{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS4431AWMW/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS4431AWMW",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF2-BinE-PCR1-Rep1_S305",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF2-BinE-PCR2-Rep1_S311",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF2-BinE-PCR3-Rep1_S323",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF2-BinE-PCR4-Rep1_S329"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS4431AWMW](/auxiliary-sets/IGVFDS4431AWMW/) has sequence file(s) [IGVFFI6867LNIV](/sequence-files/IGVFFI6867LNIV/), [IGVFFI6826RFZA](/sequence-files/IGVFFI6826RFZA/), [IGVFFI8602OLWT](/sequence-files/IGVFFI8602OLWT/), [IGVFFI9393NPUO](/sequence-files/IGVFFI9393NPUO/) 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/IGVFDS4431AWMW/"
}
]
},
"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": "2024-05-13T22:51:14.393760+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/IGVFFI6867LNIV/",
"accession": "IGVFFI6867LNIV",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF2-BinE-PCR1-Rep1_S305"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:43:23.926404+00:00",
"file_format": "fastq",
"file_size": 16532359,
"href": "/sequence-files/IGVFFI6867LNIV/@@download/IGVFFI6867LNIV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/62ebe1f8-00fd-4a1a-b1b7-8474b0ff8266/IGVFFI6867LNIV.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-BinE-PCR1-Rep1_S305_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4100DJZL/",
"accession": "IGVFFI4100DJZL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF2-BinE-PCR1-Rep1_S305"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:30:57.906372+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI4100DJZL/@@download/IGVFFI4100DJZL.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/d4edc7da-417c-4247-85ab-0869eb7da4b7/IGVFFI4100DJZL.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF2-BinE-PCR1-Rep1_S305.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6826RFZA/",
"accession": "IGVFFI6826RFZA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF2-BinE-PCR2-Rep1_S311"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:43:41.044507+00:00",
"file_format": "fastq",
"file_size": 18136219,
"href": "/sequence-files/IGVFFI6826RFZA/@@download/IGVFFI6826RFZA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/39bc7fcd-ce69-49cd-901b-7774928614ea/IGVFFI6826RFZA.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-BinE-PCR2-Rep1_S311_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8602OLWT/",
"accession": "IGVFFI8602OLWT",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF2-BinE-PCR3-Rep1_S323"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:43:58.274162+00:00",
"file_format": "fastq",
"file_size": 30074551,
"href": "/sequence-files/IGVFFI8602OLWT/@@download/IGVFFI8602OLWT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/5042cc14-0ab9-400f-ae38-d0f656123ccc/IGVFFI8602OLWT.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-BinE-PCR3-Rep1_S323_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9393NPUO/",
"accession": "IGVFFI9393NPUO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF2-BinE-PCR4-Rep1_S329"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:44:15.483412+00:00",
"file_format": "fastq",
"file_size": 30650816,
"href": "/sequence-files/IGVFFI9393NPUO/@@download/IGVFFI9393NPUO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/580d61cf-2a09-4082-aeb6-c69f6be2ae0b/IGVFFI9393NPUO.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-BinE-PCR4-Rep1_S329_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4259FZTU/",
"accession": "IGVFFI4259FZTU",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF2-BinE-PCR3-Rep1_S323"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:31:26.165532+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI4259FZTU/@@download/IGVFFI4259FZTU.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/a856de26-3562-4c6c-98c0-9ea0c53e3d94/IGVFFI4259FZTU.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF2-BinE-PCR3-Rep1_S323.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9891MKQE/",
"accession": "IGVFFI9891MKQE",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF2-BinE-PCR4-Rep1_S329"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:31:41.090385+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI9891MKQE/@@download/IGVFFI9891MKQE.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/13e71ea6-3d10-4c16-beca-988e696368c9/IGVFFI9891MKQE.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF2-BinE-PCR4-Rep1_S329.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6826LGEI/",
"accession": "IGVFFI6826LGEI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF2-BinE-PCR2-Rep1_S311"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:31:12.026561+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI6826LGEI/@@download/IGVFFI6826LGEI.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/01a400ad-5a30-4566-aeca-72b231cf1434/IGVFFI6826LGEI.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF2-BinE-PCR2-Rep1_S311.yaml",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1569RNPD/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS1027FGVK/",
"accession": "IGVFDS1027FGVK",
"aliases": [
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF2-BinE-PCR1-Rep1_S305",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF2-BinE-PCR2-Rep1_S311",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF2-BinE-PCR3-Rep1_S323",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF2-BinE-PCR4-Rep1_S329"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-07-10T20:10:22.808991+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6283XDLL/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6283XDLL",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF2-BinE-PCR1-Rep1_S305",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF2-BinE-PCR2-Rep1_S311",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF2-BinE-PCR3-Rep1_S323",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF2-BinE-PCR4-Rep1_S329"
],
"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 E for 80-90% 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": "2024-06-01T01:43:23.926404+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "d0ad1e83-09c2-4e9c-a509-989588e47846"
}