{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS6655SGOR/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS6655SGOR",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR1-Rep1_S27",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR2-Rep1_S33",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR3-Rep1_S81",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR4-Rep1_S87"
],
"audit": {
"ERROR": [
{
"category": "missing measurement set",
"detail": "Auxiliary set [IGVFDS6655SGOR](/auxiliary-sets/IGVFDS6655SGOR/) is not associated with any `measurement_sets`. Auxiliary sets are expected to be associated with a measurement set(s).",
"level": 60,
"level_name": "ERROR",
"name": "audit_missing_measurement_sets",
"path": "/auxiliary-sets/IGVFDS6655SGOR/"
},
{
"category": "missing related files",
"detail": "Auxiliary set [IGVFDS6655SGOR](/auxiliary-sets/IGVFDS6655SGOR/) has seqspec configuration file [IGVFFI1050EAZP](/configuration-files/IGVFFI1050EAZP/) which links to sequence file(s): [IGVFFI6949YOXY](/sequence-files/IGVFFI6949YOXY/) which do not link to this file set. All files associated with a seqspec (both sequencing and seqspec files) are expected to be linked to the same file set.",
"level": 60,
"level_name": "ERROR",
"name": "audit_files_associated_with_incorrect_fileset",
"path": "/auxiliary-sets/IGVFDS6655SGOR/"
}
],
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM5347ZNZW](/in-vitro-systems/IGVFSM5347ZNZW/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_sample_missing_publication",
"path": "/in-vitro-systems/IGVFSM5347ZNZW/"
},
{
"category": "mismatched status",
"detail": "Released configuration file [IGVFFI1050EAZP](/configuration-files/IGVFFI1050EAZP/) has revoked subobject auxiliary set [IGVFDS6655SGOR](/auxiliary-sets/IGVFDS6655SGOR/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/configuration-files/IGVFFI1050EAZP/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM5347ZNZW](/in-vitro-systems/IGVFSM5347ZNZW/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_nucleic_acid_delivery",
"path": "/in-vitro-systems/IGVFSM5347ZNZW/"
}
]
},
"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"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS5413RKIA/",
"accession": "IGVFDS5413RKIA",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI5130EWUZ/",
"accession": "IGVFFI5130EWUZ",
"content_type": "guide RNA sequences",
"status": "released",
"summary": "guide RNA sequences"
}
],
"status": "released",
"summary": "guide (sgRNA) library targeting accessible genome regions in many genomic loci"
}
],
"control_for": [],
"creation_timestamp": "2024-05-14T21:06:13.225144+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": "/configuration-files/IGVFFI1050EAZP/",
"accession": "IGVFFI1050EAZP",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR2-Rep1_S33"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:40:03.864646+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI1050EAZP/@@download/IGVFFI1050EAZP.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/e62459fe-18ae-48b2-bc1e-eb3603c124bc/IGVFFI1050EAZP.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF1-BinC-PCR2-Rep1_S33.yaml",
"upload_status": "validation exempted"
}
],
"input_for": [
"/analysis-sets/IGVFDS2031CTSP/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [],
"release_timestamp": "2024-07-10T20:25:22.870230+00:00",
"revoke_detail": "This auxiliary set has been revoked as its files have been moved to the measurement set: /measurement-sets/IGVFDS8837KFKM/",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5347ZNZW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5347ZNZW",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR1-Rep1_S27",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR2-Rep1_S33",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR3-Rep1_S81",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR4-Rep1_S87"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"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": "Homo sapiens (male) HCT116 cell line (sorting details: FACS bin C for 35-45% expression of SSFA2) 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/",
"purpose": "activation",
"status": "released",
"summary": "Treatment of 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours",
"treatment_type": "chemical"
}
]
}
],
"schema_version": "12",
"status": "revoked",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-11T20:40:03.864646+00:00",
"summary": "gRNA sequencing",
"uuid": "aa052c62-8779-4138-a7c2-2e2364394b26"
}