{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS4259ETEA/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS4259ETEA",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR1-Rep1_S222",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR2-Rep1_S228",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR3-Rep1_S264",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR4-Rep1_S270"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS4259ETEA](/auxiliary-sets/IGVFDS4259ETEA/) has sequence file(s) [IGVFFI9279HEMN](/sequence-files/IGVFFI9279HEMN/), [IGVFFI6818RKHX](/sequence-files/IGVFFI6818RKHX/), [IGVFFI8918ZHNH](/sequence-files/IGVFFI8918ZHNH/), [IGVFFI5127EQNC](/sequence-files/IGVFFI5127EQNC/) 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/IGVFDS4259ETEA/"
}
]
},
"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": "2024-05-13T22:38:52.466994+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/IGVFFI9279HEMN/",
"accession": "IGVFFI9279HEMN",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR1-Rep1_S222"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:36:11.253477+00:00",
"file_format": "fastq",
"file_size": 19329587,
"href": "/sequence-files/IGVFFI9279HEMN/@@download/IGVFFI9279HEMN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/7d8fbe0f-86c5-4530-9425-f83d600a47e2/IGVFFI9279HEMN.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-Auxin0hrs-FF1-BinF-PCR1-Rep1_S222_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7078QGHI/",
"accession": "IGVFFI7078QGHI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR1-Rep1_S222"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:10.610396+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI7078QGHI/@@download/IGVFFI7078QGHI.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/ed3816b8-b038-4028-a347-9072a35cabf4/IGVFFI7078QGHI.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinF-PCR1-Rep1_S222.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6818RKHX/",
"accession": "IGVFFI6818RKHX",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR2-Rep1_S228"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:36:29.478680+00:00",
"file_format": "fastq",
"file_size": 19083131,
"href": "/sequence-files/IGVFFI6818RKHX/@@download/IGVFFI6818RKHX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/ed435d61-e851-4e66-badf-b37a5d08ee8c/IGVFFI6818RKHX.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-Auxin0hrs-FF1-BinF-PCR2-Rep1_S228_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8918ZHNH/",
"accession": "IGVFFI8918ZHNH",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR3-Rep1_S264"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:36:47.423039+00:00",
"file_format": "fastq",
"file_size": 26679582,
"href": "/sequence-files/IGVFFI8918ZHNH/@@download/IGVFFI8918ZHNH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/b7a3d7f6-31b9-450a-b06a-32c1659788cd/IGVFFI8918ZHNH.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-Auxin0hrs-FF1-BinF-PCR3-Rep1_S264_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5127EQNC/",
"accession": "IGVFFI5127EQNC",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR4-Rep1_S270"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:37:05.555898+00:00",
"file_format": "fastq",
"file_size": 12550088,
"href": "/sequence-files/IGVFFI5127EQNC/@@download/IGVFFI5127EQNC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/0052ecf9-7420-446f-a14c-ea29b860250d/IGVFFI5127EQNC.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-Auxin0hrs-FF1-BinF-PCR4-Rep1_S270_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6107TILF/",
"accession": "IGVFFI6107TILF",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR2-Rep1_S228"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:24.942247+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI6107TILF/@@download/IGVFFI6107TILF.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/4f62228a-aca6-40d8-8d41-00996aed29b2/IGVFFI6107TILF.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinF-PCR2-Rep1_S228.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8036KMXA/",
"accession": "IGVFFI8036KMXA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR4-Rep1_S270"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:53.325992+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI8036KMXA/@@download/IGVFFI8036KMXA.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/d6890866-6e0a-4344-902e-a14df883ab32/IGVFFI8036KMXA.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinF-PCR4-Rep1_S270.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4912PNJI/",
"accession": "IGVFFI4912PNJI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR3-Rep1_S264"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:38.680666+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI4912PNJI/@@download/IGVFFI4912PNJI.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/9fc64df1-490b-4bd8-aea0-fbfe7f3bffb0/IGVFFI4912PNJI.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinF-PCR3-Rep1_S264.yaml",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1569RNPD/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS2241NBBY/",
"accession": "IGVFDS2241NBBY",
"aliases": [
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR1-Rep1_S222",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR2-Rep1_S228",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR3-Rep1_S264",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR4-Rep1_S270"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-07-10T20:08:24.486641+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4218VHTT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4218VHTT",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR1-Rep1_S222",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR2-Rep1_S228",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR3-Rep1_S264",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinF-PCR4-Rep1_S270"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS6351FGNG/"
],
"modifications": [
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released"
},
{
"@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
"modality": "degradation",
"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 F for 80-100% expression of CCND1) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "12",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T01:36:11.253477+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "e66ac2d2-b305-4dd7-ac89-ec60c47a2449"
}