{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS8794YVNF/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS8794YVNF",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR1_Rep1_S6",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR1_Rep2_S61",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR2_Rep1_S12",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR2_Rep2_S67",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR3_Rep1_S18",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR3_Rep2_S73",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR4_Rep1_S24",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR4_Rep2_S79"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8794YVNF](/auxiliary-sets/IGVFDS8794YVNF/) has sequence file(s) [IGVFFI2406URSZ](/sequence-files/IGVFFI2406URSZ/), [IGVFFI8406TKIY](/sequence-files/IGVFFI8406TKIY/), [IGVFFI1943WFER](/sequence-files/IGVFFI1943WFER/), [IGVFFI3544BRUD](/sequence-files/IGVFFI3544BRUD/), [IGVFFI2688NUHF](/sequence-files/IGVFFI2688NUHF/), [IGVFFI9742FWEW](/sequence-files/IGVFFI9742FWEW/), [IGVFFI2723OPXS](/sequence-files/IGVFFI2723OPXS/), [IGVFFI2265SRGR](/sequence-files/IGVFFI2265SRGR/) 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/IGVFDS8794YVNF/"
}
]
},
"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": "2024-05-21T17:12:28.022055+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"accession": "IGVFDO0384OZRW",
"aliases": [
"igvf:donor_of_HCT116"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
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{
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"accession": "IGVFFI2406URSZ",
"aliases": [
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],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6594CJQE/",
"accession": "IGVFFI6594CJQE",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR1_Rep1_S6"
],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8406TKIY/",
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"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR2_Rep1_S12"
],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8822UQNI/",
"accession": "IGVFFI8822UQNI",
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"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR3_Rep1_S18"
],
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"file_format": "yaml",
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"href": "/configuration-files/IGVFFI8822UQNI/@@download/IGVFFI8822UQNI.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/36e0bcdb-1937-4352-b267-ddf6b8fefc1c/IGVFFI8822UQNI.yaml.gz",
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9867ZSRT/",
"accession": "IGVFFI9867ZSRT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR4_Rep1_S24"
],
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"file_format": "yaml",
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"href": "/configuration-files/IGVFFI9867ZSRT/@@download/IGVFFI9867ZSRT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/54e48b52-8b8b-4a4c-84dc-6b2f2948ed71/IGVFFI9867ZSRT.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinF-PCR4_Rep1_S24.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1943WFER/",
"accession": "IGVFFI1943WFER",
"aliases": [
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],
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"creation_timestamp": "2024-06-01T01:58:37.660452+00:00",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3544BRUD/",
"accession": "IGVFFI3544BRUD",
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"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR4_Rep2_S79"
],
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"creation_timestamp": "2024-06-01T02:00:41.130596+00:00",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2688NUHF/",
"accession": "IGVFFI2688NUHF",
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],
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},
{
"@id": "/sequence-files/IGVFFI9742FWEW/",
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],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2723OPXS/",
"accession": "IGVFFI2723OPXS",
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],
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"upload_status": "validated"
},
{
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],
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},
{
"@id": "/configuration-files/IGVFFI1926CUXK/",
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],
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},
{
"@id": "/configuration-files/IGVFFI6830TVJW/",
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],
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},
{
"@id": "/configuration-files/IGVFFI3988VDKG/",
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],
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},
{
"@id": "/configuration-files/IGVFFI6628HKXW/",
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],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0668QZUU/",
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"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR4_Rep2_S79"
],
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"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4544YEQM/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS1500HTAU/",
"accession": "IGVFDS1500HTAU",
"aliases": [
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"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR1_Rep2_S61",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR2_Rep1_S12",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR2_Rep2_S67",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR3_Rep1_S18",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR3_Rep2_S73",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR4_Rep1_S24",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR4_Rep2_S79"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-07-10T20:19:50.713446+00:00",
"samples": [
{
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"@type": [
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"Biosample",
"Sample",
"Item"
],
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"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR1_Rep2_S61",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR2_Rep1_S12",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR2_Rep2_S67",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR3_Rep1_S18",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR3_Rep2_S73",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR4_Rep1_S24",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR4_Rep2_S79"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7857SYCK/"
],
"modifications": [
{
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},
{
"@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
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}
],
"sample_terms": [
{
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"@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 MYC) 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": "2024-06-01T01:58:17.438390+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "c5028f1b-d093-4f7c-bd89-b53a2fb108aa"
}