{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS6286FOBM/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS6286FOBM",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinB-PCR1-Rep1_S2",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinB-PCR2-Rep1_S8",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinB-PCR3-Rep1_S56",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinB-PCR4-Rep1_S62"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS6286FOBM](/auxiliary-sets/IGVFDS6286FOBM/) has sequence file(s) [IGVFFI5753AKDH](/sequence-files/IGVFFI5753AKDH/), [IGVFFI5649PKQE](/sequence-files/IGVFFI5649PKQE/), [IGVFFI2857MGHU](/sequence-files/IGVFFI2857MGHU/), [IGVFFI0085KGJD](/sequence-files/IGVFFI0085KGJD/) 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/IGVFDS6286FOBM/"
}
]
},
"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": "2024-05-14T20:30:53.780712+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/IGVFFI5753AKDH/",
"accession": "IGVFFI5753AKDH",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinB-PCR1-Rep1_S2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:44:38.384230+00:00",
"file_format": "fastq",
"file_size": 22218030,
"href": "/sequence-files/IGVFFI5753AKDH/@@download/IGVFFI5753AKDH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/34c8be98-b996-4923-9a7c-bf2e0f3a83e7/IGVFFI5753AKDH.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/SSFA2-Auxin0hrs-FF1-BinB-PCR1-Rep1_S2_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3700VVCG/",
"accession": "IGVFFI3700VVCG",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinB-PCR1-Rep1_S2"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:37:19.627373+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI3700VVCG/@@download/IGVFFI3700VVCG.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/69d02995-c5c0-4682-b1d9-5c280d0bc3f3/IGVFFI3700VVCG.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinB-PCR1-Rep1_S2.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5649PKQE/",
"accession": "IGVFFI5649PKQE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinB-PCR2-Rep1_S8"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:44:56.667051+00:00",
"file_format": "fastq",
"file_size": 21880116,
"href": "/sequence-files/IGVFFI5649PKQE/@@download/IGVFFI5649PKQE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/df1f543a-2dc7-4f6f-8c48-c91570d1861f/IGVFFI5649PKQE.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/SSFA2-Auxin0hrs-FF1-BinB-PCR2-Rep1_S8_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2857MGHU/",
"accession": "IGVFFI2857MGHU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinB-PCR4-Rep1_S62"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:45:32.724920+00:00",
"file_format": "fastq",
"file_size": 22118350,
"href": "/sequence-files/IGVFFI2857MGHU/@@download/IGVFFI2857MGHU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/33633dfb-bb52-4ec2-a018-a6fb8994afab/IGVFFI2857MGHU.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/SSFA2-Auxin0hrs-FF1-BinB-PCR4-Rep1_S62_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0085KGJD/",
"accession": "IGVFFI0085KGJD",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinB-PCR3-Rep1_S56"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:45:14.941134+00:00",
"file_format": "fastq",
"file_size": 21209478,
"href": "/sequence-files/IGVFFI0085KGJD/@@download/IGVFFI0085KGJD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/13ec8d97-90bd-45fa-81c7-1c196149bade/IGVFFI0085KGJD.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/SSFA2-Auxin0hrs-FF1-BinB-PCR3-Rep1_S56_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6162VIQX/",
"accession": "IGVFFI6162VIQX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinB-PCR3-Rep1_S56"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:37:49.190408+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI6162VIQX/@@download/IGVFFI6162VIQX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/102e6368-e7de-4edc-8b31-c28737234f78/IGVFFI6162VIQX.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinB-PCR3-Rep1_S56.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6404EYSK/",
"accession": "IGVFFI6404EYSK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinB-PCR4-Rep1_S62"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:38:04.728221+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI6404EYSK/@@download/IGVFFI6404EYSK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/31e518a6-97cb-44d0-b23b-ad4a44c6e9c5/IGVFFI6404EYSK.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinB-PCR4-Rep1_S62.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8066BXEB/",
"accession": "IGVFFI8066BXEB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinB-PCR2-Rep1_S8"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:37:33.866347+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI8066BXEB/@@download/IGVFFI8066BXEB.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/48f1c03f-c560-4373-8a28-daf1528e1d7a/IGVFFI8066BXEB.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinB-PCR2-Rep1_S8.yaml",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2031CTSP/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS2697OVVG/",
"accession": "IGVFDS2697OVVG",
"aliases": [
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinB-PCR1-Rep1_S2",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinB-PCR2-Rep1_S8",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinB-PCR3-Rep1_S56",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinB-PCR4-Rep1_S62"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-07-10T20:23:49.224649+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0430YSKQ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0430YSKQ",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinB-PCR1-Rep1_S2",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinB-PCR2-Rep1_S8",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinB-PCR3-Rep1_S56",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinB-PCR4-Rep1_S62"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS5413RKIA/"
],
"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 B for 10-20% expression of SSFA2) 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": "2024-06-01T01:44:38.384230+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "5c3484fa-532c-4356-a48e-b5ca2a6a1100"
}