{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS9907QGGC/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS9907QGGC",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR1_S64",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR2_S70",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR3_S160",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR4_S166"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM8586BMQG](/in-vitro-systems/IGVFSM8586BMQG/) 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/IGVFSM8586BMQG/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM8586BMQG](/in-vitro-systems/IGVFSM8586BMQG/) 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/IGVFSM8586BMQG/"
},
{
"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 [IGVFDS9907QGGC](/auxiliary-sets/IGVFDS9907QGGC/) has sequence file(s) [IGVFFI1843RRPT](/sequence-files/IGVFFI1843RRPT/), [IGVFFI3411QDKP](/sequence-files/IGVFFI3411QDKP/), [IGVFFI3360ZAFX](/sequence-files/IGVFFI3360ZAFX/), [IGVFFI8684DGZI](/sequence-files/IGVFFI8684DGZI/) 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/IGVFDS9907QGGC/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS9907QGGC](/auxiliary-sets/IGVFDS9907QGGC/) 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/IGVFDS9907QGGC/"
}
]
},
"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": "2024-05-16T17:59:37.396866+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/IGVFFI1843RRPT/",
"accession": "IGVFFI1843RRPT",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR1_S64"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:22:34.824110+00:00",
"file_format": "fastq",
"file_size": 9223559,
"href": "/sequence-files/IGVFFI1843RRPT/@@download/IGVFFI1843RRPT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/36993756-0de4-4903-9bd4-8dece0eb9c65/IGVFFI1843RRPT.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF2-BinD-PCR1_S64_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1267PVEU/",
"accession": "IGVFFI1267PVEU",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR1_S64"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:10:25.862221+00:00",
"file_format": "yaml",
"file_size": 900,
"href": "/configuration-files/IGVFFI1267PVEU/@@download/IGVFFI1267PVEU.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/57de2c76-12f9-4893-a4ae-e032bfde5afa/IGVFFI1267PVEU.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinD-PCR1_S64.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3411QDKP/",
"accession": "IGVFFI3411QDKP",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR4_S166"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:26:35.983621+00:00",
"file_format": "fastq",
"file_size": 14034354,
"href": "/sequence-files/IGVFFI3411QDKP/@@download/IGVFFI3411QDKP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/d36f07fd-7f3b-4135-9f6e-c23c20d7a0cd/IGVFFI3411QDKP.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF2-BinD-PCR4_S166_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3360ZAFX/",
"accession": "IGVFFI3360ZAFX",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR3_S160"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:26:15.151160+00:00",
"file_format": "fastq",
"file_size": 14238686,
"href": "/sequence-files/IGVFFI3360ZAFX/@@download/IGVFFI3360ZAFX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/07ba3510-a4c2-4e42-ab4f-be73833c0821/IGVFFI3360ZAFX.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF2-BinD-PCR3_S160_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8684DGZI/",
"accession": "IGVFFI8684DGZI",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR2_S70"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:22:51.353949+00:00",
"file_format": "fastq",
"file_size": 8909639,
"href": "/sequence-files/IGVFFI8684DGZI/@@download/IGVFFI8684DGZI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/3191743a-2d2f-4748-a275-d7f46da8f845/IGVFFI8684DGZI.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF2-BinD-PCR2_S70_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1486JESD/",
"accession": "IGVFFI1486JESD",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR2_S70"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:10:40.730991+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI1486JESD/@@download/IGVFFI1486JESD.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/6a1229a8-e5c1-4561-99d2-5c5af70180b4/IGVFFI1486JESD.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinD-PCR2_S70.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5749UYDF/",
"accession": "IGVFFI5749UYDF",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR4_S166"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:11:12.160222+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI5749UYDF/@@download/IGVFFI5749UYDF.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/1a3e2b55-4432-4d27-ae53-1028b6dba1b1/IGVFFI5749UYDF.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinD-PCR4_S166.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4776XMGE/",
"accession": "IGVFFI4776XMGE",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR3_S160"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:10:57.760639+00:00",
"file_format": "yaml",
"file_size": 904,
"href": "/configuration-files/IGVFFI4776XMGE/@@download/IGVFFI4776XMGE.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/a4cd95f4-0db2-4bf0-a4e9-4aa6550d0f96/IGVFFI4776XMGE.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinD-PCR3_S160.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS3328PNPV/",
"accession": "IGVFDS3328PNPV",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR1_S64",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR2_S70",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR3_S160",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR4_S166"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:17:26.040014+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8586BMQG/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8586BMQG",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR1_S64",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR2_S70",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR3_S160",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinD-PCR4_S166"
],
"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 D for 55-65% 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": "2024-06-03T15:22:34.824110+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "219f61fe-6a92-4622-9a1e-02156616c40b"
}