{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS7971RAUG/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS7971RAUG",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR1-Rep1_S40",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR2-Rep1_S46",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR3-Rep1_S94",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR4-Rep1_S100"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6811XGTM](/in-vitro-systems/IGVFSM6811XGTM/) has in progress subobject degron modification [95081d1b-08b4-49ed-b324-e53fc43d8456](/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM6811XGTM/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6811XGTM](/in-vitro-systems/IGVFSM6811XGTM/) 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/IGVFSM6811XGTM/"
},
{
"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/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS7971RAUG](/auxiliary-sets/IGVFDS7971RAUG/) has sequence file(s) [IGVFFI6303UTLS](/sequence-files/IGVFFI6303UTLS/), [IGVFFI8668YDHW](/sequence-files/IGVFFI8668YDHW/), [IGVFFI6234KUHQ](/sequence-files/IGVFFI6234KUHQ/), [IGVFFI0065HIAT](/sequence-files/IGVFFI0065HIAT/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 40,
"level_name": "WARNING",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS7971RAUG/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS7971RAUG](/auxiliary-sets/IGVFDS7971RAUG/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_file_set_for",
"path": "/auxiliary-sets/IGVFDS7971RAUG/"
}
]
},
"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": "2024-05-14T21:06:45.927878+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/IGVFFI6303UTLS/",
"accession": "IGVFFI6303UTLS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR1-Rep1_S40"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:48:27.294717+00:00",
"file_format": "fastq",
"file_size": 10545827,
"href": "/sequence-files/IGVFFI6303UTLS/@@download/IGVFFI6303UTLS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/e94ef069-e49a-4b11-8820-0d48030bbe5d/IGVFFI6303UTLS.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin6hrs-FF2-BinD-PCR1-Rep1_S40_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2542AYLY/",
"accession": "IGVFFI2542AYLY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR1-Rep1_S40"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:40:52.877820+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI2542AYLY/@@download/IGVFFI2542AYLY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/c3fb14bb-0593-4f98-9c91-d26bb9299de4/IGVFFI2542AYLY.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF2-BinD-PCR1-Rep1_S40.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8668YDHW/",
"accession": "IGVFFI8668YDHW",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR2-Rep1_S46"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:48:45.131380+00:00",
"file_format": "fastq",
"file_size": 1352904,
"href": "/sequence-files/IGVFFI8668YDHW/@@download/IGVFFI8668YDHW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/9e34a7cb-f2f2-4dfa-b7bc-782bffab9851/IGVFFI8668YDHW.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin6hrs-FF2-BinD-PCR2-Rep1_S46_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6234KUHQ/",
"accession": "IGVFFI6234KUHQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR4-Rep1_S100"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:49:21.411416+00:00",
"file_format": "fastq",
"file_size": 1568355,
"href": "/sequence-files/IGVFFI6234KUHQ/@@download/IGVFFI6234KUHQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/265de1c7-576b-4025-bf6f-0fb1bfe164e8/IGVFFI6234KUHQ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin6hrs-FF2-BinD-PCR4-Rep1_S100_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0065HIAT/",
"accession": "IGVFFI0065HIAT",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR3-Rep1_S94"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:49:02.203495+00:00",
"file_format": "fastq",
"file_size": 19082795,
"href": "/sequence-files/IGVFFI0065HIAT/@@download/IGVFFI0065HIAT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/14b7d4a5-f1f4-42ec-8fcc-f3cd32807ddc/IGVFFI0065HIAT.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin6hrs-FF2-BinD-PCR3-Rep1_S94_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3258XDEX/",
"accession": "IGVFFI3258XDEX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR2-Rep1_S46"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:41:09.232044+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI3258XDEX/@@download/IGVFFI3258XDEX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/5b5a354a-e437-4dc5-848f-4ce7483e3756/IGVFFI3258XDEX.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF2-BinD-PCR2-Rep1_S46.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1542IONW/",
"accession": "IGVFFI1542IONW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR3-Rep1_S94"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:41:24.783028+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI1542IONW/@@download/IGVFFI1542IONW.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/41d3f9da-9be3-440b-ab48-099f9607bab4/IGVFFI1542IONW.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF2-BinD-PCR3-Rep1_S94.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6800DDJL/",
"accession": "IGVFFI6800DDJL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR4-Rep1_S100"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:41:40.208575+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI6800DDJL/@@download/IGVFFI6800DDJL.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/9b7ef02b-a228-4eb5-a7b9-c9a9534748c4/IGVFFI6800DDJL.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF2-BinD-PCR4-Rep1_S100.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS2363BVTQ/",
"accession": "IGVFDS2363BVTQ",
"aliases": [
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR1-Rep1_S40",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR2-Rep1_S46",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR3-Rep1_S94",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR4-Rep1_S100"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:26:14.630773+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6811XGTM/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6811XGTM",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR1-Rep1_S40",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR2-Rep1_S46",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR3-Rep1_S94",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR4-Rep1_S100"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS5413RKIA/"
],
"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 D for 55-65% expression of SSFA2) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified 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": "2024-06-01T01:48:27.294717+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "c674f601-b534-4065-a72e-8f8e51088080"
}