{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS0720TXUF/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS0720TXUF",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR1-Rep1_S306",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR2-Rep1_S312",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR3-Rep1_S324",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR4-Rep1_S330"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM0402MSVI](/in-vitro-systems/IGVFSM0402MSVI/) 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/IGVFSM0402MSVI/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM0402MSVI](/in-vitro-systems/IGVFSM0402MSVI/) 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/IGVFSM0402MSVI/"
},
{
"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 [IGVFDS0720TXUF](/auxiliary-sets/IGVFDS0720TXUF/) has sequence file(s) [IGVFFI4262NYMF](/sequence-files/IGVFFI4262NYMF/), [IGVFFI1935DBLW](/sequence-files/IGVFFI1935DBLW/), [IGVFFI8971PQCM](/sequence-files/IGVFFI8971PQCM/), [IGVFFI9698DUHO](/sequence-files/IGVFFI9698DUHO/) 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/IGVFDS0720TXUF/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS0720TXUF](/auxiliary-sets/IGVFDS0720TXUF/) 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/IGVFDS0720TXUF/"
}
]
},
"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": "2024-05-13T22:51:15.337013+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/IGVFFI4262NYMF/",
"accession": "IGVFFI4262NYMF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR1-Rep1_S306"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:43:26.766525+00:00",
"file_format": "fastq",
"file_size": 13369840,
"href": "/sequence-files/IGVFFI4262NYMF/@@download/IGVFFI4262NYMF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/f31ba84a-08c2-416c-927b-fe114cdcce4c/IGVFFI4262NYMF.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin6hrs-FF2-BinF-PCR1-Rep1_S306_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5413XAFZ/",
"accession": "IGVFFI5413XAFZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR1-Rep1_S306"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:31:00.244067+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI5413XAFZ/@@download/IGVFFI5413XAFZ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/d6d122ad-3d65-44cf-ba19-2567e3084283/IGVFFI5413XAFZ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF2-BinF-PCR1-Rep1_S306.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1935DBLW/",
"accession": "IGVFFI1935DBLW",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR2-Rep1_S312"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:43:43.848038+00:00",
"file_format": "fastq",
"file_size": 12237502,
"href": "/sequence-files/IGVFFI1935DBLW/@@download/IGVFFI1935DBLW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/c4f1bfe9-19b4-4451-95f7-3924bf9cc2b2/IGVFFI1935DBLW.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin6hrs-FF2-BinF-PCR2-Rep1_S312_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8971PQCM/",
"accession": "IGVFFI8971PQCM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR3-Rep1_S324"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:44:01.287728+00:00",
"file_format": "fastq",
"file_size": 30900481,
"href": "/sequence-files/IGVFFI8971PQCM/@@download/IGVFFI8971PQCM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/2f4fa433-abde-41eb-a61f-1377af9011d6/IGVFFI8971PQCM.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin6hrs-FF2-BinF-PCR3-Rep1_S324_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9698DUHO/",
"accession": "IGVFFI9698DUHO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR4-Rep1_S330"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:44:18.304916+00:00",
"file_format": "fastq",
"file_size": 25446426,
"href": "/sequence-files/IGVFFI9698DUHO/@@download/IGVFFI9698DUHO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/ca260c91-a986-46fe-b76b-0e2ddd064c1b/IGVFFI9698DUHO.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin6hrs-FF2-BinF-PCR4-Rep1_S330_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0256YXOJ/",
"accession": "IGVFFI0256YXOJ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR4-Rep1_S330"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:31:43.549118+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI0256YXOJ/@@download/IGVFFI0256YXOJ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/f3d79659-52ea-46da-bdae-744f2ee39782/IGVFFI0256YXOJ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF2-BinF-PCR4-Rep1_S330.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2184MRDQ/",
"accession": "IGVFFI2184MRDQ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR2-Rep1_S312"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:31:14.396214+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI2184MRDQ/@@download/IGVFFI2184MRDQ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/b86deb38-986f-44c6-84f8-6d3705e8942c/IGVFFI2184MRDQ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF2-BinF-PCR2-Rep1_S312.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7503ZAVZ/",
"accession": "IGVFFI7503ZAVZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR3-Rep1_S324"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:31:28.488829+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI7503ZAVZ/@@download/IGVFFI7503ZAVZ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/c5ab8c48-3ad4-4b23-9228-ae1a8a8774ff/IGVFFI7503ZAVZ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF2-BinF-PCR3-Rep1_S324.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS5387BSQH/",
"accession": "IGVFDS5387BSQH",
"aliases": [
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR1-Rep1_S306",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR2-Rep1_S312",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR3-Rep1_S324",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR4-Rep1_S330"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:10:30.543955+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0402MSVI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0402MSVI",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR1-Rep1_S306",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR2-Rep1_S312",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR3-Rep1_S324",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF2-BinF-PCR4-Rep1_S330"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS6351FGNG/"
],
"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 CCND1) 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": "2024-06-01T01:43:26.766525+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "bf925fe9-f9b7-494e-bf06-ab964b400f51"
}