{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS5616WTVS/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS5616WTVS",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR1_S90",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR2_S96",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR3_S186",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR4_S192"
],
"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 [IGVFSM1655HPGH](/in-vitro-systems/IGVFSM1655HPGH/) 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/IGVFSM1655HPGH/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM1655HPGH](/in-vitro-systems/IGVFSM1655HPGH/) 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/IGVFSM1655HPGH/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS5616WTVS](/auxiliary-sets/IGVFDS5616WTVS/) has sequence file(s) [IGVFFI0227JJOM](/sequence-files/IGVFFI0227JJOM/), [IGVFFI9673DFOR](/sequence-files/IGVFFI9673DFOR/), [IGVFFI4429ZJPV](/sequence-files/IGVFFI4429ZJPV/), [IGVFFI8610SEGJ](/sequence-files/IGVFFI8610SEGJ/) 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/IGVFDS5616WTVS/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS5616WTVS](/auxiliary-sets/IGVFDS5616WTVS/) 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/IGVFDS5616WTVS/"
}
]
},
"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": "2024-05-16T18:01:22.964668+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/IGVFFI0227JJOM/",
"accession": "IGVFFI0227JJOM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR1_S90"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:28:04.494504+00:00",
"file_format": "fastq",
"file_size": 4872644,
"href": "/sequence-files/IGVFFI0227JJOM/@@download/IGVFFI0227JJOM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/ebdbb1e7-ad48-41ec-965c-71f399afc726/IGVFFI0227JJOM.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF4-BinF-PCR1_S90_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2020ZSYY/",
"accession": "IGVFFI2020ZSYY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR1_S90"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:12:29.153459+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI2020ZSYY/@@download/IGVFFI2020ZSYY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/8a034352-bf70-4994-bc3d-4b9b04f581e8/IGVFFI2020ZSYY.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinF-PCR1_S90.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9673DFOR/",
"accession": "IGVFFI9673DFOR",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR2_S96"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:28:20.522798+00:00",
"file_format": "fastq",
"file_size": 3890654,
"href": "/sequence-files/IGVFFI9673DFOR/@@download/IGVFFI9673DFOR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/a38d2320-9db1-4174-82d5-260d1cb66315/IGVFFI9673DFOR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF4-BinF-PCR2_S96_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4429ZJPV/",
"accession": "IGVFFI4429ZJPV",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR4_S192"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:28:54.040158+00:00",
"file_format": "fastq",
"file_size": 20726500,
"href": "/sequence-files/IGVFFI4429ZJPV/@@download/IGVFFI4429ZJPV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/e62c92b5-6515-43f5-9efa-dd5a3b233648/IGVFFI4429ZJPV.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF4-BinF-PCR4_S192_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8610SEGJ/",
"accession": "IGVFFI8610SEGJ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR3_S186"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:28:37.414938+00:00",
"file_format": "fastq",
"file_size": 6631250,
"href": "/sequence-files/IGVFFI8610SEGJ/@@download/IGVFFI8610SEGJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/99121842-3ed4-46cb-b378-3469e037f3df/IGVFFI8610SEGJ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF4-BinF-PCR3_S186_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2753RZSU/",
"accession": "IGVFFI2753RZSU",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR2_S96"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:12:44.032171+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI2753RZSU/@@download/IGVFFI2753RZSU.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/ee5b09d1-7e70-4f22-b6aa-72f01da0320f/IGVFFI2753RZSU.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinF-PCR2_S96.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4600EVHN/",
"accession": "IGVFFI4600EVHN",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR3_S186"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:12:58.548861+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI4600EVHN/@@download/IGVFFI4600EVHN.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/d33d0314-b457-4b89-9dd7-cd1eda56ddf8/IGVFFI4600EVHN.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinF-PCR3_S186.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1208IBPS/",
"accession": "IGVFFI1208IBPS",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR4_S192"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:13:13.298182+00:00",
"file_format": "yaml",
"file_size": 904,
"href": "/configuration-files/IGVFFI1208IBPS/@@download/IGVFFI1208IBPS.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/ee6e2ae8-3df0-4465-b01e-92188e5602b8/IGVFFI1208IBPS.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinF-PCR4_S192.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS9183CPVF/",
"accession": "IGVFDS9183CPVF",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR1_S90",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR2_S96",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR3_S186",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR4_S192"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:19:06.744728+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1655HPGH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1655HPGH",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR1_S90",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR2_S96",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR3_S186",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR4_S192"
],
"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 F for 80-100% 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": "2024-06-03T15:28:04.494504+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "ee884fcc-b7da-41fb-9482-695a60b919a0"
}