{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS0791JOAT/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS0791JOAT",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR1-Rep1_S28",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR2-Rep1_S34",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR3-Rep1_S82",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR4-Rep1_S88"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6629TXKH](/in-vitro-systems/IGVFSM6629TXKH/) 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/IGVFSM6629TXKH/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6629TXKH](/in-vitro-systems/IGVFSM6629TXKH/) 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/IGVFSM6629TXKH/"
},
{
"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 [IGVFDS0791JOAT](/auxiliary-sets/IGVFDS0791JOAT/) has sequence file(s) [IGVFFI4529YFBY](/sequence-files/IGVFFI4529YFBY/), [IGVFFI0315AYNG](/sequence-files/IGVFFI0315AYNG/), [IGVFFI5357ACRU](/sequence-files/IGVFFI5357ACRU/), [IGVFFI9488COAD](/sequence-files/IGVFFI9488COAD/) 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/IGVFDS0791JOAT/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS0791JOAT](/auxiliary-sets/IGVFDS0791JOAT/) 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/IGVFDS0791JOAT/"
}
]
},
"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": "2024-05-14T21:06:14.363922+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/IGVFFI4529YFBY/",
"accession": "IGVFFI4529YFBY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR1-Rep1_S28"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:47:14.110692+00:00",
"file_format": "fastq",
"file_size": 17739882,
"href": "/sequence-files/IGVFFI4529YFBY/@@download/IGVFFI4529YFBY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/c9530500-38be-45c4-bf47-98ed65d23a24/IGVFFI4529YFBY.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-FF1-BinD-PCR1-Rep1_S28_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4931FRCX/",
"accession": "IGVFFI4931FRCX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR1-Rep1_S28"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:39:50.866992+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI4931FRCX/@@download/IGVFFI4931FRCX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/15edf48c-e15a-4d12-bfb7-ce8d603a2982/IGVFFI4931FRCX.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF1-BinD-PCR1-Rep1_S28.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5152ILXJ/",
"accession": "IGVFFI5152ILXJ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR2-Rep1_S34"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:40:06.452882+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI5152ILXJ/@@download/IGVFFI5152ILXJ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/27404c44-2f76-48a8-b0cc-490da7f5cb4a/IGVFFI5152ILXJ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF1-BinD-PCR2-Rep1_S34.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0315AYNG/",
"accession": "IGVFFI0315AYNG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR2-Rep1_S34"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:47:32.363139+00:00",
"file_format": "fastq",
"file_size": 16567622,
"href": "/sequence-files/IGVFFI0315AYNG/@@download/IGVFFI0315AYNG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/df90e240-b153-42df-bd65-c19233f778c2/IGVFFI0315AYNG.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-FF1-BinD-PCR2-Rep1_S34_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5357ACRU/",
"accession": "IGVFFI5357ACRU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR3-Rep1_S82"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:47:50.570946+00:00",
"file_format": "fastq",
"file_size": 26008308,
"href": "/sequence-files/IGVFFI5357ACRU/@@download/IGVFFI5357ACRU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/a88f1e2b-fa50-49f4-98ff-8ad9fb51866b/IGVFFI5357ACRU.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-FF1-BinD-PCR3-Rep1_S82_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9488COAD/",
"accession": "IGVFFI9488COAD",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR4-Rep1_S88"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:48:09.079191+00:00",
"file_format": "fastq",
"file_size": 21674394,
"href": "/sequence-files/IGVFFI9488COAD/@@download/IGVFFI9488COAD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/d658e637-4f85-4b0e-9c49-9f3ff149fea8/IGVFFI9488COAD.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-FF1-BinD-PCR4-Rep1_S88_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9103TGSJ/",
"accession": "IGVFFI9103TGSJ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR3-Rep1_S82"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:40:21.484640+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI9103TGSJ/@@download/IGVFFI9103TGSJ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/8c041cfc-6f96-423e-b150-3456c45d577d/IGVFFI9103TGSJ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF1-BinD-PCR3-Rep1_S82.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6811NNBT/",
"accession": "IGVFFI6811NNBT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR4-Rep1_S88"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:40:37.409077+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI6811NNBT/@@download/IGVFFI6811NNBT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/e148f6bf-93ae-4290-aecc-858fa7b83a30/IGVFFI6811NNBT.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF1-BinD-PCR4-Rep1_S88.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS1334EHAI/",
"accession": "IGVFDS1334EHAI",
"aliases": [
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR1-Rep1_S28",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR2-Rep1_S34",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR3-Rep1_S82",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR4-Rep1_S88"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:25:30.350121+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6629TXKH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6629TXKH",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR1-Rep1_S28",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR2-Rep1_S34",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR3-Rep1_S82",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR4-Rep1_S88"
],
"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": "2024-06-01T01:47:14.110692+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "b12431d6-605e-466d-a0eb-a6cf15af6739"
}