{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS2452BXCK/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS2452BXCK",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF1-BinD-PCR1_S52",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF1-BinD-PCR2_S58",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF1-BinD-PCR3_S148",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF1-BinD-PCR4_S154"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM8244VKAL](/in-vitro-systems/IGVFSM8244VKAL/) 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/IGVFSM8244VKAL/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM8244VKAL](/in-vitro-systems/IGVFSM8244VKAL/) 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/IGVFSM8244VKAL/"
},
{
"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 [IGVFDS2452BXCK](/auxiliary-sets/IGVFDS2452BXCK/) has sequence file(s) [IGVFFI3469NFLH](/sequence-files/IGVFFI3469NFLH/), [IGVFFI6997WQGE](/sequence-files/IGVFFI6997WQGE/), [IGVFFI4752YNUH](/sequence-files/IGVFFI4752YNUH/), [IGVFFI5272HZEO](/sequence-files/IGVFFI5272HZEO/) 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/IGVFDS2452BXCK/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS2452BXCK](/auxiliary-sets/IGVFDS2452BXCK/) 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/IGVFDS2452BXCK/"
}
]
},
"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": "2024-05-16T17:58:58.121514+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/IGVFFI3469NFLH/",
"accession": "IGVFFI3469NFLH",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF1-BinD-PCR1_S52"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:20:07.876173+00:00",
"file_format": "fastq",
"file_size": 11472810,
"href": "/sequence-files/IGVFFI3469NFLH/@@download/IGVFFI3469NFLH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/ff7ada83-00bf-49e1-980f-224685fa2c10/IGVFFI3469NFLH.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF1-BinD-PCR1_S52_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1548FRKP/",
"accession": "IGVFFI1548FRKP",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF1-BinD-PCR1_S52"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:09:26.593131+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI1548FRKP/@@download/IGVFFI1548FRKP.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/4a0187d0-95b7-4379-8321-770f2cfd3af9/IGVFFI1548FRKP.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF1-BinD-PCR1_S52.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6997WQGE/",
"accession": "IGVFFI6997WQGE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF1-BinD-PCR2_S58"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:20:28.679259+00:00",
"file_format": "fastq",
"file_size": 8120739,
"href": "/sequence-files/IGVFFI6997WQGE/@@download/IGVFFI6997WQGE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/3653fed3-c244-4086-89a7-893647d1235d/IGVFFI6997WQGE.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF1-BinD-PCR2_S58_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4752YNUH/",
"accession": "IGVFFI4752YNUH",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF1-BinD-PCR3_S148"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:20:46.500135+00:00",
"file_format": "fastq",
"file_size": 19546331,
"href": "/sequence-files/IGVFFI4752YNUH/@@download/IGVFFI4752YNUH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/f15540f4-442b-49e1-83c5-56cc1930445b/IGVFFI4752YNUH.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF1-BinD-PCR3_S148_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9534EMLB/",
"accession": "IGVFFI9534EMLB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF1-BinD-PCR3_S148"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:09:56.079037+00:00",
"file_format": "yaml",
"file_size": 904,
"href": "/configuration-files/IGVFFI9534EMLB/@@download/IGVFFI9534EMLB.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/dc6995d8-ac50-4027-991f-a6a36f7f761a/IGVFFI9534EMLB.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF1-BinD-PCR3_S148.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1780SMTF/",
"accession": "IGVFFI1780SMTF",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF1-BinD-PCR4_S154"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:10:11.135462+00:00",
"file_format": "yaml",
"file_size": 904,
"href": "/configuration-files/IGVFFI1780SMTF/@@download/IGVFFI1780SMTF.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/cc9b4988-709d-4723-acad-bae1b729ae40/IGVFFI1780SMTF.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF1-BinD-PCR4_S154.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5272HZEO/",
"accession": "IGVFFI5272HZEO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF1-BinD-PCR4_S154"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:21:04.564150+00:00",
"file_format": "fastq",
"file_size": 13663379,
"href": "/sequence-files/IGVFFI5272HZEO/@@download/IGVFFI5272HZEO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/46b54fee-f08a-4b05-b568-0c9582099e3f/IGVFFI5272HZEO.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF1-BinD-PCR4_S154_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7104CBKD/",
"accession": "IGVFFI7104CBKD",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF1-BinD-PCR2_S58"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:09:41.237261+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI7104CBKD/@@download/IGVFFI7104CBKD.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/afe2ae84-1309-4b4a-bd3e-79baf7a73b8a/IGVFFI7104CBKD.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF1-BinD-PCR2_S58.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS7960YGMN/",
"accession": "IGVFDS7960YGMN",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinD-PCR1_S52",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinD-PCR2_S58",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinD-PCR3_S148",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinD-PCR4_S154"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:16:41.526310+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8244VKAL/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8244VKAL",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF1-BinD-PCR1_S52",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF1-BinD-PCR2_S58",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF1-BinD-PCR3_S148",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF1-BinD-PCR4_S154"
],
"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": "2024-06-01T02:20:07.876173+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "b53d65cc-9574-4cdc-b0ea-e48980f4ad36"
}