{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS2486FLEH/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS2486FLEH",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR1_S73",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR2_S79",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR3_S169",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR4_S175"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM5527SWPI](/in-vitro-systems/IGVFSM5527SWPI/) 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/IGVFSM5527SWPI/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM5527SWPI](/in-vitro-systems/IGVFSM5527SWPI/) 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/IGVFSM5527SWPI/"
},
{
"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 [IGVFDS2486FLEH](/auxiliary-sets/IGVFDS2486FLEH/) has sequence file(s) [IGVFFI4055KBRJ](/sequence-files/IGVFFI4055KBRJ/), [IGVFFI9532FPLV](/sequence-files/IGVFFI9532FPLV/), [IGVFFI8139XLPP](/sequence-files/IGVFFI8139XLPP/), [IGVFFI6385TRDU](/sequence-files/IGVFFI6385TRDU/) 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/IGVFDS2486FLEH/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS2486FLEH](/auxiliary-sets/IGVFDS2486FLEH/) 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/IGVFDS2486FLEH/"
}
]
},
"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": "2024-05-16T17:59:54.926912+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/IGVFFI4055KBRJ/",
"accession": "IGVFFI4055KBRJ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR1_S73"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:26:44.938512+00:00",
"file_format": "fastq",
"file_size": 6909652,
"href": "/sequence-files/IGVFFI4055KBRJ/@@download/IGVFFI4055KBRJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/7598ed17-e1fd-45d4-ae2a-b8bfff8251f4/IGVFFI4055KBRJ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF3-BinA-PCR1_S73_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0193GCPM/",
"accession": "IGVFFI0193GCPM",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR1_S73"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:11:19.327232+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI0193GCPM/@@download/IGVFFI0193GCPM.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/01cf0f23-1913-4007-9b98-d3df6c16a4e7/IGVFFI0193GCPM.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF3-BinA-PCR1_S73.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9532FPLV/",
"accession": "IGVFFI9532FPLV",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR4_S175"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:27:34.034339+00:00",
"file_format": "fastq",
"file_size": 9835599,
"href": "/sequence-files/IGVFFI9532FPLV/@@download/IGVFFI9532FPLV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/8cb11afd-498d-4502-89b6-331be6a4d012/IGVFFI9532FPLV.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF3-BinA-PCR4_S175_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2538KHLW/",
"accession": "IGVFFI2538KHLW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR3_S169"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:11:48.333703+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI2538KHLW/@@download/IGVFFI2538KHLW.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/6b3559de-9c7f-4ef0-95d7-8fb9b923b995/IGVFFI2538KHLW.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF3-BinA-PCR3_S169.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0188JCNR/",
"accession": "IGVFFI0188JCNR",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR2_S79"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:11:33.676095+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI0188JCNR/@@download/IGVFFI0188JCNR.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/55409adb-d877-4624-b13f-e41e2a4701c7/IGVFFI0188JCNR.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF3-BinA-PCR2_S79.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8139XLPP/",
"accession": "IGVFFI8139XLPP",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR2_S79"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:27:01.221570+00:00",
"file_format": "fastq",
"file_size": 4477129,
"href": "/sequence-files/IGVFFI8139XLPP/@@download/IGVFFI8139XLPP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/804fbc70-fb59-4beb-8b16-5962422143f9/IGVFFI8139XLPP.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF3-BinA-PCR2_S79_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6385TRDU/",
"accession": "IGVFFI6385TRDU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR3_S169"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:27:16.909657+00:00",
"file_format": "fastq",
"file_size": 11750327,
"href": "/sequence-files/IGVFFI6385TRDU/@@download/IGVFFI6385TRDU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/ee124551-bf64-4942-97d2-7014aed8604f/IGVFFI6385TRDU.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF3-BinA-PCR3_S169_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4861EWNQ/",
"accession": "IGVFFI4861EWNQ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR4_S175"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:12:03.013322+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI4861EWNQ/@@download/IGVFFI4861EWNQ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/258ac20a-2947-41ee-99af-bee49a1f0057/IGVFFI4861EWNQ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF3-BinA-PCR4_S175.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS2213NJWP/",
"accession": "IGVFDS2213NJWP",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR1_S73",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR2_S79",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR3_S169",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR4_S175"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:17:47.319684+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5527SWPI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5527SWPI",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR1_S73",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR2_S79",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR3_S169",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF3-BinA-PCR4_S175"
],
"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 A for 0-10% 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": "2024-06-03T15:26:44.938512+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "d8fbc675-2805-4ee3-b1c6-852be2964d88"
}