{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS3773NYHJ/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS3773NYHJ",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR1_Rep1_S135",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR1_Rep2_S190",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR2_Rep1_S141",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR2_Rep2_S196",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR3_Rep1_S147",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR3_Rep2_S202",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR4_Rep1_S153",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR4_Rep2_S208"
],
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS3773NYHJ](/auxiliary-sets/IGVFDS3773NYHJ/) has sequence file(s) [IGVFFI0625IJAQ](/sequence-files/IGVFFI0625IJAQ/), [IGVFFI9925PDQT](/sequence-files/IGVFFI9925PDQT/), [IGVFFI5272TWLQ](/sequence-files/IGVFFI5272TWLQ/), [IGVFFI1923OXRY](/sequence-files/IGVFFI1923OXRY/), [IGVFFI2912HULO](/sequence-files/IGVFFI2912HULO/), [IGVFFI7847XCEY](/sequence-files/IGVFFI7847XCEY/), [IGVFFI0779HVAM](/sequence-files/IGVFFI0779HVAM/), [IGVFFI7772BVHA](/sequence-files/IGVFFI7772BVHA/) 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/IGVFDS3773NYHJ/"
}
]
},
"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"
},
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"creation_timestamp": "2024-05-21T17:39:57.275820+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"accession": "IGVFDO0384OZRW",
"aliases": [
"igvf:donor_of_HCT116"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
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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"
},
{
"@id": "/configuration-files/IGVFFI6092JPSK/",
"accession": "IGVFFI6092JPSK",
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"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR2_Rep1_S141"
],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5272TWLQ/",
"accession": "IGVFFI5272TWLQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR1_Rep2_S190"
],
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"s3_uri": "s3://igvf-files/2024/06/01/56666d9c-c3a3-437a-8954-77a5f6125169/IGVFFI5272TWLQ.fastq.gz",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1923OXRY/",
"accession": "IGVFFI1923OXRY",
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"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR4_Rep2_S208"
],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2912HULO/",
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"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR3_Rep1_S147"
],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0240BUEF/",
"accession": "IGVFFI0240BUEF",
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],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7847XCEY/",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0779HVAM/",
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"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR3_Rep2_S202"
],
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"upload_status": "validated"
},
{
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},
{
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},
{
"@id": "/configuration-files/IGVFFI8226ETLT/",
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},
{
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],
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"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF2-BinA-PCR1_Rep2_S190.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6953RQCU/",
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],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1138TVPD/",
"accession": "IGVFFI1138TVPD",
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],
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"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4544YEQM/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS9717YXWE/",
"accession": "IGVFDS9717YXWE",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR1_Rep1_S135",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR1_Rep2_S190",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR2_Rep1_S141",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR2_Rep2_S196",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR3_Rep1_S147",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR3_Rep2_S202",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR4_Rep1_S153",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR4_Rep2_S208"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:21:32.218942+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9689GGGO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9689GGGO",
"aliases": [
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"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR1_Rep2_S190",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR2_Rep1_S141",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR2_Rep2_S196",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR3_Rep1_S147",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR3_Rep2_S202",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR4_Rep1_S153",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR4_Rep2_S208"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7857SYCK/"
],
"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 A for 0-10% 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/",
"treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
}
]
}
],
"schema_version": "11",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T02:06:12.280802+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "34ceeb44-77f1-4761-be4d-3535d706f4fc"
}