{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS2394VMWJ/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS2394VMWJ",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR1_Rep1_S115",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR1_Rep2_S170",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR2_Rep1_S121",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR2_Rep2_S176",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR3_Rep1_S127",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR3_Rep2_S182",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR4_Rep1_S133",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR4_Rep2_S188"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2394VMWJ](/auxiliary-sets/IGVFDS2394VMWJ/) has sequence file(s) [IGVFFI4083RNOM](/sequence-files/IGVFFI4083RNOM/), [IGVFFI6531JUDM](/sequence-files/IGVFFI6531JUDM/), [IGVFFI0145XWMG](/sequence-files/IGVFFI0145XWMG/), [IGVFFI1648DHDD](/sequence-files/IGVFFI1648DHDD/), [IGVFFI6318MDEU](/sequence-files/IGVFFI6318MDEU/), [IGVFFI3208UFEI](/sequence-files/IGVFFI3208UFEI/), [IGVFFI3894LVNC](/sequence-files/IGVFFI3894LVNC/), [IGVFFI1771JOTI](/sequence-files/IGVFFI1771JOTI/) 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/IGVFDS2394VMWJ/"
}
]
},
"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": "2024-05-21T17:39:10.943480+00:00",
"donors": [
{
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"accession": "IGVFDO0384OZRW",
"aliases": [
"igvf:donor_of_HCT116"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
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{
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"accession": "IGVFFI4083RNOM",
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],
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"file_format": "fastq",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9911GLNJ/",
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"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR1_Rep1_S115"
],
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"upload_status": "validated"
},
{
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"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR4_Rep1_S133"
],
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"creation_timestamp": "2024-06-01T02:05:47.337602+00:00",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0145XWMG/",
"accession": "IGVFFI0145XWMG",
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"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR3_Rep2_S182"
],
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"file_size": 16200094,
"href": "/sequence-files/IGVFFI0145XWMG/@@download/IGVFFI0145XWMG.fastq.gz",
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"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1069NYSB/",
"accession": "IGVFFI1069NYSB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR2_Rep2_S176"
],
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"creation_timestamp": "2024-06-11T20:50:15.277099+00:00",
"file_format": "yaml",
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"href": "/configuration-files/IGVFFI1069NYSB/@@download/IGVFFI1069NYSB.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/58394ca9-7cbb-47a7-a640-ad9cc188496d/IGVFFI1069NYSB.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF1-BinE-PCR2_Rep2_S176.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1648DHDD/",
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"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR4_Rep2_S188"
],
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"creation_timestamp": "2024-06-01T02:06:06.043694+00:00",
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"file_size": 16867401,
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6318MDEU/",
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],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3208UFEI/",
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],
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},
{
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],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1771JOTI/",
"accession": "IGVFFI1771JOTI",
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],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7855SBQR/",
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],
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},
{
"@id": "/configuration-files/IGVFFI5081MANB/",
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},
{
"@id": "/configuration-files/IGVFFI7235MAKP/",
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},
{
"@id": "/configuration-files/IGVFFI3321WGQE/",
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],
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},
{
"@id": "/configuration-files/IGVFFI0663NHPJ/",
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],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9027LRAF/",
"accession": "IGVFFI9027LRAF",
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"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR4_Rep2_S188"
],
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"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4544YEQM/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
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"accession": "IGVFDS0310XYPS",
"aliases": [
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"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR1_Rep2_S170",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR2_Rep1_S121",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR2_Rep2_S176",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR3_Rep1_S127",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR3_Rep2_S182",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR4_Rep1_S133",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR4_Rep2_S188"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-07-10T20:21:17.948628+00:00",
"samples": [
{
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"@type": [
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"Biosample",
"Sample",
"Item"
],
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"aliases": [
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"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR1_Rep2_S170",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR2_Rep1_S121",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR2_Rep2_S176",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR3_Rep1_S127",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR3_Rep2_S182",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR4_Rep1_S133",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR4_Rep2_S188"
],
"classifications": [
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],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7857SYCK/"
],
"modifications": [
{
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},
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
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}
],
"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 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": "2024-06-01T02:03:48.475864+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "52908b80-5c55-42cb-80a6-fff0b41d1348"
}