{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS1380VYWN/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS1380VYWN",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR1-Rep1_S26",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR2-Rep1_S32",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR3-Rep1_S80",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR4-Rep1_S86"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM8531AKQD](/in-vitro-systems/IGVFSM8531AKQD/) 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/IGVFSM8531AKQD/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM8531AKQD](/in-vitro-systems/IGVFSM8531AKQD/) 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/IGVFSM8531AKQD/"
},
{
"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 [IGVFDS1380VYWN](/auxiliary-sets/IGVFDS1380VYWN/) has sequence file(s) [IGVFFI1233TQNL](/sequence-files/IGVFFI1233TQNL/), [IGVFFI1079QGZM](/sequence-files/IGVFFI1079QGZM/), [IGVFFI9364JMZY](/sequence-files/IGVFFI9364JMZY/), [IGVFFI9695GFTP](/sequence-files/IGVFFI9695GFTP/) 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/IGVFDS1380VYWN/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS1380VYWN](/auxiliary-sets/IGVFDS1380VYWN/) 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/IGVFDS1380VYWN/"
}
]
},
"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": "2024-05-14T21:06:12.074635+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/IGVFFI1233TQNL/",
"accession": "IGVFFI1233TQNL",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR1-Rep1_S26"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:47:08.052605+00:00",
"file_format": "fastq",
"file_size": 11893852,
"href": "/sequence-files/IGVFFI1233TQNL/@@download/IGVFFI1233TQNL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/30e720e3-cdd9-48c6-8e95-ae25ba9966b2/IGVFFI1233TQNL.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-BinB-PCR1-Rep1_S26_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2269TFRI/",
"accession": "IGVFFI2269TFRI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR1-Rep1_S26"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:39:45.714418+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI2269TFRI/@@download/IGVFFI2269TFRI.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/1c21485b-12d1-4d34-8181-38b47f9368c2/IGVFFI2269TFRI.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF1-BinB-PCR1-Rep1_S26.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4536MNTO/",
"accession": "IGVFFI4536MNTO",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR2-Rep1_S32"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:40:01.343958+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI4536MNTO/@@download/IGVFFI4536MNTO.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/d1094865-0bf7-406a-a199-d08bafcc0bdb/IGVFFI4536MNTO.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF1-BinB-PCR2-Rep1_S32.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6904JXET/",
"accession": "IGVFFI6904JXET",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR3-Rep1_S80"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:40:16.606923+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI6904JXET/@@download/IGVFFI6904JXET.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/e227e839-c8da-41ab-9fd9-d2cef8c5e599/IGVFFI6904JXET.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF1-BinB-PCR3-Rep1_S80.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1079QGZM/",
"accession": "IGVFFI1079QGZM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR2-Rep1_S32"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:47:26.364604+00:00",
"file_format": "fastq",
"file_size": 12234670,
"href": "/sequence-files/IGVFFI1079QGZM/@@download/IGVFFI1079QGZM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/e26863d5-01fd-4713-b850-0582512bbfaf/IGVFFI1079QGZM.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-BinB-PCR2-Rep1_S32_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9364JMZY/",
"accession": "IGVFFI9364JMZY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR3-Rep1_S80"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:47:44.581782+00:00",
"file_format": "fastq",
"file_size": 22861403,
"href": "/sequence-files/IGVFFI9364JMZY/@@download/IGVFFI9364JMZY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/59df6e18-feac-45d2-b253-b34965bb49e2/IGVFFI9364JMZY.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-BinB-PCR3-Rep1_S80_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9695GFTP/",
"accession": "IGVFFI9695GFTP",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR4-Rep1_S86"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:48:02.808912+00:00",
"file_format": "fastq",
"file_size": 20227298,
"href": "/sequence-files/IGVFFI9695GFTP/@@download/IGVFFI9695GFTP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/f9517372-73a1-4e75-9185-3a763b8402ef/IGVFFI9695GFTP.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-BinB-PCR4-Rep1_S86_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0605XPPL/",
"accession": "IGVFFI0605XPPL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR4-Rep1_S86"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:40:31.748189+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI0605XPPL/@@download/IGVFFI0605XPPL.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/d9f26d35-b2b5-4c74-a224-f45eebcb6add/IGVFFI0605XPPL.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF1-BinB-PCR4-Rep1_S86.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS8391VNJE/",
"accession": "IGVFDS8391VNJE",
"aliases": [
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR1-Rep1_S26",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR2-Rep1_S32",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR3-Rep1_S80",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR4-Rep1_S86"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:25:16.297042+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8531AKQD/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8531AKQD",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR1-Rep1_S26",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR2-Rep1_S32",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR3-Rep1_S80",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR4-Rep1_S86"
],
"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 B for 10-20% 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": "2024-06-01T01:47:08.052605+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "f90a1806-7184-4a62-9ec6-62531bd5c29d"
}