{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS2620FWYA/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS2620FWYA",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinD-PCR1_S4",
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinD-PCR2_S100",
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinD-PCR3_S196",
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinD-PCR4_S292"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2620FWYA](/auxiliary-sets/IGVFDS2620FWYA/) has sequence file(s) [IGVFFI4992AQIL](/sequence-files/IGVFFI4992AQIL/), [IGVFFI4867LJQY](/sequence-files/IGVFFI4867LJQY/), [IGVFFI5071KMPM](/sequence-files/IGVFFI5071KMPM/), [IGVFFI9120FVRY](/sequence-files/IGVFFI9120FVRY/) 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/IGVFDS2620FWYA/"
}
]
},
"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": "2024-05-06T23:13:28.987122+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/IGVFFI4992AQIL/",
"accession": "IGVFFI4992AQIL",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinD-PCR1_S4"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:24:46.925428+00:00",
"file_format": "fastq",
"file_size": 4794532,
"href": "/sequence-files/IGVFFI4992AQIL/@@download/IGVFFI4992AQIL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/8977010c-23af-4f1d-a5b1-21ab6ce97b32/IGVFFI4992AQIL.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-BinD-PCR1_S4_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0857GNWK/",
"accession": "IGVFFI0857GNWK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinD-PCR1_S4"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:00.313988+00:00",
"file_format": "yaml",
"file_size": 906,
"href": "/configuration-files/IGVFFI0857GNWK/@@download/IGVFFI0857GNWK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/db0a8205-4cd7-4467-9efc-4e3bf5e53074/IGVFFI0857GNWK.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin6hrs-FF1-BinD-PCR1_S4.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4867LJQY/",
"accession": "IGVFFI4867LJQY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinD-PCR2_S100"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:25:03.246716+00:00",
"file_format": "fastq",
"file_size": 8144652,
"href": "/sequence-files/IGVFFI4867LJQY/@@download/IGVFFI4867LJQY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/95d1cc98-e233-4a13-b405-a18f01b08c4b/IGVFFI4867LJQY.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-BinD-PCR2_S100_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3229YGRY/",
"accession": "IGVFFI3229YGRY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinD-PCR4_S292"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:41.677913+00:00",
"file_format": "yaml",
"file_size": 909,
"href": "/configuration-files/IGVFFI3229YGRY/@@download/IGVFFI3229YGRY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/92539a4e-7ef8-4d1a-8c2f-d3ae7cd96a2a/IGVFFI3229YGRY.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin6hrs-FF1-BinD-PCR4_S292.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5071KMPM/",
"accession": "IGVFFI5071KMPM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinD-PCR3_S196"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:25:19.561553+00:00",
"file_format": "fastq",
"file_size": 8251586,
"href": "/sequence-files/IGVFFI5071KMPM/@@download/IGVFFI5071KMPM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/a9e8b488-42c9-4db9-9cdb-96602c9c7c86/IGVFFI5071KMPM.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-BinD-PCR3_S196_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9120FVRY/",
"accession": "IGVFFI9120FVRY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinD-PCR4_S292"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:25:34.856011+00:00",
"file_format": "fastq",
"file_size": 8753395,
"href": "/sequence-files/IGVFFI9120FVRY/@@download/IGVFFI9120FVRY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/23e22963-a36f-413e-8111-d46f799c9ecb/IGVFFI9120FVRY.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-BinD-PCR4_S292_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9673HHQT/",
"accession": "IGVFFI9673HHQT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinD-PCR3_S196"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:28.056602+00:00",
"file_format": "yaml",
"file_size": 909,
"href": "/configuration-files/IGVFFI9673HHQT/@@download/IGVFFI9673HHQT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/ec61f7b1-ed30-405c-8ba3-a8073bb263db/IGVFFI9673HHQT.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin6hrs-FF1-BinD-PCR3_S196.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1093CRUS/",
"accession": "IGVFFI1093CRUS",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinD-PCR2_S100"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:14.272559+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI1093CRUS/@@download/IGVFFI1093CRUS.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/9450167c-a88b-478c-a75f-9bc8128ed767/IGVFFI1093CRUS.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin6hrs-FF1-BinD-PCR2_S100.yaml",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2982SJGW/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS5146ALYO/",
"accession": "IGVFDS5146ALYO",
"aliases": [
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinD-PCR1_S4",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinD-PCR2_S100",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinD-PCR3_S196",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinD-PCR4_S292"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-07-10T20:23:19.772266+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7735WAOD/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7735WAOD",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinD-PCR1_S4",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinD-PCR2_S100",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinD-PCR3_S196",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinD-PCR4_S292"
],
"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 D for 55-65% 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": "2024-06-01T01:24:46.925428+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in 36 genomic loci",
"uuid": "db4a813d-7dc2-4a1d-8c59-47f95563b2d4"
}