{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS4894APIT/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS4894APIT",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR1_Rep1_S114",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR1_Rep2_S169",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR2_Rep1_S120",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR2_Rep2_S175",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR3_Rep1_S126",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR3_Rep2_S181",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR4_Rep1_S132",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR4_Rep2_S187"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS4894APIT](/auxiliary-sets/IGVFDS4894APIT/) has sequence file(s) [IGVFFI6767UOHJ](/sequence-files/IGVFFI6767UOHJ/), [IGVFFI1838TDNU](/sequence-files/IGVFFI1838TDNU/), [IGVFFI5888TLGJ](/sequence-files/IGVFFI5888TLGJ/), [IGVFFI4501LVHP](/sequence-files/IGVFFI4501LVHP/), [IGVFFI4677UICJ](/sequence-files/IGVFFI4677UICJ/), [IGVFFI1659OMPY](/sequence-files/IGVFFI1659OMPY/), [IGVFFI1400XMFH](/sequence-files/IGVFFI1400XMFH/), [IGVFFI7202ZYZL](/sequence-files/IGVFFI7202ZYZL/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS4894APIT/"
}
]
},
"award": {
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"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"
},
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"donors": [
{
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"aliases": [
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],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
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{
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],
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"upload_status": "validated"
},
{
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],
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"upload_status": "validated"
},
{
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],
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"upload_status": "validated"
},
{
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],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5910EETS/",
"accession": "IGVFFI5910EETS",
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],
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"s3_uri": "s3://igvf-files/2024/06/11/f8588a9b-e786-4530-aff8-40fc96b7d2c3/IGVFFI5910EETS.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4501LVHP/",
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],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4677UICJ/",
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],
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},
{
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],
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},
{
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],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7202ZYZL/",
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],
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},
{
"@id": "/configuration-files/IGVFFI4121BJCJ/",
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],
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},
{
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},
{
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},
{
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],
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},
{
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],
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},
{
"@id": "/configuration-files/IGVFFI2204VYTD/",
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],
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"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4544YEQM/"
],
"lab": {
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"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
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"accession": "IGVFDS2690TTFH",
"aliases": [
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"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR1_Rep2_S169",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR2_Rep1_S120",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR2_Rep2_S175",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR3_Rep1_S126",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR3_Rep2_S181",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR4_Rep1_S132",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR4_Rep2_S187"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-07-10T20:21:10.325514+00:00",
"samples": [
{
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"Biosample",
"Sample",
"Item"
],
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"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR1_Rep2_S169",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR2_Rep1_S120",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR2_Rep2_S175",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR3_Rep1_S126",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR3_Rep2_S181",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR4_Rep1_S132",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR4_Rep2_S187"
],
"classifications": [
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],
"construct_library_sets": [
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],
"modifications": [
{
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},
{
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}
],
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{
"@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 D for 55-65% expression of MYC) 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/",
"status": "released",
"treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
}
]
}
],
"schema_version": "12",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T02:03:45.203043+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "5dfd3991-e8d8-4c94-9aaa-be67bdf3ff18"
}