{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3270YULL/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3270YULL",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep2-FFRep2-BinD_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS3270YULL](/measurement-sets/IGVFDS3270YULL/) has sequence file(s) [IGVFFI1784XXXD](/sequence-files/IGVFFI1784XXXD/), [IGVFFI1796ZBYH](/sequence-files/IGVFFI1796ZBYH/), [IGVFFI2479EEFZ](/sequence-files/IGVFFI2479EEFZ/), [IGVFFI4412HYBG](/sequence-files/IGVFFI4412HYBG/), [IGVFFI2937FXDU](/sequence-files/IGVFFI2937FXDU/), [IGVFFI5834VJCP](/sequence-files/IGVFFI5834VJCP/), [IGVFFI5976GJEL](/sequence-files/IGVFFI5976GJEL/), [IGVFFI8750GATQ](/sequence-files/IGVFFI8750GATQ/), [IGVFFI7221QEEY](/sequence-files/IGVFFI7221QEEY/), [IGVFFI3357WOVZ](/sequence-files/IGVFFI3357WOVZ/), [IGVFFI6362ZLIJ](/sequence-files/IGVFFI6362ZLIJ/), [IGVFFI9084NOCR](/sequence-files/IGVFFI9084NOCR/), [IGVFFI3894EIDH](/sequence-files/IGVFFI3894EIDH/), [IGVFFI2612FTDR](/sequence-files/IGVFFI2612FTDR/), [IGVFFI0745HTWN](/sequence-files/IGVFFI0745HTWN/), [IGVFFI9367FDBM](/sequence-files/IGVFFI9367FDBM/), [IGVFFI0813WRDR](/sequence-files/IGVFFI0813WRDR/), [IGVFFI3646LAMB](/sequence-files/IGVFFI3646LAMB/), [IGVFFI2596TNJS](/sequence-files/IGVFFI2596TNJS/), [IGVFFI6744CAKE](/sequence-files/IGVFFI6744CAKE/), [IGVFFI6644EAID](/sequence-files/IGVFFI6644EAID/), [IGVFFI3525LSZD](/sequence-files/IGVFFI3525LSZD/), [IGVFFI3949VTFG](/sequence-files/IGVFFI3949VTFG/), [IGVFFI7867ALVM](/sequence-files/IGVFFI7867ALVM/), [IGVFFI5644ZQSK](/sequence-files/IGVFFI5644ZQSK/), [IGVFFI2958IRAU](/sequence-files/IGVFFI2958IRAU/), [IGVFFI4629PDYT](/sequence-files/IGVFFI4629PDYT/), [IGVFFI0370PIQO](/sequence-files/IGVFFI0370PIQO/), [IGVFFI1359DPBP](/sequence-files/IGVFFI1359DPBP/), [IGVFFI6631ISOS](/sequence-files/IGVFFI6631ISOS/), [IGVFFI4624EEZX](/sequence-files/IGVFFI4624EEZX/), [IGVFFI4348YXIW](/sequence-files/IGVFFI4348YXIW/) 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": "/measurement-sets/IGVFDS3270YULL/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3270YULL](/measurement-sets/IGVFDS3270YULL/) has sequence file(s): [IGVFFI1784XXXD](/sequence-files/IGVFFI1784XXXD/), [IGVFFI1796ZBYH](/sequence-files/IGVFFI1796ZBYH/), [IGVFFI2479EEFZ](/sequence-files/IGVFFI2479EEFZ/), [IGVFFI4412HYBG](/sequence-files/IGVFFI4412HYBG/), [IGVFFI2937FXDU](/sequence-files/IGVFFI2937FXDU/), [IGVFFI5834VJCP](/sequence-files/IGVFFI5834VJCP/), [IGVFFI5976GJEL](/sequence-files/IGVFFI5976GJEL/), [IGVFFI8750GATQ](/sequence-files/IGVFFI8750GATQ/), [IGVFFI7221QEEY](/sequence-files/IGVFFI7221QEEY/), [IGVFFI3357WOVZ](/sequence-files/IGVFFI3357WOVZ/), [IGVFFI6362ZLIJ](/sequence-files/IGVFFI6362ZLIJ/), [IGVFFI9084NOCR](/sequence-files/IGVFFI9084NOCR/), [IGVFFI3894EIDH](/sequence-files/IGVFFI3894EIDH/), [IGVFFI2612FTDR](/sequence-files/IGVFFI2612FTDR/), [IGVFFI0745HTWN](/sequence-files/IGVFFI0745HTWN/), [IGVFFI9367FDBM](/sequence-files/IGVFFI9367FDBM/), [IGVFFI0813WRDR](/sequence-files/IGVFFI0813WRDR/), [IGVFFI3646LAMB](/sequence-files/IGVFFI3646LAMB/), [IGVFFI2596TNJS](/sequence-files/IGVFFI2596TNJS/), [IGVFFI6744CAKE](/sequence-files/IGVFFI6744CAKE/), [IGVFFI6644EAID](/sequence-files/IGVFFI6644EAID/), [IGVFFI3525LSZD](/sequence-files/IGVFFI3525LSZD/), [IGVFFI3949VTFG](/sequence-files/IGVFFI3949VTFG/), [IGVFFI7867ALVM](/sequence-files/IGVFFI7867ALVM/), [IGVFFI5644ZQSK](/sequence-files/IGVFFI5644ZQSK/), [IGVFFI2958IRAU](/sequence-files/IGVFFI2958IRAU/), [IGVFFI4629PDYT](/sequence-files/IGVFFI4629PDYT/), [IGVFFI0370PIQO](/sequence-files/IGVFFI0370PIQO/), [IGVFFI1359DPBP](/sequence-files/IGVFFI1359DPBP/), [IGVFFI6631ISOS](/sequence-files/IGVFFI6631ISOS/), [IGVFFI4624EEZX](/sequence-files/IGVFFI4624EEZX/), [IGVFFI4348YXIW](/sequence-files/IGVFFI4348YXIW/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS3270YULL/"
