{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS0078EAAP/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS0078EAAP",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR1_S66",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR2_S72",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR3_S162",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR4_S168"
],
"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 [IGVFSM4713PHAB](/in-vitro-systems/IGVFSM4713PHAB/) 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/IGVFSM4713PHAB/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS0078EAAP](/auxiliary-sets/IGVFDS0078EAAP/) has sequence file(s) [IGVFFI0574QGWX](/sequence-files/IGVFFI0574QGWX/), [IGVFFI7101MEEN](/sequence-files/IGVFFI7101MEEN/), [IGVFFI2836GXUE](/sequence-files/IGVFFI2836GXUE/), [IGVFFI8827QTFJ](/sequence-files/IGVFFI8827QTFJ/) 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/IGVFDS0078EAAP/"
}
]
},
"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": "2024-05-16T17:59:38.856195+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",
"files": [
{
"@id": "/sequence-files/IGVFFI0574QGWX/",
"accession": "IGVFFI0574QGWX",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR1_S66"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:22:40.455461+00:00",
"file_format": "fastq",
"file_size": 7190465,
"href": "/sequence-files/IGVFFI0574QGWX/@@download/IGVFFI0574QGWX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/9d77375f-9544-4bc0-b557-2771696b7ed4/IGVFFI0574QGWX.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF2-BinF-PCR1_S66_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1999NLYB/",
"accession": "IGVFFI1999NLYB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR1_S66"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:10:30.809820+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI1999NLYB/@@download/IGVFFI1999NLYB.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/00bc944e-64f3-421e-962d-b7eab6d981df/IGVFFI1999NLYB.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinF-PCR1_S66.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7101MEEN/",
"accession": "IGVFFI7101MEEN",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR2_S72"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:22:57.025875+00:00",
"file_format": "fastq",
"file_size": 13013915,
"href": "/sequence-files/IGVFFI7101MEEN/@@download/IGVFFI7101MEEN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/c7b74f92-4016-4c75-a4a3-5f927205528f/IGVFFI7101MEEN.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF2-BinF-PCR2_S72_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2836GXUE/",
"accession": "IGVFFI2836GXUE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR3_S162"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:26:24.459928+00:00",
"file_format": "fastq",
"file_size": 16180873,
"href": "/sequence-files/IGVFFI2836GXUE/@@download/IGVFFI2836GXUE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/1937eec8-b3fd-44af-b9fd-d802981edb56/IGVFFI2836GXUE.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF2-BinF-PCR3_S162_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8827QTFJ/",
"accession": "IGVFFI8827QTFJ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR4_S168"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:26:42.124213+00:00",
"file_format": "fastq",
"file_size": 28437769,
"href": "/sequence-files/IGVFFI8827QTFJ/@@download/IGVFFI8827QTFJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/82fe7be8-bfdd-4844-b23f-88393b6695f8/IGVFFI8827QTFJ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF2-BinF-PCR4_S168_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2875SNJW/",
"accession": "IGVFFI2875SNJW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR2_S72"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:10:45.597684+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI2875SNJW/@@download/IGVFFI2875SNJW.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/116ad698-cabe-42ff-9ebb-8c97c1a77407/IGVFFI2875SNJW.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinF-PCR2_S72.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8909CZJU/",
"accession": "IGVFFI8909CZJU",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR3_S162"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:11:02.635611+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI8909CZJU/@@download/IGVFFI8909CZJU.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/d64dd6cc-f5ca-43f2-bcf7-978e83c0865d/IGVFFI8909CZJU.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinF-PCR3_S162.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5051VBYP/",
"accession": "IGVFFI5051VBYP",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR4_S168"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:11:16.922592+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI5051VBYP/@@download/IGVFFI5051VBYP.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/8892ef60-e13a-4e8e-b71f-2220e05f8c6a/IGVFFI5051VBYP.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinF-PCR4_S168.yaml",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS6482AXWW/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS8445NSWZ/",
"accession": "IGVFDS8445NSWZ",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR1_S66",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR2_S72",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR3_S162",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR4_S168"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:17:40.455079+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4713PHAB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4713PHAB",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR1_S66",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR2_S72",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR3_S162",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinF-PCR4_S168"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7846UISG/"
],
"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 F for 80-100% expression of KITLG) 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": [
"/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": "2024-06-03T15:22:40.455461+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "f35880a7-bca0-4049-8a1d-30f137477c08"
}