{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS6655SGOR/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS6655SGOR",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR1-Rep1_S27",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR2-Rep1_S33",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR3-Rep1_S81",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR4-Rep1_S87"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM5347ZNZW](/in-vitro-systems/IGVFSM5347ZNZW/) 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/IGVFSM5347ZNZW/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM5347ZNZW](/in-vitro-systems/IGVFSM5347ZNZW/) 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/IGVFSM5347ZNZW/"
},
{
"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 [IGVFDS6655SGOR](/auxiliary-sets/IGVFDS6655SGOR/) has sequence file(s) [IGVFFI9942MBPU](/sequence-files/IGVFFI9942MBPU/), [IGVFFI6949YOXY](/sequence-files/IGVFFI6949YOXY/), [IGVFFI5485UKSW](/sequence-files/IGVFFI5485UKSW/), [IGVFFI3791DPCW](/sequence-files/IGVFFI3791DPCW/) 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/IGVFDS6655SGOR/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS6655SGOR](/auxiliary-sets/IGVFDS6655SGOR/) 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/IGVFDS6655SGOR/"
}
]
},
"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": "2024-05-14T21:06:13.225144+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/IGVFFI9942MBPU/",
"accession": "IGVFFI9942MBPU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR1-Rep1_S27"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:47:11.078698+00:00",
"file_format": "fastq",
"file_size": 15539789,
"href": "/sequence-files/IGVFFI9942MBPU/@@download/IGVFFI9942MBPU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/e82c6741-d7a3-460d-bd76-c99a38072700/IGVFFI9942MBPU.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin6hrs-FF1-BinC-PCR1-Rep1_S27_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5931KOIF/",
"accession": "IGVFFI5931KOIF",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR1-Rep1_S27"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:39:48.321650+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI5931KOIF/@@download/IGVFFI5931KOIF.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/0eed2e1a-98ea-40b1-baac-ff618c98f8a5/IGVFFI5931KOIF.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF1-BinC-PCR1-Rep1_S27.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9401XGMS/",
"accession": "IGVFFI9401XGMS",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR4-Rep1_S87"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:40:34.488356+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI9401XGMS/@@download/IGVFFI9401XGMS.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/03555d92-92c9-4c50-8ab3-135216c62cd2/IGVFFI9401XGMS.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF1-BinC-PCR4-Rep1_S87.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6949YOXY/",
"accession": "IGVFFI6949YOXY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR2-Rep1_S33"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:47:29.366184+00:00",
"file_format": "fastq",
"file_size": 18518813,
"href": "/sequence-files/IGVFFI6949YOXY/@@download/IGVFFI6949YOXY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/25be7aca-554d-404b-8c42-d4e06789ff80/IGVFFI6949YOXY.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin6hrs-FF1-BinC-PCR2-Rep1_S33_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5485UKSW/",
"accession": "IGVFFI5485UKSW",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR4-Rep1_S87"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:48:05.880288+00:00",
"file_format": "fastq",
"file_size": 23038811,
"href": "/sequence-files/IGVFFI5485UKSW/@@download/IGVFFI5485UKSW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/ea709a3e-e5ca-40c8-9571-2228145c5dcd/IGVFFI5485UKSW.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin6hrs-FF1-BinC-PCR4-Rep1_S87_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3791DPCW/",
"accession": "IGVFFI3791DPCW",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR3-Rep1_S81"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:47:47.588569+00:00",
"file_format": "fastq",
"file_size": 19766225,
"href": "/sequence-files/IGVFFI3791DPCW/@@download/IGVFFI3791DPCW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/971d1bd6-9b72-491e-b46e-8d4740ce15eb/IGVFFI3791DPCW.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin6hrs-FF1-BinC-PCR3-Rep1_S81_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7432WZRT/",
"accession": "IGVFFI7432WZRT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR3-Rep1_S81"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:40:19.052656+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI7432WZRT/@@download/IGVFFI7432WZRT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/17b39e58-60d3-4384-803c-b9cfc5b54b35/IGVFFI7432WZRT.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF1-BinC-PCR3-Rep1_S81.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1050EAZP/",
"accession": "IGVFFI1050EAZP",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR2-Rep1_S33"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:40:03.864646+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI1050EAZP/@@download/IGVFFI1050EAZP.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/e62459fe-18ae-48b2-bc1e-eb3603c124bc/IGVFFI1050EAZP.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF1-BinC-PCR2-Rep1_S33.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS8837KFKM/",
"accession": "IGVFDS8837KFKM",
"aliases": [
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR1-Rep1_S27",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR2-Rep1_S33",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR3-Rep1_S81",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR4-Rep1_S87"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:25:22.870230+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5347ZNZW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5347ZNZW",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR1-Rep1_S27",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR2-Rep1_S33",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR3-Rep1_S81",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR4-Rep1_S87"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS5413RKIA/"
],
"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 C for 35-45% expression of SSFA2) 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": "2024-06-01T01:47:11.078698+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "aa052c62-8779-4138-a7c2-2e2364394b26"
}