{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS6678UHIV/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS6678UHIV",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR1_Rep1_S138",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR1_Rep2_S193",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR2_Rep1_S144",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR2_Rep2_S199",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR3_Rep1_S150",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR3_Rep2_S205",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR4_Rep1_S156",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR4_Rep2_S211"
],
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS6678UHIV](/auxiliary-sets/IGVFDS6678UHIV/) has sequence file(s) [IGVFFI7000MNXU](/sequence-files/IGVFFI7000MNXU/), [IGVFFI9023KXQX](/sequence-files/IGVFFI9023KXQX/), [IGVFFI1607CWVS](/sequence-files/IGVFFI1607CWVS/), [IGVFFI1491AZEG](/sequence-files/IGVFFI1491AZEG/), [IGVFFI1233YJYR](/sequence-files/IGVFFI1233YJYR/), [IGVFFI9919VFXO](/sequence-files/IGVFFI9919VFXO/), [IGVFFI0578DOVK](/sequence-files/IGVFFI0578DOVK/), [IGVFFI7502XORW](/sequence-files/IGVFFI7502XORW/) 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/IGVFDS6678UHIV/"
}
]
},
"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": "2024-05-21T17:39:59.870279+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/IGVFFI7000MNXU/",
"accession": "IGVFFI7000MNXU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR1_Rep1_S138"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:06:25.038440+00:00",
"file_format": "fastq",
"file_size": 20765805,
"href": "/sequence-files/IGVFFI7000MNXU/@@download/IGVFFI7000MNXU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/78d2488c-c421-47e9-bc60-2773562d92a9/IGVFFI7000MNXU.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF2-BinD-PCR1-Rep1_S138_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1104IEKV/",
"accession": "IGVFFI1104IEKV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR1_Rep1_S138"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:51:28.391387+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI1104IEKV/@@download/IGVFFI1104IEKV.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/380ecdd4-2190-4ac5-9aad-1c8a6f9e510c/IGVFFI1104IEKV.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF2-BinD-PCR1_Rep1_S138.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9023KXQX/",
"accession": "IGVFFI9023KXQX",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR4_Rep1_S156"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:08:18.776412+00:00",
"file_format": "fastq",
"file_size": 25105170,
"href": "/sequence-files/IGVFFI9023KXQX/@@download/IGVFFI9023KXQX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/81c2c6c6-d1bb-4413-aa0a-19f2a5621c21/IGVFFI9023KXQX.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF2-BinD-PCR4-Rep1_S156_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4503UDHR/",
"accession": "IGVFFI4503UDHR",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR3_Rep1_S150"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:52:27.750677+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI4503UDHR/@@download/IGVFFI4503UDHR.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/03362151-835f-4511-8b76-99589f27aac9/IGVFFI4503UDHR.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF2-BinD-PCR3_Rep1_S150.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2254QOGJ/",
"accession": "IGVFFI2254QOGJ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR4_Rep1_S156"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:52:56.661052+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI2254QOGJ/@@download/IGVFFI2254QOGJ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/a94605b5-5bdf-4a75-a383-349a769ec38a/IGVFFI2254QOGJ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF2-BinD-PCR4_Rep1_S156.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1607CWVS/",
"accession": "IGVFFI1607CWVS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR2_Rep2_S199"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:07:22.691041+00:00",
"file_format": "fastq",
"file_size": 23189951,
"href": "/sequence-files/IGVFFI1607CWVS/@@download/IGVFFI1607CWVS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/8e34e06c-5eca-4b2a-943e-0ab2c37d08be/IGVFFI1607CWVS.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF2-BinD-PCR2-Rep2_S199_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1491AZEG/",
"accession": "IGVFFI1491AZEG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR3_Rep2_S205"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:07:59.838430+00:00",
"file_format": "fastq",
"file_size": 22094580,
"href": "/sequence-files/IGVFFI1491AZEG/@@download/IGVFFI1491AZEG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/ac7287b8-0983-4e85-97d1-46a1d2655a44/IGVFFI1491AZEG.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1233YJYR/",
"accession": "IGVFFI1233YJYR",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR1_Rep2_S193"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:06:43.977041+00:00",
"file_format": "fastq",
"file_size": 22135977,
"href": "/sequence-files/IGVFFI1233YJYR/@@download/IGVFFI1233YJYR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/ab7bae09-215f-4300-bf30-326480ceec93/IGVFFI1233YJYR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF2-BinD-PCR1-Rep2_S193_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9919VFXO/",
