPR screen using single-cell RNA-seq"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM9983LVUX](/in-vitro-systems/IGVFSM9983LVUX/) has in progress subobject degron modification [95081d1b-08b4-49ed-b324-e53fc43d8456](/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/).",
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"name": "audit_item_status",
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},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM9983LVUX](/in-vitro-systems/IGVFSM9983LVUX/) has in progress subobject treatment [d35868d1-c45b-49ae-8ff3-a9c0c22551c2](/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/).",
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"name": "audit_item_status",
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},
{
"category": "mismatched status",
"detail": "Released human donor [IGVFDO0384OZRW](/human-donors/IGVFDO0384OZRW/) has in progress subobject publication [155f24ce-5c2c-4400-8651-da9447eaca25](/publications/155f24ce-5c2c-4400-8651-da9447eaca25/).",
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"name": "audit_item_status",
"path": "/human-donors/IGVFDO0384OZRW/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS5533XJRU](/auxiliary-sets/IGVFDS5533XJRU/) has sequence file(s) [IGVFFI7012CCWR](/sequence-files/IGVFFI7012CCWR/), [IGVFFI7666EOCK](/sequence-files/IGVFFI7666EOCK/), [IGVFFI4762FVTH](/sequence-files/IGVFFI4762FVTH/), [IGVFFI0675WIPQ](/sequence-files/IGVFFI0675WIPQ/), [IGVFFI4105QVFH](/sequence-files/IGVFFI4105QVFH/), [IGVFFI1421DDQV](/sequence-files/IGVFFI1421DDQV/), [IGVFFI8910PMMH](/sequence-files/IGVFFI8910PMMH/), [IGVFFI5484ZXJH](/sequence-files/IGVFFI5484ZXJH/), [IGVFFI7147GVXA](/sequence-files/IGVFFI7147GVXA/), [IGVFFI2954POWQ](/sequence-files/IGVFFI2954POWQ/), [IGVFFI2914SEZO](/sequence-files/IGVFFI2914SEZO/), [IGVFFI1192NXTI](/sequence-files/IGVFFI1192NXTI/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 40,
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"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS5533XJRU/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS6896VSKX](/measurement-sets/IGVFDS6896VSKX/) has sequence file(s) [IGVFFI9778ISFP](/sequence-files/IGVFFI9778ISFP/), [IGVFFI9026YNOD](/sequence-files/IGVFFI9026YNOD/), [IGVFFI7012DKGV](/sequence-files/IGVFFI7012DKGV/), [IGVFFI9585YHED](/sequence-files/IGVFFI9585YHED/), [IGVFFI2763QTWE](/sequence-files/IGVFFI2763QTWE/), [IGVFFI2367JOHE](/sequence-files/IGVFFI2367JOHE/), [IGVFFI8354TIRT](/sequence-files/IGVFFI8354TIRT/), [IGVFFI4212DNWG](/sequence-files/IGVFFI4212DNWG/), [IGVFFI1732ALVS](/sequence-files/IGVFFI1732ALVS/), [IGVFFI4474HZGX](/sequence-files/IGVFFI4474HZGX/), [IGVFFI4606KWZQ](/sequence-files/IGVFFI4606KWZQ/), [IGVFFI4195HNMX](/sequence-files/IGVFFI4195HNMX/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 40,
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"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS6896VSKX/"
}
]
},
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],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 86015c12-b9a6-43ba-9601-5d75aab4d39c was removed from this measurement set.",
"preferred_assay_title": "TAP-seq",
"protocols": [
"https://www.protocols.io/view/crispri-of-regulatory-elements-upon-degron-operati-5jyl82d59l2w/v1"
],
"release_timestamp": "2024-07-10T19:53:36.270241+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9983LVUX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9983LVUX",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_TAPseq-Auxin6hrs-Rep1"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS9869EMNE/",
"accession": "IGVFDS9869EMNE",
"file_set_type": "guide library",
"summary": "Guide (sgRNA) library targeting accessible genome regions in 29 genomic loci"
}
],
"modifications": [
{
"@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"modality": "degradation"
},
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HCT116"
],
"status": "released",
"summary": "HCT116",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
"purpose": "activation",
"summary": "Treatment of 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours",
"treatment_type": "chemical"
}
]
}
],
"schema_version": "21",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-03T19:09:45.640392+00:00",
"summary": "mixed TAP-seq integrating a guide (sgRNA) library targeting accessible genome regions in 29 genomic loci",
"uuid": "b5bdfc71-7a84-4ab6-a9c5-e4eee8ea194c"
}