{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9444MPCG/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9444MPCG",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep2-FFRep1-BinA_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 [IGVFDS9444MPCG](/measurement-sets/IGVFDS9444MPCG/) has sequence file(s) [IGVFFI7009WUQO](/sequence-files/IGVFFI7009WUQO/), [IGVFFI5473EOUW](/sequence-files/IGVFFI5473EOUW/), [IGVFFI0814OELU](/sequence-files/IGVFFI0814OELU/), [IGVFFI0996WHAU](/sequence-files/IGVFFI0996WHAU/), [IGVFFI8510STTP](/sequence-files/IGVFFI8510STTP/), [IGVFFI7019QYJK](/sequence-files/IGVFFI7019QYJK/), [IGVFFI4065GLXW](/sequence-files/IGVFFI4065GLXW/), [IGVFFI0201FAOW](/sequence-files/IGVFFI0201FAOW/), [IGVFFI1627EONJ](/sequence-files/IGVFFI1627EONJ/), [IGVFFI2273WMSQ](/sequence-files/IGVFFI2273WMSQ/), [IGVFFI8381NPDT](/sequence-files/IGVFFI8381NPDT/), [IGVFFI9049LFKK](/sequence-files/IGVFFI9049LFKK/), [IGVFFI9410BDLG](/sequence-files/IGVFFI9410BDLG/), [IGVFFI6367JMPD](/sequence-files/IGVFFI6367JMPD/), [IGVFFI7809KCGI](/sequence-files/IGVFFI7809KCGI/), [IGVFFI8000WOMP](/sequence-files/IGVFFI8000WOMP/), [IGVFFI3576ZDJD](/sequence-files/IGVFFI3576ZDJD/), [IGVFFI0492UXDY](/sequence-files/IGVFFI0492UXDY/), [IGVFFI0102VUIE](/sequence-files/IGVFFI0102VUIE/), [IGVFFI1366IZBY](/sequence-files/IGVFFI1366IZBY/), [IGVFFI6408GOIO](/sequence-files/IGVFFI6408GOIO/), [IGVFFI5806PKVO](/sequence-files/IGVFFI5806PKVO/), [IGVFFI0872SIOH](/sequence-files/IGVFFI0872SIOH/), [IGVFFI8634BXNJ](/sequence-files/IGVFFI8634BXNJ/), [IGVFFI7556RJEM](/sequence-files/IGVFFI7556RJEM/), [IGVFFI4348ZWJH](/sequence-files/IGVFFI4348ZWJH/), [IGVFFI3757LWTU](/sequence-files/IGVFFI3757LWTU/), [IGVFFI7526RQZV](/sequence-files/IGVFFI7526RQZV/), [IGVFFI9257KFKP](/sequence-files/IGVFFI9257KFKP/), [IGVFFI9993OJWO](/sequence-files/IGVFFI9993OJWO/), [IGVFFI5375KJRO](/sequence-files/IGVFFI5375KJRO/), [IGVFFI2123GOJJ](/sequence-files/IGVFFI2123GOJJ/) 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/IGVFDS9444MPCG/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9444MPCG](/measurement-sets/IGVFDS9444MPCG/) has sequence file(s): [IGVFFI7009WUQO](/sequence-files/IGVFFI7009WUQO/), [IGVFFI5473EOUW](/sequence-files/IGVFFI5473EOUW/), [IGVFFI0814OELU](/sequence-files/IGVFFI0814OELU/), [IGVFFI0996WHAU](/sequence-files/IGVFFI0996WHAU/), [IGVFFI8510STTP](/sequence-files/IGVFFI8510STTP/), [IGVFFI7019QYJK](/sequence-files/IGVFFI7019QYJK/), [IGVFFI4065GLXW](/sequence-files/IGVFFI4065GLXW/), [IGVFFI0201FAOW](/sequence-files/IGVFFI0201FAOW/), [IGVFFI1627EONJ](/sequence-files/IGVFFI1627EONJ/), [IGVFFI2273WMSQ](/sequence-files/IGVFFI2273WMSQ/), [IGVFFI8381NPDT](/sequence-files/IGVFFI8381NPDT/), [IGVFFI9049LFKK](/sequence-files/IGVFFI9049LFKK/), [IGVFFI9410BDLG](/sequence-files/IGVFFI9410BDLG/), [IGVFFI6367JMPD](/sequence-files/IGVFFI6367JMPD/), [IGVFFI7809KCGI](/sequence-files/IGVFFI7809KCGI/), [IGVFFI8000WOMP](/sequence-files/IGVFFI8000WOMP/), [IGVFFI3576ZDJD](/sequence-files/IGVFFI3576ZDJD/), [IGVFFI0492UXDY](/sequence-files/IGVFFI0492UXDY/), [IGVFFI0102VUIE](/sequence-files/IGVFFI0102VUIE/), [IGVFFI1366IZBY](/sequence-files/IGVFFI1366IZBY/), [IGVFFI6408GOIO](/sequence-files/IGVFFI6408GOIO/), [IGVFFI5806PKVO](/sequence-files/IGVFFI5806PKVO/), [IGVFFI0872SIOH](/sequence-files/IGVFFI0872SIOH/), [IGVFFI8634BXNJ](/sequence-files/IGVFFI8634BXNJ/), [IGVFFI7556RJEM](/sequence-files/IGVFFI7556RJEM/), [IGVFFI4348ZWJH](/sequence-files/IGVFFI4348ZWJH/), [IGVFFI3757LWTU](/sequence-files/IGVFFI3757LWTU/), [IGVFFI7526RQZV](/sequence-files/IGVFFI7526RQZV/), [IGVFFI9257KFKP](/sequence-files/IGVFFI9257KFKP/), [IGVFFI9993OJWO](/sequence-files/IGVFFI9993OJWO/), [IGVFFI5375KJRO](/sequence-files/IGVFFI5375KJRO/), [IGVFFI2123GOJJ](/sequence-files/IGVFFI2123GOJJ/) 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/IGVFDS9444MPCG/"
},
{
"category": "mismatched status",
"detail": "Preview in vitro system [IGVFSM7312DZBH](/in-vitro-systems/IGVFSM7312DZBH/) 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/IGVFSM7312DZBH/"
},
{
"category": "mismatched status",
"detail": "Preview in vitro system [IGVFSM7312DZBH](/in-vitro-systems/IGVFSM7312DZBH/) 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/IGVFSM7312DZBH/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS9444MPCG](/measurement-sets/IGVFDS9444MPCG/) 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/IGVFDS9444MPCG/"
}
]
},
"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": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-NegControl_AmpliconSequencing"
],
"status": "preview"
}
],
"control_for": [],
"creation_timestamp": "2024-11-22T00:48:06.582757+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1080XFGV/",
"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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},
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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": "/treatments/cf87f410-54ee-48ef-b654-8443c4fee032/",
"status": "in progress",
"treatment_term_name": "T-cell surface glycoprotein CD3 gamma chain"
}
]
}
],
"schema_version": "23",
"status": "preview",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2024-11-22T06:18:23.049790+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": "5a064bac-c577-4c9e-a4d5-4153f564957e"
}