{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS3120IRAP/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS3120IRAP",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF1-BinC-PCR1-Rep1_S243",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF1-BinC-PCR2-Rep1_S249",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF1-BinC-PCR3-Rep1_S285",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF1-BinC-PCR4-Rep1_S291"
],
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS3120IRAP](/auxiliary-sets/IGVFDS3120IRAP/) has sequence file(s) [IGVFFI1822HTFR](/sequence-files/IGVFFI1822HTFR/), [IGVFFI4815RJIT](/sequence-files/IGVFFI4815RJIT/), [IGVFFI5154USHE](/sequence-files/IGVFFI5154USHE/), [IGVFFI9181YPZG](/sequence-files/IGVFFI9181YPZG/) 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/IGVFDS3120IRAP/"
}
]
},
"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": "2024-05-13T22:50:45.105836+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/IGVFFI1822HTFR/",
"accession": "IGVFFI1822HTFR",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinC-PCR1-Rep1_S243"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:42:06.604856+00:00",
"file_format": "fastq",
"file_size": 14278365,
"href": "/sequence-files/IGVFFI1822HTFR/@@download/IGVFFI1822HTFR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/f3127739-e58d-4a5a-9c33-8e7d7558119e/IGVFFI1822HTFR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin6hrs-FF1-BinC-PCR1-Rep1_S243_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2287BUST/",
"accession": "IGVFFI2287BUST",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinC-PCR1-Rep1_S243"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:29:56.774806+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI2287BUST/@@download/IGVFFI2287BUST.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/e6b0b27a-30ec-450a-bdc9-fb75a14aa630/IGVFFI2287BUST.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinC-PCR1-Rep1_S243.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4815RJIT/",
"accession": "IGVFFI4815RJIT",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinC-PCR2-Rep1_S249"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:42:24.307093+00:00",
"file_format": "fastq",
"file_size": 13692997,
"href": "/sequence-files/IGVFFI4815RJIT/@@download/IGVFFI4815RJIT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/92d90ecc-e4ed-4599-b198-f2e193df4f18/IGVFFI4815RJIT.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin6hrs-FF1-BinC-PCR2-Rep1_S249_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5154USHE/",
"accession": "IGVFFI5154USHE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinC-PCR3-Rep1_S285"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:42:40.824548+00:00",
"file_format": "fastq",
"file_size": 25660281,
"href": "/sequence-files/IGVFFI5154USHE/@@download/IGVFFI5154USHE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/ac96ddec-539f-4aae-b14a-36bbc1b59a5a/IGVFFI5154USHE.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin6hrs-FF1-BinC-PCR3-Rep1_S285_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9181YPZG/",
"accession": "IGVFFI9181YPZG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinC-PCR4-Rep1_S291"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:42:59.603037+00:00",
"file_format": "fastq",
"file_size": 29718656,
"href": "/sequence-files/IGVFFI9181YPZG/@@download/IGVFFI9181YPZG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/508139dd-33f5-408e-ad6e-0a64c0e2e5b0/IGVFFI9181YPZG.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin6hrs-FF1-BinC-PCR4-Rep1_S291_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7447YRKM/",
"accession": "IGVFFI7447YRKM",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinC-PCR3-Rep1_S285"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:30:25.190772+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI7447YRKM/@@download/IGVFFI7447YRKM.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/cdfc9713-a646-4d6f-b627-9aaaf1374519/IGVFFI7447YRKM.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinC-PCR3-Rep1_S285.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6283ZAYL/",
"accession": "IGVFFI6283ZAYL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinC-PCR4-Rep1_S291"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:30:39.608599+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI6283ZAYL/@@download/IGVFFI6283ZAYL.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/4b331ff2-0360-49a1-b4d0-ea10586e2b22/IGVFFI6283ZAYL.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinC-PCR4-Rep1_S291.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5770SSOD/",
"accession": "IGVFFI5770SSOD",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinC-PCR2-Rep1_S249"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:30:11.057070+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI5770SSOD/@@download/IGVFFI5770SSOD.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/f04bd725-7b38-4c75-9e45-1041c1287673/IGVFFI5770SSOD.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinC-PCR2-Rep1_S249.yaml",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1569RNPD/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS6865SDZA/",
"accession": "IGVFDS6865SDZA",
"aliases": [
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinC-PCR1-Rep1_S243",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinC-PCR2-Rep1_S249",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinC-PCR3-Rep1_S285",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinC-PCR4-Rep1_S291"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:09:25.529379+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2025NTWT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2025NTWT",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinC-PCR1-Rep1_S243",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinC-PCR2-Rep1_S249",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinC-PCR3-Rep1_S285",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinC-PCR4-Rep1_S291"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS6351FGNG/"
],
"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 C for 35-45% expression of CCND1) 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": "2024-06-01T01:42:06.604856+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "fc23e237-cefd-4218-9b9a-817a676d5b8d"
}