{
"@context": "/terms/",
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"TabularFile",
"File",
"Item"
],
"accession": "IGVFFI7448MNPA",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_file_CRUDO_CCND1_Auxin6hrs-FF2"
],
"assay_titles": [
"CRISPR FlowFISH screen"
],
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing file format specifications",
"detail": "Tabular file [IGVFFI7448MNPA](/tabular-files/IGVFFI7448MNPA/) has no `file_format_specifications`. Tabular files are expected to link to a file format specifications document describing the headers of the file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_tabular_file_no_file_format_specifications",
"path": "/tabular-files/IGVFFI7448MNPA/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization"
},
"barcode_map_for": [],
"content_md5sum": "850fcc164dbd87f7a3aabee8690a9b3f",
"content_type": "sample sort parameters",
"controlled_access": false,
"creation_timestamp": "2024-07-03T00:35:23.481238+00:00",
"file_format": "tsv",
"file_set": {
"@id": "/auxiliary-sets/IGVFDS1065WJDZ/",
"accession": "IGVFDS1065WJDZ",
"file_set_type": "cell sorting",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5974NFSN/",
"accession": "IGVFSM5974NFSN",
"classifications": [
"cell line"
],
"modifications": [
{
"@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"modality": "degradation",
"status": "released",
"summary": "AID system targeting RAD21"
},
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released",
"summary": "CRISPRi Sp-dCas9-KOX1-KRAB"
}
],
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{
"@id": "/sample-terms/EFO_0002824/",
"status": "released",
"term_name": "HCT116"
}
],
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"summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin A for 0-10% 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",
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{
"@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
"purpose": "activation",
"status": "released",
"summary": "Treatment of 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours",
"treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
}
]
},
{
"@id": "/in-vitro-systems/IGVFSM7955GCNG/",
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"classifications": [
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],
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{
"@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
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"summary": "AID system targeting RAD21"
},
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released",
"summary": "CRISPRi Sp-dCas9-KOX1-KRAB"
}
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{
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"status": "released",
"term_name": "HCT116"
}
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"summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin B for 10-20% 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",
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{
"@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
"purpose": "activation",
"status": "released",
"summary": "Treatment of 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours",
"treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
}
]
},
{
"@id": "/in-vitro-systems/IGVFSM1476QKIB/",
"accession": "IGVFSM1476QKIB",
"classifications": [
"cell line"
],
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{
"@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
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"summary": "AID system targeting RAD21"
},
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released",
"summary": "CRISPRi Sp-dCas9-KOX1-KRAB"
}
],
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{
"@id": "/sample-terms/EFO_0002824/",
"status": "released",
"term_name": "HCT116"
}
],
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"taxa": "Homo sapiens",
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{
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"purpose": "activation",
"status": "released",
"summary": "Treatment of 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours",
"treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
}
]
},
{
"@id": "/in-vitro-systems/IGVFSM5076QTOJ/",
"accession": "IGVFSM5076QTOJ",
"classifications": [
"cell line"
],
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{
"@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"modality": "degradation",
"status": "released",
"summary": "AID system targeting RAD21"
},
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released",
"summary": "CRISPRi Sp-dCas9-KOX1-KRAB"
}
],
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{
"@id": "/sample-terms/EFO_0002824/",
"status": "released",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin D for 55-65% 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",
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{
"@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
"purpose": "activation",
"status": "released",
"summary": "Treatment of 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours",
"treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
}
]
},
{
"@id": "/in-vitro-systems/IGVFSM6283XDLL/",
"accession": "IGVFSM6283XDLL",
"classifications": [
"cell line"
],
"modifications": [
{
"@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"modality": "degradation",
"status": "released",
"summary": "AID system targeting RAD21"
},
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released",
"summary": "CRISPRi Sp-dCas9-KOX1-KRAB"
}
],
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{
"@id": "/sample-terms/EFO_0002824/",
"status": "released",
"term_name": "HCT116"
}
],
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{
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"purpose": "activation",
"status": "released",
"summary": "Treatment of 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours",
"treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
}
]
},
{
"@id": "/in-vitro-systems/IGVFSM0402MSVI/",
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],
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{
"@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"modality": "degradation",
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"summary": "AID system targeting RAD21"
},
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released",
"summary": "CRISPRi Sp-dCas9-KOX1-KRAB"
}
],
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{
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"status": "released",
"term_name": "HCT116"
}
],
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"taxa": "Homo sapiens",
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{
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"purpose": "activation",
"status": "released",
"summary": "Treatment of 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours",
"treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
}
]
}
],
"status": "released",
"summary": "cell sorting for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci, mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci, ... and 4 more measurement sets"
},
"file_size": 483,
"gene_list_for": [],
"href": "/tabular-files/IGVFFI7448MNPA/@@download/IGVFFI7448MNPA.tsv.gz",
"input_file_for": [
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],
"integrated_in": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
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"md5sum": "05776d38ad9a634bdf0e4de9c3ca4617",
"release_timestamp": "2024-07-10T20:27:25.219489+00:00",
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"title": "Benjamin Doughty"
},
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/sortparams2/220307B014_15.tsv.gz",
"summary": "sample sort parameters",
"upload_status": "validated",
"uuid": "1c2d6efe-1285-4355-adfa-449c1fed842e"
}