{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3802XLBV/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3802XLBV",
"aliases": [
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR1_S5",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR2_S101",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR3_S197",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR4_S293"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM9116DXLY](/in-vitro-systems/IGVFSM9116DXLY/) has in progress subobject treatment [d35868d1-c45b-49ae-8ff3-a9c0c22551c2](/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM9116DXLY/"
},
{
"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/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO0384OZRW/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8896GBSX](/auxiliary-sets/IGVFDS8896GBSX/) has sequence file(s) [IGVFFI7202YFCO](/sequence-files/IGVFFI7202YFCO/), [IGVFFI6253BEMU](/sequence-files/IGVFFI6253BEMU/), [IGVFFI8588OWHR](/sequence-files/IGVFFI8588OWHR/), [IGVFFI4477VBFK](/sequence-files/IGVFFI4477VBFK/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS8896GBSX/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS5877TZTD/",
"accession": "IGVFDS5877TZTD",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_PILOT_CCND1-Auxin6hrs-FF1"
],
"file_set_type": "cell sorting"
},
{
"@id": "/auxiliary-sets/IGVFDS8896GBSX/",
"accession": "IGVFDS8896GBSX",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR1_S5",
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR2_S101",
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR3_S197",
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR4_S293"
],
"file_set_type": "gRNA sequencing"
}
],
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
"control_for": [],
"creation_timestamp": "2024-05-06T22:19:09.014126+00:00",
"documents": [
"/documents/74d53b9c-ab1d-42e3-b679-d3a00ae3d842/"
],
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"accession": "IGVFDO0384OZRW",
"aliases": [
"igvf:donor_of_HCT116"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [],
"input_for": [
"/analysis-sets/IGVFDS2982SJGW/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set.",
"preferred_assay_title": "CRISPR FlowFISH screen",
"protocols": [
"https://www.protocols.io/view/crispri-of-regulatory-elements-upon-degron-operati-5jyl82d59l2w/v1"
],
"release_timestamp": "2024-07-10T19:50:27.997338+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9116DXLY/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9116DXLY",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR1_S5",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR2_S101",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR3_S197",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR4_S293"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS0392OWNZ/",
"accession": "IGVFDS0392OWNZ",
"file_set_type": "guide library",
"summary": "Guide (sgRNA) library targeting accessible genome regions in 36 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 (sorting details: FACS bin E for 80-90% expression of CCND1) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected 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": "22",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T01:24:49.779269+00:00",
"summary": "mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in 36 genomic loci",
"targeted_genes": [
{
"@id": "/genes/ENSG00000110092/",
"geneid": "ENSG00000110092",
"name": "cyclin D1",
"symbol": "CCND1",
"synonyms": [
"BCL1",
"PRAD1",
"D11S287E",
"B-cell CLL/lymphoma 1",
"PRAD1 oncogene",
"BCL-1 oncogene",
"G1/S-specific cyclin-D1",
"B-cell lymphoma 1 protein",
"U21B31"
]
}
],
"uuid": "ced33de3-10b4-4a6f-935d-50df16820ef5"
}