{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS0244COUW/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS0244COUW",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF2-BinC-PCR1-Rep1_S303",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF2-BinC-PCR2-Rep1_S309",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF2-BinC-PCR3-Rep1_S321",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF2-BinC-PCR4-Rep1_S327"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS0244COUW](/auxiliary-sets/IGVFDS0244COUW/) has sequence file(s) [IGVFFI9232LIOS](/sequence-files/IGVFFI9232LIOS/), [IGVFFI2596GDWU](/sequence-files/IGVFFI2596GDWU/), [IGVFFI7782DEGB](/sequence-files/IGVFFI7782DEGB/), [IGVFFI0642YKDD](/sequence-files/IGVFFI0642YKDD/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS0244COUW/"
}
]
},
"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": "2024-05-13T22:51:11.949257+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/IGVFFI9232LIOS/",
"accession": "IGVFFI9232LIOS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF2-BinC-PCR1-Rep1_S303"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:43:18.284595+00:00",
"file_format": "fastq",
"file_size": 22195375,
"href": "/sequence-files/IGVFFI9232LIOS/@@download/IGVFFI9232LIOS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/4765ac8c-da0c-425e-bbde-f8e02546751e/IGVFFI9232LIOS.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin6hrs-FF2-BinC-PCR1-Rep1_S303_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6899YSXN/",
"accession": "IGVFFI6899YSXN",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF2-BinC-PCR1-Rep1_S303"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:30:53.396119+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI6899YSXN/@@download/IGVFFI6899YSXN.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/85f56c7c-6faf-409f-8ae0-4f3236ed9f90/IGVFFI6899YSXN.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF2-BinC-PCR1-Rep1_S303.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2596GDWU/",
"accession": "IGVFFI2596GDWU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF2-BinC-PCR2-Rep1_S309"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:43:35.534036+00:00",
"file_format": "fastq",
"file_size": 17629190,
"href": "/sequence-files/IGVFFI2596GDWU/@@download/IGVFFI2596GDWU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/a380236e-de59-4bfc-a6c0-1a46c72401a2/IGVFFI2596GDWU.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin6hrs-FF2-BinC-PCR2-Rep1_S309_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7782DEGB/",
"accession": "IGVFFI7782DEGB",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF2-BinC-PCR3-Rep1_S321"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:43:52.368644+00:00",
"file_format": "fastq",
"file_size": 35728792,
"href": "/sequence-files/IGVFFI7782DEGB/@@download/IGVFFI7782DEGB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/f0846e12-7054-4ad4-8621-1c1e0dfb5229/IGVFFI7782DEGB.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin6hrs-FF2-BinC-PCR3-Rep1_S321_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0642YKDD/",
"accession": "IGVFFI0642YKDD",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF2-BinC-PCR4-Rep1_S327"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:44:09.889692+00:00",
"file_format": "fastq",
"file_size": 30868785,
"href": "/sequence-files/IGVFFI0642YKDD/@@download/IGVFFI0642YKDD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/f96e7abf-c5f7-498e-af4d-479411d9bed4/IGVFFI0642YKDD.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin6hrs-FF2-BinC-PCR4-Rep1_S327_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5749XZRQ/",
"accession": "IGVFFI5749XZRQ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF2-BinC-PCR4-Rep1_S327"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:31:35.646016+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI5749XZRQ/@@download/IGVFFI5749XZRQ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/9976ad71-48d3-4b5a-8708-cae6fce749ad/IGVFFI5749XZRQ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF2-BinC-PCR4-Rep1_S327.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5901URTV/",
"accession": "IGVFFI5901URTV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF2-BinC-PCR3-Rep1_S321"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:31:21.559997+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI5901URTV/@@download/IGVFFI5901URTV.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/2cb5f75f-db2a-4cac-b59f-4af8f42bebe2/IGVFFI5901URTV.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF2-BinC-PCR3-Rep1_S321.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1789VZTD/",
"accession": "IGVFFI1789VZTD",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF2-BinC-PCR2-Rep1_S309"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:31:07.191137+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI1789VZTD/@@download/IGVFFI1789VZTD.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/2f3c656f-b0af-414f-aebc-b6b820928f4f/IGVFFI1789VZTD.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF2-BinC-PCR2-Rep1_S309.yaml",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1569RNPD/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS8484TQSR/",
"accession": "IGVFDS8484TQSR",
"aliases": [
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF2-BinC-PCR1-Rep1_S303",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF2-BinC-PCR2-Rep1_S309",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF2-BinC-PCR3-Rep1_S321",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF2-BinC-PCR4-Rep1_S327"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-07-10T20:10:09.058591+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1476QKIB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1476QKIB",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF2-BinC-PCR1-Rep1_S303",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF2-BinC-PCR2-Rep1_S309",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF2-BinC-PCR3-Rep1_S321",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF2-BinC-PCR4-Rep1_S327"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS6351FGNG/"
],
"modifications": [
{
"@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"modality": "degradation",
"status": "released"
},
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released"
}
],
"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 CCND1) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
"status": "released",
"treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
}
]
}
],
"schema_version": "12",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T01:43:18.284595+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "217cec93-1ba9-409c-b043-dcae9b8d0811"
}