{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS1906FZZS/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS1906FZZS",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF2-BinA-PCR1-Rep1_S301",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF2-BinA-PCR2-Rep1_S307",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF2-BinA-PCR3-Rep1_S319",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF2-BinA-PCR4-Rep1_S325"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM5974NFSN](/in-vitro-systems/IGVFSM5974NFSN/) 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/IGVFSM5974NFSN/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM5974NFSN](/in-vitro-systems/IGVFSM5974NFSN/) 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/IGVFSM5974NFSN/"
},
{
"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 [IGVFDS1906FZZS](/auxiliary-sets/IGVFDS1906FZZS/) has sequence file(s) [IGVFFI3169FYVS](/sequence-files/IGVFFI3169FYVS/), [IGVFFI8992FUGP](/sequence-files/IGVFFI8992FUGP/), [IGVFFI1703SUAL](/sequence-files/IGVFFI1703SUAL/), [IGVFFI3150KUCM](/sequence-files/IGVFFI3150KUCM/) 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/IGVFDS1906FZZS/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS1906FZZS](/auxiliary-sets/IGVFDS1906FZZS/) 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/IGVFDS1906FZZS/"
}
]
},
"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": "2024-05-13T22:51:09.839691+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/IGVFFI3169FYVS/",
"accession": "IGVFFI3169FYVS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF2-BinA-PCR1-Rep1_S301"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:43:12.548956+00:00",
"file_format": "fastq",
"file_size": 16494623,
"href": "/sequence-files/IGVFFI3169FYVS/@@download/IGVFFI3169FYVS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/7857153c-da4d-4df9-b69a-1f231f6ec8d0/IGVFFI3169FYVS.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-BinA-PCR1-Rep1_S301_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4227NHQH/",
"accession": "IGVFFI4227NHQH",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF2-BinA-PCR1-Rep1_S301"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:30:48.730511+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI4227NHQH/@@download/IGVFFI4227NHQH.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/fed2a29d-2a02-4f96-a6a8-f5637be02a3d/IGVFFI4227NHQH.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF2-BinA-PCR1-Rep1_S301.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8992FUGP/",
"accession": "IGVFFI8992FUGP",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF2-BinA-PCR2-Rep1_S307"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:43:29.651013+00:00",
"file_format": "fastq",
"file_size": 12597327,
"href": "/sequence-files/IGVFFI8992FUGP/@@download/IGVFFI8992FUGP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/f436bb2d-938e-4f80-ae09-cdd18e133f76/IGVFFI8992FUGP.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-BinA-PCR2-Rep1_S307_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1703SUAL/",
"accession": "IGVFFI1703SUAL",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF2-BinA-PCR3-Rep1_S319"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:43:46.868379+00:00",
"file_format": "fastq",
"file_size": 23124020,
"href": "/sequence-files/IGVFFI1703SUAL/@@download/IGVFFI1703SUAL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/fce9e556-911b-40ec-b526-21cbcbf5714e/IGVFFI1703SUAL.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-BinA-PCR3-Rep1_S319_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3150KUCM/",
"accession": "IGVFFI3150KUCM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF2-BinA-PCR4-Rep1_S325"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:44:04.187841+00:00",
"file_format": "fastq",
"file_size": 21061854,
"href": "/sequence-files/IGVFFI3150KUCM/@@download/IGVFFI3150KUCM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/ce54fa06-d7be-4636-bf53-17e8602981f9/IGVFFI3150KUCM.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-BinA-PCR4-Rep1_S325_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2383CPOX/",
"accession": "IGVFFI2383CPOX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF2-BinA-PCR4-Rep1_S325"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:31:30.768148+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI2383CPOX/@@download/IGVFFI2383CPOX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/de9da9aa-46b9-4a2c-8a24-ea7876bd8249/IGVFFI2383CPOX.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF2-BinA-PCR4-Rep1_S325.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8091LBKA/",
"accession": "IGVFFI8091LBKA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF2-BinA-PCR2-Rep1_S307"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:31:02.565819+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI8091LBKA/@@download/IGVFFI8091LBKA.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/8438ecd1-f618-4714-b61d-7c8e889fbdfd/IGVFFI8091LBKA.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF2-BinA-PCR2-Rep1_S307.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6629TDFL/",
"accession": "IGVFFI6629TDFL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF2-BinA-PCR3-Rep1_S319"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:31:16.866375+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI6629TDFL/@@download/IGVFFI6629TDFL.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/7ef44518-7c9e-4fb1-ba5c-11d753a1fd15/IGVFFI6629TDFL.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF2-BinA-PCR3-Rep1_S319.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS5384IANT/",
"accession": "IGVFDS5384IANT",
"aliases": [
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF2-BinA-PCR1-Rep1_S301",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF2-BinA-PCR2-Rep1_S307",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF2-BinA-PCR3-Rep1_S319",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF2-BinA-PCR4-Rep1_S325"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:09:55.581481+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5974NFSN/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5974NFSN",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF2-BinA-PCR1-Rep1_S301",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF2-BinA-PCR2-Rep1_S307",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF2-BinA-PCR3-Rep1_S319",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF2-BinA-PCR4-Rep1_S325"
],
"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 A for 0-10% 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": "2024-06-01T01:43:12.548956+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "cb70f17f-5bc8-453b-b442-f21d208bf007"
}