{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS5647VZOO/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS5647VZOO",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF3-BinB-PCR1_S74",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF3-BinB-PCR2_S80",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF3-BinB-PCR3_S170",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF3-BinB-PCR4_S176"
],
"audit": {
"INTERNAL_ACTION": [
{
"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/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM3595PQEE](/in-vitro-systems/IGVFSM3595PQEE/) 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/IGVFSM3595PQEE/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM3595PQEE](/in-vitro-systems/IGVFSM3595PQEE/) 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/IGVFSM3595PQEE/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS5647VZOO](/auxiliary-sets/IGVFDS5647VZOO/) has sequence file(s) [IGVFFI3703CFWX](/sequence-files/IGVFFI3703CFWX/), [IGVFFI6765CFEW](/sequence-files/IGVFFI6765CFEW/), [IGVFFI7197IOZO](/sequence-files/IGVFFI7197IOZO/), [IGVFFI1748KJOU](/sequence-files/IGVFFI1748KJOU/) 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/IGVFDS5647VZOO/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS5647VZOO](/auxiliary-sets/IGVFDS5647VZOO/) 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/IGVFDS5647VZOO/"
}
]
},
"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": "2024-05-16T17:59:55.618235+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/IGVFFI3703CFWX/",
"accession": "IGVFFI3703CFWX",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF3-BinB-PCR1_S74"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:26:47.564684+00:00",
"file_format": "fastq",
"file_size": 15092016,
"href": "/sequence-files/IGVFFI3703CFWX/@@download/IGVFFI3703CFWX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/3942c86e-59ce-44d9-96a7-5469a654f861/IGVFFI3703CFWX.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF3-BinB-PCR1_S74_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5756WIKZ/",
"accession": "IGVFFI5756WIKZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF3-BinB-PCR1_S74"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:11:21.644727+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI5756WIKZ/@@download/IGVFFI5756WIKZ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/6efc588a-4a7b-4fc9-ae34-92b16d90e844/IGVFFI5756WIKZ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF3-BinB-PCR1_S74.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6765CFEW/",
"accession": "IGVFFI6765CFEW",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF3-BinB-PCR3_S170"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:27:19.784847+00:00",
"file_format": "fastq",
"file_size": 29973431,
"href": "/sequence-files/IGVFFI6765CFEW/@@download/IGVFFI6765CFEW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/0d7c576e-1ca8-4beb-8148-d9df1060bd01/IGVFFI6765CFEW.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF3-BinB-PCR3_S170_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7197IOZO/",
"accession": "IGVFFI7197IOZO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF3-BinB-PCR4_S176"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:27:36.806285+00:00",
"file_format": "fastq",
"file_size": 10692107,
"href": "/sequence-files/IGVFFI7197IOZO/@@download/IGVFFI7197IOZO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/72818c25-3bee-4215-93ae-e842198af737/IGVFFI7197IOZO.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF3-BinB-PCR4_S176_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1748KJOU/",
"accession": "IGVFFI1748KJOU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF3-BinB-PCR2_S80"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:27:03.791199+00:00",
"file_format": "fastq",
"file_size": 5060628,
"href": "/sequence-files/IGVFFI1748KJOU/@@download/IGVFFI1748KJOU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/ed02ba40-eecf-4b97-b289-fe35a0f3f193/IGVFFI1748KJOU.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF3-BinB-PCR2_S80_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9976PFGF/",
"accession": "IGVFFI9976PFGF",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF3-BinB-PCR2_S80"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:11:36.221263+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI9976PFGF/@@download/IGVFFI9976PFGF.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/1e48e5d0-4b05-416d-88cc-d078eaab90de/IGVFFI9976PFGF.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF3-BinB-PCR2_S80.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5669XSUH/",
"accession": "IGVFFI5669XSUH",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF3-BinB-PCR4_S176"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:12:05.336471+00:00",
"file_format": "yaml",
"file_size": 904,
"href": "/configuration-files/IGVFFI5669XSUH/@@download/IGVFFI5669XSUH.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/97e7ebd0-da25-4c1d-a3cc-9b5ad69c4236/IGVFFI5669XSUH.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF3-BinB-PCR4_S176.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5618VLDR/",
"accession": "IGVFFI5618VLDR",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF3-BinB-PCR3_S170"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:11:51.130754+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI5618VLDR/@@download/IGVFFI5618VLDR.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/0324eb8c-53aa-4302-ac82-779412d69c0e/IGVFFI5618VLDR.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF3-BinB-PCR3_S170.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS2629TAZT/",
"accession": "IGVFDS2629TAZT",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF3-BinB-PCR1_S74",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF3-BinB-PCR2_S80",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF3-BinB-PCR3_S170",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF3-BinB-PCR4_S176"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:17:54.259600+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3595PQEE/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3595PQEE",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF3-BinB-PCR1_S74",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF3-BinB-PCR2_S80",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF3-BinB-PCR3_S170",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF3-BinB-PCR4_S176"
],
"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": "2024-06-03T15:26:47.564684+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "73f52d47-42c3-484e-8360-0100463a06d7"
}