{
"@context": "/terms/",
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"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS6339VOWW",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF1-BinE-PCR1-Rep1_S137",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF1-BinE-PCR2-Rep1_S143",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF1-BinE-PCR3-Rep1_S191",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF1-BinE-PCR4-Rep1_S197"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS6339VOWW](/auxiliary-sets/IGVFDS6339VOWW/) has sequence file(s) [IGVFFI8876DUSQ](/sequence-files/IGVFFI8876DUSQ/), [IGVFFI5201ODGZ](/sequence-files/IGVFFI5201ODGZ/), [IGVFFI7203LQPW](/sequence-files/IGVFFI7203LQPW/), [IGVFFI0863TIZV](/sequence-files/IGVFFI0863TIZV/) 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/IGVFDS6339VOWW/"
}
]
},
"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": "2024-05-14T16:51:11.411183+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/IGVFFI8876DUSQ/",
"accession": "IGVFFI8876DUSQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinE-PCR1-Rep1_S137"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:53:31.814487+00:00",
"file_format": "fastq",
"file_size": 24238076,
"href": "/sequence-files/IGVFFI8876DUSQ/@@download/IGVFFI8876DUSQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/ce733ab4-9e80-4de3-bd65-ddcd87f8d11d/IGVFFI8876DUSQ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6050YPJF/",
"accession": "IGVFFI6050YPJF",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinE-PCR1-Rep1_S137"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:50.879718+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI6050YPJF/@@download/IGVFFI6050YPJF.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/541bf080-81c7-4f45-b08a-5688a383eee6/IGVFFI6050YPJF.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinE-PCR1-Rep1_S137.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7266DDSV/",
"accession": "IGVFFI7266DDSV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinE-PCR2-Rep1_S143"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:44:04.941317+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI7266DDSV/@@download/IGVFFI7266DDSV.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/d24f4da1-69b7-460a-b09b-507fe1c6956e/IGVFFI7266DDSV.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinE-PCR2-Rep1_S143.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5201ODGZ/",
"accession": "IGVFFI5201ODGZ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinE-PCR2-Rep1_S143"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:53:49.996408+00:00",
"file_format": "fastq",
"file_size": 17376371,
"href": "/sequence-files/IGVFFI5201ODGZ/@@download/IGVFFI5201ODGZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/b1b95d57-d500-472a-956d-97a74f4b9b85/IGVFFI5201ODGZ.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-FF1-BinE-PCR2-Rep1_S143_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0576GUNB/",
"accession": "IGVFFI0576GUNB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinE-PCR3-Rep1_S191"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:44:18.610157+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI0576GUNB/@@download/IGVFFI0576GUNB.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/24252cf9-da2d-46f1-a061-ed0cd1c5fcb4/IGVFFI0576GUNB.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinE-PCR3-Rep1_S191.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1168ECOQ/",
"accession": "IGVFFI1168ECOQ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinE-PCR4-Rep1_S197"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:44:32.142342+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI1168ECOQ/@@download/IGVFFI1168ECOQ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/716dc743-f405-44f7-b4ae-832823e0038c/IGVFFI1168ECOQ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinE-PCR4-Rep1_S197.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7203LQPW/",
"accession": "IGVFFI7203LQPW",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinE-PCR3-Rep1_S191"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:54:08.405870+00:00",
"file_format": "fastq",
"file_size": 33558346,
"href": "/sequence-files/IGVFFI7203LQPW/@@download/IGVFFI7203LQPW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/9b6eaac4-8391-4014-950a-8aaabc0ae02b/IGVFFI7203LQPW.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-FF1-BinE-PCR3-Rep1_S191_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0863TIZV/",
"accession": "IGVFFI0863TIZV",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinE-PCR4-Rep1_S197"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:54:27.029163+00:00",
"file_format": "fastq",
"file_size": 20442317,
"href": "/sequence-files/IGVFFI0863TIZV/@@download/IGVFFI0863TIZV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/b0373081-befe-48f5-8cfc-c80ec4acb70e/IGVFFI0863TIZV.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-FF1-BinE-PCR4-Rep1_S197_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/IGVFDS3892SCNX/",
"accession": "IGVFDS3892SCNX",
"aliases": [
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinE-PCR1-Rep1_S137",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinE-PCR2-Rep1_S143",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinE-PCR3-Rep1_S191",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinE-PCR4-Rep1_S197"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-07-10T20:12:33.126439+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1988DOCZ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1988DOCZ",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinE-PCR1-Rep1_S137",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinE-PCR2-Rep1_S143",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinE-PCR3-Rep1_S191",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinE-PCR4-Rep1_S197"
],
"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 E for 80-90% 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": "2024-06-01T01:53:31.814487+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "b5cb00c9-eaf9-4a8f-9a68-d0204de929b6"
}