"accession": "IGVFFI9919VFXO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR2_Rep1_S144"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:07:03.628724+00:00",
"file_format": "fastq",
"file_size": 24031827,
"href": "/sequence-files/IGVFFI9919VFXO/@@download/IGVFFI9919VFXO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/ebad9051-cefe-45d4-b25e-26cfb309bbcd/IGVFFI9919VFXO.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF2-BinD-PCR2-Rep1_S144_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0578DOVK/",
"accession": "IGVFFI0578DOVK",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR3_Rep1_S150"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:07:40.994774+00:00",
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"file_size": 15656832,
"href": "/sequence-files/IGVFFI0578DOVK/@@download/IGVFFI0578DOVK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/2c09dd6a-e919-4091-8c9f-df9e83bd1c4a/IGVFFI0578DOVK.fastq.gz",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7502XORW/",
"accession": "IGVFFI7502XORW",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR4_Rep2_S211"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:08:37.414951+00:00",
"file_format": "fastq",
"file_size": 31375283,
"href": "/sequence-files/IGVFFI7502XORW/@@download/IGVFFI7502XORW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/17d280a7-d184-451b-9853-0ccfed6124c6/IGVFFI7502XORW.fastq.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1754CREX/",
"accession": "IGVFFI1754CREX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR3_Rep2_S205"
],
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"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI1754CREX/@@download/IGVFFI1754CREX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/948b3928-6b20-489b-8bcc-661bbd63be03/IGVFFI1754CREX.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0718UKFU/",
"accession": "IGVFFI0718UKFU",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR4_Rep2_S211"
],
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"href": "/configuration-files/IGVFFI0718UKFU/@@download/IGVFFI0718UKFU.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/8d812c2d-5e31-46c4-aca6-2ab0e2e89d63/IGVFFI0718UKFU.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3762GXYM/",
"accession": "IGVFFI3762GXYM",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR2_Rep1_S144"
],
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"creation_timestamp": "2024-06-11T20:51:58.183052+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI3762GXYM/@@download/IGVFFI3762GXYM.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/b2dd0c1c-9d99-4c8d-9835-782784307de4/IGVFFI3762GXYM.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF2-BinD-PCR2_Rep1_S144.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8553LUVP/",
"accession": "IGVFFI8553LUVP",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR2_Rep2_S199"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:52:12.935709+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI8553LUVP/@@download/IGVFFI8553LUVP.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/5daa82d2-84fe-46c2-9a2f-34cab12fd8c3/IGVFFI8553LUVP.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF2-BinD-PCR2_Rep2_S199.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7908DGCU/",
"accession": "IGVFFI7908DGCU",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR1_Rep2_S193"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:51:43.340248+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI7908DGCU/@@download/IGVFFI7908DGCU.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/ccb922db-135e-4b85-a906-4f4f767f0445/IGVFFI7908DGCU.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF2-BinD-PCR1_Rep2_S193.yaml",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4544YEQM/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS0955GQMF/",
"accession": "IGVFDS0955GQMF",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR1_Rep1_S138",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR1_Rep2_S193",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR2_Rep1_S144",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR2_Rep2_S199",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR3_Rep1_S150",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR3_Rep2_S205",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR4_Rep1_S156",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR4_Rep2_S211"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:21:55.755926+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4390QYVS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4390QYVS",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR1_Rep1_S138",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR1_Rep2_S193",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR2_Rep1_S144",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR2_Rep2_S199",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR3_Rep1_S150",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR3_Rep2_S205",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR4_Rep1_S156",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR4_Rep2_S211"
],
"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 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/",
"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": "2024-06-01T02:06:25.038440+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "fab08936-6c04-432f-a070-361b3c31a60d"
}