{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS2726RPEW/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS2726RPEW",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR1_S77",
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR2_S173",
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR3_S269",
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR4_S365"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2726RPEW](/auxiliary-sets/IGVFDS2726RPEW/) has sequence file(s) [IGVFFI1351KSFG](/sequence-files/IGVFFI1351KSFG/), [IGVFFI2718BNTR](/sequence-files/IGVFFI2718BNTR/), [IGVFFI0509HCWG](/sequence-files/IGVFFI0509HCWG/), [IGVFFI5740TOCS](/sequence-files/IGVFFI5740TOCS/) 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/IGVFDS2726RPEW/"
}
]
},
"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": "2024-05-06T23:13:51.388388+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/IGVFFI1351KSFG/",
"accession": "IGVFFI1351KSFG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR1_S77"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:29:22.856337+00:00",
"file_format": "fastq",
"file_size": 5621093,
"href": "/sequence-files/IGVFFI1351KSFG/@@download/IGVFFI1351KSFG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/3ef076da-aadd-4d3f-89d0-648feaf8dc00/IGVFFI1351KSFG.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin0hrs-FF1-BinE-PCR1_S77_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4005IDLG/",
"accession": "IGVFFI4005IDLG",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR1_S77"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:57.199207+00:00",
"file_format": "yaml",
"file_size": 907,
"href": "/configuration-files/IGVFFI4005IDLG/@@download/IGVFFI4005IDLG.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/b2776d0c-1ad2-4350-9685-dc5445b9ba1a/IGVFFI4005IDLG.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinE-PCR1_S77.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2718BNTR/",
"accession": "IGVFFI2718BNTR",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR4_S365"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:30:11.668951+00:00",
"file_format": "fastq",
"file_size": 9102960,
"href": "/sequence-files/IGVFFI2718BNTR/@@download/IGVFFI2718BNTR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/1ed45f62-a741-4e93-8ea7-802cb300a387/IGVFFI2718BNTR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin0hrs-FF1-BinE-PCR4_S365_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0509HCWG/",
"accession": "IGVFFI0509HCWG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR3_S269"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:29:55.335598+00:00",
"file_format": "fastq",
"file_size": 10826442,
"href": "/sequence-files/IGVFFI0509HCWG/@@download/IGVFFI0509HCWG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/c61ad7e2-59fb-40c7-96e8-31672ee5802a/IGVFFI0509HCWG.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin0hrs-FF1-BinE-PCR3_S269_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2623ANUZ/",
"accession": "IGVFFI2623ANUZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR3_S269"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:24:23.564092+00:00",
"file_format": "yaml",
"file_size": 908,
"href": "/configuration-files/IGVFFI2623ANUZ/@@download/IGVFFI2623ANUZ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/7bbfe4fc-1d54-4fa1-97fb-7551aa0911c8/IGVFFI2623ANUZ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinE-PCR3_S269.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5740TOCS/",
"accession": "IGVFFI5740TOCS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR2_S173"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:29:38.615861+00:00",
"file_format": "fastq",
"file_size": 7503769,
"href": "/sequence-files/IGVFFI5740TOCS/@@download/IGVFFI5740TOCS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/edec47c4-e919-4374-8f4b-40d2585ec691/IGVFFI5740TOCS.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin0hrs-FF1-BinE-PCR2_S173_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8761WVJE/",
"accession": "IGVFFI8761WVJE",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR2_S173"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:24:10.288107+00:00",
"file_format": "yaml",
"file_size": 907,
"href": "/configuration-files/IGVFFI8761WVJE/@@download/IGVFFI8761WVJE.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/70e60d0a-2f91-436f-a5e0-32d88872d303/IGVFFI8761WVJE.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinE-PCR2_S173.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0038OXWJ/",
"accession": "IGVFFI0038OXWJ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR4_S365"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:24:36.938742+00:00",
"file_format": "yaml",
"file_size": 908,
"href": "/configuration-files/IGVFFI0038OXWJ/@@download/IGVFFI0038OXWJ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/ea1e9f0e-0883-4430-90b5-95f5b3389f49/IGVFFI0038OXWJ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinE-PCR4_S365.yaml",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2982SJGW/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS3741DKGN/",
"accession": "IGVFDS3741DKGN",
"aliases": [
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR1_S77",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR2_S173",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR3_S269",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR4_S365"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-07-10T20:22:45.644889+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1617PVUY/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1617PVUY",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR1_S77",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR2_S173",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR3_S269",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR4_S365"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS0392OWNZ/"
],
"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 E for 80-90% 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": "2024-06-01T01:29:22.856337+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in 36 genomic loci",
"uuid": "925bcf5a-f214-4e02-8187-318d0c964175"
}