{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS5482SFKX/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS5482SFKX",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF1-BinB-PCR1_S50",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF1-BinB-PCR2_S56",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF1-BinB-PCR3_S146",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF1-BinB-PCR4_S152"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM9603ZYAW](/in-vitro-systems/IGVFSM9603ZYAW/) 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/IGVFSM9603ZYAW/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM9603ZYAW](/in-vitro-systems/IGVFSM9603ZYAW/) 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/IGVFSM9603ZYAW/"
},
{
"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 [IGVFDS5482SFKX](/auxiliary-sets/IGVFDS5482SFKX/) has sequence file(s) [IGVFFI2260MGVP](/sequence-files/IGVFFI2260MGVP/), [IGVFFI0595UXSF](/sequence-files/IGVFFI0595UXSF/), [IGVFFI7452OWTH](/sequence-files/IGVFFI7452OWTH/), [IGVFFI9853OBLJ](/sequence-files/IGVFFI9853OBLJ/) 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/IGVFDS5482SFKX/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS5482SFKX](/auxiliary-sets/IGVFDS5482SFKX/) 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/IGVFDS5482SFKX/"
}
]
},
"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": "2024-05-16T17:58:55.918783+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/IGVFFI2260MGVP/",
"accession": "IGVFFI2260MGVP",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF1-BinB-PCR1_S50"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:20:01.684657+00:00",
"file_format": "fastq",
"file_size": 8999923,
"href": "/sequence-files/IGVFFI2260MGVP/@@download/IGVFFI2260MGVP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/40f7f2c2-f0a0-4178-93fb-3e82ac2bd178/IGVFFI2260MGVP.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF1-BinB-PCR1_S50_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4948EKHU/",
"accession": "IGVFFI4948EKHU",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF1-BinB-PCR1_S50"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:09:20.726852+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI4948EKHU/@@download/IGVFFI4948EKHU.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/4a88a29b-5e44-4e79-a5c1-19ada072e885/IGVFFI4948EKHU.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF1-BinB-PCR1_S50.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0595UXSF/",
"accession": "IGVFFI0595UXSF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF1-BinB-PCR4_S152"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:20:58.370423+00:00",
"file_format": "fastq",
"file_size": 18716751,
"href": "/sequence-files/IGVFFI0595UXSF/@@download/IGVFFI0595UXSF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/256b999c-325f-444a-a9be-385cc7e002c0/IGVFFI0595UXSF.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF1-BinB-PCR4_S152_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7452OWTH/",
"accession": "IGVFFI7452OWTH",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF1-BinB-PCR2_S56"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:20:19.336325+00:00",
"file_format": "fastq",
"file_size": 7318208,
"href": "/sequence-files/IGVFFI7452OWTH/@@download/IGVFFI7452OWTH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/37dcee15-dd93-4bc0-acec-5beda6b20947/IGVFFI7452OWTH.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF1-BinB-PCR2_S56_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0205SXGF/",
"accession": "IGVFFI0205SXGF",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF1-BinB-PCR2_S56"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:09:36.318908+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI0205SXGF/@@download/IGVFFI0205SXGF.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/2e8e707b-c106-4e28-bb81-8fabbcaa84db/IGVFFI0205SXGF.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF1-BinB-PCR2_S56.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9853OBLJ/",
"accession": "IGVFFI9853OBLJ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF1-BinB-PCR3_S146"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:20:40.527810+00:00",
"file_format": "fastq",
"file_size": 19088312,
"href": "/sequence-files/IGVFFI9853OBLJ/@@download/IGVFFI9853OBLJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/e3b41b43-7094-4d80-964a-cfb4f6cbe4db/IGVFFI9853OBLJ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF1-BinB-PCR3_S146_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0103DRAT/",
"accession": "IGVFFI0103DRAT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF1-BinB-PCR4_S152"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:10:06.115443+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI0103DRAT/@@download/IGVFFI0103DRAT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/8b30f092-28f9-4224-8a82-f8311f4abdff/IGVFFI0103DRAT.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF1-BinB-PCR4_S152.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8152WVOT/",
"accession": "IGVFFI8152WVOT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF1-BinB-PCR3_S146"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:09:51.161616+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI8152WVOT/@@download/IGVFFI8152WVOT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/ca7e33c2-3edc-4438-a6c9-ae1fbe2d8cd3/IGVFFI8152WVOT.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF1-BinB-PCR3_S146.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS1621QIUZ/",
"accession": "IGVFDS1621QIUZ",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinB-PCR1_S50",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinB-PCR2_S56",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinB-PCR3_S146",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinB-PCR4_S152"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:16:27.868466+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9603ZYAW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9603ZYAW",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF1-BinB-PCR1_S50",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF1-BinB-PCR2_S56",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF1-BinB-PCR3_S146",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF1-BinB-PCR4_S152"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7846UISG/"
],
"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 B for 10-20% expression of KITLG) 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": "2024-06-01T02:20:01.684657+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "008ebbf4-3a2d-4a9c-a833-f1f550762b48"
}