{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS2834VAYS/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS2834VAYS",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR1_Rep1_S26",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR1_Rep2_S81",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR2_Rep1_S32",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR2_Rep2_S87",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR3_Rep1_S38",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR3_Rep2_S93",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR4_Rep1_S44",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR4_Rep2_S99"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2834VAYS](/auxiliary-sets/IGVFDS2834VAYS/) has sequence file(s) [IGVFFI7807KLUU](/sequence-files/IGVFFI7807KLUU/), [IGVFFI3275WQZQ](/sequence-files/IGVFFI3275WQZQ/), [IGVFFI4298DZIN](/sequence-files/IGVFFI4298DZIN/), [IGVFFI2362LKOQ](/sequence-files/IGVFFI2362LKOQ/), [IGVFFI5870UCTK](/sequence-files/IGVFFI5870UCTK/), [IGVFFI1545RRLD](/sequence-files/IGVFFI1545RRLD/), [IGVFFI9245IPZR](/sequence-files/IGVFFI9245IPZR/), [IGVFFI9172PREQ](/sequence-files/IGVFFI9172PREQ/) 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/IGVFDS2834VAYS/"
}
]
},
"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"
},
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"creation_timestamp": "2024-05-21T17:13:07.300301+00:00",
"donors": [
{
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"accession": "IGVFDO0384OZRW",
"aliases": [
"igvf:donor_of_HCT116"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
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{
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],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8168MZFJ/",
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],
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"upload_status": "validated"
},
{
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],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4298DZIN/",
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],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1435OZLL/",
"accession": "IGVFFI1435OZLL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR4_Rep1_S44"
],
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"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinB-PCR4_Rep1_S44.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2362LKOQ/",
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],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7331TUOS/",
"accession": "IGVFFI7331TUOS",
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],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5870UCTK/",
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],
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"upload_status": "validated"
},
{
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],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9245IPZR/",
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],
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},
{
"@id": "/sequence-files/IGVFFI9172PREQ/",
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],
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},
{
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},
{
"@id": "/configuration-files/IGVFFI2068XJOM/",
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},
{
"@id": "/configuration-files/IGVFFI2467IQLT/",
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],
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"href": "/configuration-files/IGVFFI2467IQLT/@@download/IGVFFI2467IQLT.yaml.gz",
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},
{
"@id": "/configuration-files/IGVFFI8314LAZS/",
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],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2350VRGN/",
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],
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"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4544YEQM/"
],
"lab": {
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"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
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"accession": "IGVFDS0398KCYH",
"aliases": [
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"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR1_Rep2_S81",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR2_Rep1_S32",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR2_Rep2_S87",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR3_Rep1_S38",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR3_Rep2_S93",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR4_Rep1_S44",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR4_Rep2_S99"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-07-10T20:20:06.844779+00:00",
"samples": [
{
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"Biosample",
"Sample",
"Item"
],
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"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR1_Rep2_S81",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR2_Rep1_S32",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR2_Rep2_S87",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR3_Rep1_S38",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR3_Rep2_S93",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR4_Rep1_S44",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinB-PCR4_Rep2_S99"
],
"classifications": [
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],
"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": [
{
"@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 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": "2024-06-01T02:00:48.191718+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "97595564-a0c8-4dc3-8969-0d92c2bfcee5"
}