{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS1012DWQM/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS1012DWQM",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF2-BinB-PCR1-Rep1_S146",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF2-BinB-PCR2-Rep1_S152",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF2-BinB-PCR3-Rep1_S200",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF2-BinB-PCR4-Rep1_S206"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS1012DWQM](/auxiliary-sets/IGVFDS1012DWQM/) has sequence file(s) [IGVFFI7817VEUU](/sequence-files/IGVFFI7817VEUU/), [IGVFFI7633XNAY](/sequence-files/IGVFFI7633XNAY/), [IGVFFI9300EOBH](/sequence-files/IGVFFI9300EOBH/), [IGVFFI6135TIGK](/sequence-files/IGVFFI6135TIGK/) 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/IGVFDS1012DWQM/"
}
]
},
"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": "2024-05-14T16:51:33.704831+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/IGVFFI7817VEUU/",
"accession": "IGVFFI7817VEUU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF2-BinB-PCR1-Rep1_S146"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:54:36.099319+00:00",
"file_format": "fastq",
"file_size": 23522597,
"href": "/sequence-files/IGVFFI7817VEUU/@@download/IGVFFI7817VEUU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/1ed39aef-39c0-439a-99bf-881cd3ad8ba7/IGVFFI7817VEUU.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/FAM3C-Auxin6hrs-FF2-BinB-PCR1-Rep1_S146_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0173LWNL/",
"accession": "IGVFFI0173LWNL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF2-BinB-PCR1-Rep1_S146"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:44:39.029469+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI0173LWNL/@@download/IGVFFI0173LWNL.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/79f87535-92b3-46f3-bb64-66b39bc3afbf/IGVFFI0173LWNL.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF2-BinB-PCR1-Rep1_S146.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7633XNAY/",
"accession": "IGVFFI7633XNAY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF2-BinB-PCR4-Rep1_S206"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:55:31.206568+00:00",
"file_format": "fastq",
"file_size": 20773054,
"href": "/sequence-files/IGVFFI7633XNAY/@@download/IGVFFI7633XNAY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/b09f92ac-37ce-48a2-984d-30a5100ea5af/IGVFFI7633XNAY.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/FAM3C-Auxin6hrs-FF2-BinB-PCR4-Rep1_S206_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9300EOBH/",
"accession": "IGVFFI9300EOBH",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF2-BinB-PCR2-Rep1_S152"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:54:54.301023+00:00",
"file_format": "fastq",
"file_size": 14521908,
"href": "/sequence-files/IGVFFI9300EOBH/@@download/IGVFFI9300EOBH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/8b147ec6-9551-4dbc-a804-a6d840503e97/IGVFFI9300EOBH.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/FAM3C-Auxin6hrs-FF2-BinB-PCR2-Rep1_S152_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5798UHAG/",
"accession": "IGVFFI5798UHAG",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF2-BinB-PCR2-Rep1_S152"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:44:53.683871+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI5798UHAG/@@download/IGVFFI5798UHAG.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/f7263bbe-e5f7-4d05-a0d8-cc055c1695cc/IGVFFI5798UHAG.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF2-BinB-PCR2-Rep1_S152.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3660FXUN/",
"accession": "IGVFFI3660FXUN",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF2-BinB-PCR3-Rep1_S200"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:45:07.512042+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI3660FXUN/@@download/IGVFFI3660FXUN.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/5810d46a-7a7f-4403-96dd-5e911be3ee0f/IGVFFI3660FXUN.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF2-BinB-PCR3-Rep1_S200.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1431PSHL/",
"accession": "IGVFFI1431PSHL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF2-BinB-PCR4-Rep1_S206"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:45:20.815946+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI1431PSHL/@@download/IGVFFI1431PSHL.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/733baa96-1c7c-431c-9ccb-2fd5cbf0b9ba/IGVFFI1431PSHL.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF2-BinB-PCR4-Rep1_S206.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6135TIGK/",
"accession": "IGVFFI6135TIGK",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF2-BinB-PCR3-Rep1_S200"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:55:12.454503+00:00",
"file_format": "fastq",
"file_size": 28704538,
"href": "/sequence-files/IGVFFI6135TIGK/@@download/IGVFFI6135TIGK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/7a5bccfa-24ad-421d-ade0-ae716fa847d5/IGVFFI6135TIGK.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/FAM3C-Auxin6hrs-FF2-BinB-PCR3-Rep1_S200_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5239VQTN/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS1173ZRMB/",
"accession": "IGVFDS1173ZRMB",
"aliases": [
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF2-BinB-PCR1-Rep1_S146",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF2-BinB-PCR2-Rep1_S152",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF2-BinB-PCR3-Rep1_S200",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF2-BinB-PCR4-Rep1_S206"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-07-10T20:12:56.770247+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9676AELV/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9676AELV",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF2-BinB-PCR1-Rep1_S146",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF2-BinB-PCR2-Rep1_S152",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF2-BinB-PCR3-Rep1_S200",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF2-BinB-PCR4-Rep1_S206"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS1891GTLU/"
],
"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 B for 10-20% expression of FAM3C) 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": "2024-06-01T01:54:36.099319+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "8c9d5ade-9c0a-4c41-93b8-c05c5b8318dd"
}