},
{
"category": "mismatched status",
"detail": "Preview in vitro system [IGVFSM4553KVCE](/in-vitro-systems/IGVFSM4553KVCE/) has in progress subobject treatment [cf87f410-54ee-48ef-b654-8443c4fee032](/treatments/cf87f410-54ee-48ef-b654-8443c4fee032/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM4553KVCE/"
},
{
"category": "mismatched status",
"detail": "Preview in vitro system [IGVFSM4553KVCE](/in-vitro-systems/IGVFSM4553KVCE/) has in progress subobject treatment [4b5f0d13-ec20-4b91-85f5-a009cd91451f](/treatments/4b5f0d13-ec20-4b91-85f5-a009cd91451f/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM4553KVCE/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3270YULL](/measurement-sets/IGVFDS3270YULL/) has no cell sorting `auxiliary_sets`. CRISPR-based measurement sets that utilize flow cytometry are expected to link to a cell sorting auxiliary set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS3270YULL/"
}
]
},
"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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{
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"accession": "IGVFDS6874YIXA",
"aliases": [
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],
"status": "preview"
}
],
"control_for": [],
"creation_timestamp": "2024-11-22T00:48:50.251503+00:00",
"donors": [
{
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"accession": "IGVFDO1080XFGV",
"aliases": [
"igvf:donor_of_Jurkat"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
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{
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"accession": "IGVFFI1784XXXD",
"aliases": [
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],
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"creation_timestamp": "2024-11-22T06:40:08.876912+00:00",
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},
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},
{
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},
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},
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},
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},
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},
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},
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},
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},
{
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],
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"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2024-11-22T06:36:09.505850+00:00",
"summary": "CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"targeted_genes": [
{
"@id": "/genes/ENSG00000134460/",
"geneid": "ENSG00000134460",
"name": "interleukin 2 receptor subunit alpha",
"status": "released",
"symbol": "IL2RA",
"synonyms": [
"interleukin-2 receptor subunit alpha",
"IL2R",
"TAC antigen",
"IMD41",
"IL-2R subunit alpha",
"CD25",
"IL-2 receptor subunit alpha",
"IDDM10",
"TCGFR",
"p55",
"interleukin 2 receptor, alpha"
]
}
],
"uuid": "825bb579-fbe0-4d9f-9326-0fd775cbd44e"
}