{
"@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": "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/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM0264XNND](/in-vitro-systems/IGVFSM0264XNND/) has in progress subobject degron modification [95081d1b-08b4-49ed-b324-e53fc43d8456](/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM0264XNND/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM0264XNND](/in-vitro-systems/IGVFSM0264XNND/) 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/IGVFSM0264XNND/"
}
],
"WARNING": [
{
"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": 40,
"level_name": "WARNING",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS2394VMWJ/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS2394VMWJ](/auxiliary-sets/IGVFDS2394VMWJ/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_file_set_for",
"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": [
{
"@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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"accession": "IGVFFI4083RNOM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR1_Rep1_S115"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:03:48.475864+00:00",
"file_format": "fastq",
"file_size": 25554537,
"href": "/sequence-files/IGVFFI4083RNOM/@@download/IGVFFI4083RNOM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/6c66ad7f-4444-4edc-9a3c-ce5debf28d0a/IGVFFI4083RNOM.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9911GLNJ/",
"accession": "IGVFFI9911GLNJ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR1_Rep1_S115"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:49:31.177352+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI9911GLNJ/@@download/IGVFFI9911GLNJ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/e3acd580-0efe-4a5b-b782-d18656f14eaa/IGVFFI9911GLNJ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF1-BinE-PCR1_Rep1_S115.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6531JUDM/",
"accession": "IGVFFI6531JUDM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR4_Rep1_S133"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:05:47.337602+00:00",
"file_format": "fastq",
"file_size": 20557061,
"href": "/sequence-files/IGVFFI6531JUDM/@@download/IGVFFI6531JUDM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/25c9d544-e7d4-41a8-b679-6ab83602838d/IGVFFI6531JUDM.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF1-BinE-PCR4-Rep1_S133_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0145XWMG/",
"accession": "IGVFFI0145XWMG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR3_Rep2_S182"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:05:28.235937+00:00",
"file_format": "fastq",
"file_size": 16200094,
"href": "/sequence-files/IGVFFI0145XWMG/@@download/IGVFFI0145XWMG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/50f4207d-60d7-47ba-9c29-7ada8ee4a584/IGVFFI0145XWMG.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF1-BinE-PCR3-Rep2_S182_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1069NYSB/",
"accession": "IGVFFI1069NYSB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR2_Rep2_S176"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:50:15.277099+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI1069NYSB/@@download/IGVFFI1069NYSB.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/58394ca9-7cbb-47a7-a640-ad9cc188496d/IGVFFI1069NYSB.yaml.gz",
"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/",
"accession": "IGVFFI1648DHDD",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR4_Rep2_S188"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:06:06.043694+00:00",
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"href": "/sequence-files/IGVFFI1648DHDD/@@download/IGVFFI1648DHDD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/dfd23610-d8e4-46d2-b659-3b005fbcf003/IGVFFI1648DHDD.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF1-BinE-PCR4-Rep2_S188_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6318MDEU/",
"accession": "IGVFFI6318MDEU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR2_Rep1_S121"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:04:28.959421+00:00",
"file_format": "fastq",
"file_size": 29797652,
"href": "/sequence-files/IGVFFI6318MDEU/@@download/IGVFFI6318MDEU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/e40741de-b2b3-45b3-9372-f915c999cf03/IGVFFI6318MDEU.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF1-BinE-PCR2-Rep1_S121_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3208UFEI/",
"accession": "IGVFFI3208UFEI",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR2_Rep2_S176"
],
"content_type": "reads",
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"href": "/sequence-files/IGVFFI3208UFEI/@@download/IGVFFI3208UFEI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/a76eca6f-7e4d-4e98-babe-57c7fbb47310/IGVFFI3208UFEI.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3894LVNC/",
"accession": "IGVFFI3894LVNC",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR1_Rep2_S170"
],
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"href": "/sequence-files/IGVFFI3894LVNC/@@download/IGVFFI3894LVNC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/49d5a413-eeea-40a6-8d77-0e221febf5a7/IGVFFI3894LVNC.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF1-BinE-PCR1-Rep2_S170_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1771JOTI/",
"accession": "IGVFFI1771JOTI",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR3_Rep1_S127"
],
"content_type": "reads",
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"href": "/sequence-files/IGVFFI1771JOTI/@@download/IGVFFI1771JOTI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/dee821a6-5207-407e-80ea-16a099b8ced0/IGVFFI1771JOTI.fastq.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7855SBQR/",
"accession": "IGVFFI7855SBQR",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR1_Rep2_S170"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:49:45.744452+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI7855SBQR/@@download/IGVFFI7855SBQR.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/33f5e9e2-64bf-4312-b8fa-82e49a172948/IGVFFI7855SBQR.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF1-BinE-PCR1_Rep2_S170.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5081MANB/",
"accession": "IGVFFI5081MANB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR3_Rep1_S127"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:50:30.320399+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI5081MANB/@@download/IGVFFI5081MANB.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/3ab2346a-ef65-4fce-9c2f-66b23884a78f/IGVFFI5081MANB.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF1-BinE-PCR3_Rep1_S127.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7235MAKP/",
"accession": "IGVFFI7235MAKP",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR2_Rep1_S121"
],
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"href": "/configuration-files/IGVFFI7235MAKP/@@download/IGVFFI7235MAKP.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3321WGQE/",
"accession": "IGVFFI3321WGQE",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR3_Rep2_S182"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:50:44.881055+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI3321WGQE/@@download/IGVFFI3321WGQE.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/3bb79cd4-a25a-444a-9a17-6e54e1b92ced/IGVFFI3321WGQE.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF1-BinE-PCR3_Rep2_S182.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0663NHPJ/",
"accession": "IGVFFI0663NHPJ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR4_Rep1_S133"
],
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"file_format": "yaml",
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"href": "/configuration-files/IGVFFI0663NHPJ/@@download/IGVFFI0663NHPJ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/0950f70e-a601-4298-8c28-595f1d8944cb/IGVFFI0663NHPJ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF1-BinE-PCR4_Rep1_S133.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9027LRAF/",
"accession": "IGVFFI9027LRAF",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR4_Rep2_S188"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:51:16.232634+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI9027LRAF/@@download/IGVFFI9027LRAF.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/8e3f2df4-4a5d-4271-83f8-963ad34198cd/IGVFFI9027LRAF.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF1-BinE-PCR4_Rep2_S188.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS0310XYPS/",
"accession": "IGVFDS0310XYPS",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR1_Rep1_S115",
"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"
}
],
"release_timestamp": "2024-07-10T20:21:17.948628+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0264XNND/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0264XNND",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR1_Rep1_S115",
"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": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7857SYCK/"
],
"modifications": [
"/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/"
],
"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 a guide library",
"taxa": "Homo sapiens",
"treatments": [
"/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/"
]
}
],
"schema_version": "11",
"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"
}