{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS3144WFJD/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS3144WFJD",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinB-PCR1_S2",
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinB-PCR2_S98",
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinB-PCR3_S194",
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinB-PCR4_S290"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS3144WFJD](/auxiliary-sets/IGVFDS3144WFJD/) has sequence file(s) [IGVFFI3797FUXG](/sequence-files/IGVFFI3797FUXG/), [IGVFFI9579XYYD](/sequence-files/IGVFFI9579XYYD/), [IGVFFI9001JJGS](/sequence-files/IGVFFI9001JJGS/), [IGVFFI0478CFIW](/sequence-files/IGVFFI0478CFIW/) 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/IGVFDS3144WFJD/"
}
]
},
"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": "2024-05-06T23:13:26.796278+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/IGVFFI3797FUXG/",
"accession": "IGVFFI3797FUXG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinB-PCR1_S2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:24:40.437307+00:00",
"file_format": "fastq",
"file_size": 3919437,
"href": "/sequence-files/IGVFFI3797FUXG/@@download/IGVFFI3797FUXG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/5a1fca67-94c1-4110-a700-3440584fd3a5/IGVFFI3797FUXG.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin6hrs-FF1-BinB-PCR1_S2_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7930JXGK/",
"accession": "IGVFFI7930JXGK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinB-PCR1_S2"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:22:54.905958+00:00",
"file_format": "yaml",
"file_size": 907,
"href": "/configuration-files/IGVFFI7930JXGK/@@download/IGVFFI7930JXGK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/e6bb5408-0202-4007-90af-ad69bea84fe0/IGVFFI7930JXGK.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin6hrs-FF1-BinB-PCR1_S2.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0799SHQK/",
"accession": "IGVFFI0799SHQK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinB-PCR4_S290"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:37.134245+00:00",
"file_format": "yaml",
"file_size": 907,
"href": "/configuration-files/IGVFFI0799SHQK/@@download/IGVFFI0799SHQK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/7f3d904d-c7d3-421f-be60-460d49fabf4a/IGVFFI0799SHQK.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin6hrs-FF1-BinB-PCR4_S290.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9579XYYD/",
"accession": "IGVFFI9579XYYD",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinB-PCR2_S98"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:24:57.885077+00:00",
"file_format": "fastq",
"file_size": 7980285,
"href": "/sequence-files/IGVFFI9579XYYD/@@download/IGVFFI9579XYYD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/5ddd5ee9-bd11-4ed4-a5b3-8701b9b8f1c4/IGVFFI9579XYYD.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin6hrs-FF1-BinB-PCR2_S98_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9001JJGS/",
"accession": "IGVFFI9001JJGS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinB-PCR4_S290"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:25:29.811287+00:00",
"file_format": "fastq",
"file_size": 6274100,
"href": "/sequence-files/IGVFFI9001JJGS/@@download/IGVFFI9001JJGS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/fd2df6fb-07e5-4a45-a92e-6c79a9e57315/IGVFFI9001JJGS.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin6hrs-FF1-BinB-PCR4_S290_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0478CFIW/",
"accession": "IGVFFI0478CFIW",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinB-PCR3_S194"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:25:13.902727+00:00",
"file_format": "fastq",
"file_size": 9727938,
"href": "/sequence-files/IGVFFI0478CFIW/@@download/IGVFFI0478CFIW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/6f23210b-3f8f-4207-9e13-5324ef0f0df8/IGVFFI0478CFIW.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin6hrs-FF1-BinB-PCR3_S194_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3514NTOV/",
"accession": "IGVFFI3514NTOV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinB-PCR2_S98"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:09.705577+00:00",
"file_format": "yaml",
"file_size": 909,
"href": "/configuration-files/IGVFFI3514NTOV/@@download/IGVFFI3514NTOV.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/23ffd5e7-719e-44df-8149-68ade251f70a/IGVFFI3514NTOV.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin6hrs-FF1-BinB-PCR2_S98.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7227CNQO/",
"accession": "IGVFFI7227CNQO",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinB-PCR3_S194"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:23.653448+00:00",
"file_format": "yaml",
"file_size": 908,
"href": "/configuration-files/IGVFFI7227CNQO/@@download/IGVFFI7227CNQO.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/81567fa7-4042-4108-b0b9-a89d136bb287/IGVFFI7227CNQO.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin6hrs-FF1-BinB-PCR3_S194.yaml",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2982SJGW/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS9594DNWM/",
"accession": "IGVFDS9594DNWM",
"aliases": [
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinB-PCR1_S2",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinB-PCR2_S98",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinB-PCR3_S194",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinB-PCR4_S290"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-07-10T20:23:06.527429+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8104CCIE/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8104CCIE",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinB-PCR1_S2",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinB-PCR2_S98",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinB-PCR3_S194",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinB-PCR4_S290"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS0392OWNZ/"
],
"modifications": [
{
"@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"modality": "degradation",
"status": "released"
},
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released"
}
],
"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 B for 10-20% 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/",
"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": "2024-06-01T01:24:40.437307+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in 36 genomic loci",
"uuid": "57faf920-c419-4bcd-8295-bb1c6158cc5b"
}