{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS5266DCYG/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS5266DCYG",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF2-BinD-PCR1-Rep1_S304",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF2-BinD-PCR2-Rep1_S310",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF2-BinD-PCR3-Rep1_S322",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF2-BinD-PCR4-Rep1_S328"
],
"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 [IGVFSM5076QTOJ](/in-vitro-systems/IGVFSM5076QTOJ/) 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/IGVFSM5076QTOJ/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM5076QTOJ](/in-vitro-systems/IGVFSM5076QTOJ/) 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/IGVFSM5076QTOJ/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS5266DCYG](/auxiliary-sets/IGVFDS5266DCYG/) has sequence file(s) [IGVFFI1342QUYQ](/sequence-files/IGVFFI1342QUYQ/), [IGVFFI2545NMVB](/sequence-files/IGVFFI2545NMVB/), [IGVFFI9314TZQD](/sequence-files/IGVFFI9314TZQD/), [IGVFFI3687EZGL](/sequence-files/IGVFFI3687EZGL/) 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/IGVFDS5266DCYG/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS5266DCYG](/auxiliary-sets/IGVFDS5266DCYG/) 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/IGVFDS5266DCYG/"
}
]
},
"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": "2024-05-13T22:51:13.098760+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/IGVFFI1342QUYQ/",
"accession": "IGVFFI1342QUYQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF2-BinD-PCR1-Rep1_S304"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:43:21.122009+00:00",
"file_format": "fastq",
"file_size": 12832843,
"href": "/sequence-files/IGVFFI1342QUYQ/@@download/IGVFFI1342QUYQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/0eb86618-d21b-47ce-a533-a0659aac4d01/IGVFFI1342QUYQ.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-BinD-PCR1-Rep1_S304_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3926ROSH/",
"accession": "IGVFFI3926ROSH",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF2-BinD-PCR1-Rep1_S304"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:30:55.607497+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI3926ROSH/@@download/IGVFFI3926ROSH.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/6e5b2cac-0c78-42b3-ae40-38c69508a002/IGVFFI3926ROSH.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF2-BinD-PCR1-Rep1_S304.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2545NMVB/",
"accession": "IGVFFI2545NMVB",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF2-BinD-PCR2-Rep1_S310"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:43:38.397037+00:00",
"file_format": "fastq",
"file_size": 11800389,
"href": "/sequence-files/IGVFFI2545NMVB/@@download/IGVFFI2545NMVB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/81cdaf92-a53f-41d4-9160-e0ff1b1fcd46/IGVFFI2545NMVB.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-BinD-PCR2-Rep1_S310_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9314TZQD/",
"accession": "IGVFFI9314TZQD",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF2-BinD-PCR3-Rep1_S322"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:43:55.309248+00:00",
"file_format": "fastq",
"file_size": 24359857,
"href": "/sequence-files/IGVFFI9314TZQD/@@download/IGVFFI9314TZQD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/0d3d0283-c1ec-473f-aee7-5f2a7ad7549e/IGVFFI9314TZQD.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-BinD-PCR3-Rep1_S322_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3687EZGL/",
"accession": "IGVFFI3687EZGL",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF2-BinD-PCR4-Rep1_S328"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:44:12.689800+00:00",
"file_format": "fastq",
"file_size": 28670607,
"href": "/sequence-files/IGVFFI3687EZGL/@@download/IGVFFI3687EZGL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/15d5dd76-cccd-4c03-8fa8-8ddd09a6211f/IGVFFI3687EZGL.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-BinD-PCR4-Rep1_S328_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2012GXFD/",
"accession": "IGVFFI2012GXFD",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF2-BinD-PCR2-Rep1_S310"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:31:09.559842+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI2012GXFD/@@download/IGVFFI2012GXFD.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/fa4c29ab-4d17-4fa0-8184-31125c3e186a/IGVFFI2012GXFD.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF2-BinD-PCR2-Rep1_S310.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2045TCIH/",
"accession": "IGVFFI2045TCIH",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF2-BinD-PCR4-Rep1_S328"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:31:38.527525+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI2045TCIH/@@download/IGVFFI2045TCIH.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/aa2e3aa3-67f6-481e-9e90-5b45801f97bb/IGVFFI2045TCIH.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF2-BinD-PCR4-Rep1_S328.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0437FCWG/",
"accession": "IGVFFI0437FCWG",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF2-BinD-PCR3-Rep1_S322"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:31:23.818260+00:00",
"file_format": "yaml",
"file_size": 916,
"href": "/configuration-files/IGVFFI0437FCWG/@@download/IGVFFI0437FCWG.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/bcdfa3b6-e207-460a-bfb9-fe60c946c09d/IGVFFI0437FCWG.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF2-BinD-PCR3-Rep1_S322.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS5758LPME/",
"accession": "IGVFDS5758LPME",
"aliases": [
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF2-BinD-PCR1-Rep1_S304",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF2-BinD-PCR2-Rep1_S310",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF2-BinD-PCR3-Rep1_S322",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF2-BinD-PCR4-Rep1_S328"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:10:15.576025+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5076QTOJ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5076QTOJ",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF2-BinD-PCR1-Rep1_S304",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF2-BinD-PCR2-Rep1_S310",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF2-BinD-PCR3-Rep1_S322",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF2-BinD-PCR4-Rep1_S328"
],
"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 D for 55-65% 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": "2024-06-01T01:43:21.122009+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "2ec8a7bf-31a2-413e-9c53-0712d562b998"
}