{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6967UVNI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6967UVNI",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-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 [IGVFDS6967UVNI](/measurement-sets/IGVFDS6967UVNI/) has sequence file(s) [IGVFFI1821ZCUE](/sequence-files/IGVFFI1821ZCUE/), [IGVFFI5431HRCO](/sequence-files/IGVFFI5431HRCO/), [IGVFFI0736JJDC](/sequence-files/IGVFFI0736JJDC/), [IGVFFI2899FICN](/sequence-files/IGVFFI2899FICN/), [IGVFFI4008WEEF](/sequence-files/IGVFFI4008WEEF/), [IGVFFI7395ASXQ](/sequence-files/IGVFFI7395ASXQ/), [IGVFFI6123MSQD](/sequence-files/IGVFFI6123MSQD/), [IGVFFI3338GVBN](/sequence-files/IGVFFI3338GVBN/), [IGVFFI4171GVTP](/sequence-files/IGVFFI4171GVTP/), [IGVFFI8603OFKJ](/sequence-files/IGVFFI8603OFKJ/), [IGVFFI4428UHFM](/sequence-files/IGVFFI4428UHFM/), [IGVFFI9760HACC](/sequence-files/IGVFFI9760HACC/), [IGVFFI8727TUOH](/sequence-files/IGVFFI8727TUOH/), [IGVFFI3192PEAI](/sequence-files/IGVFFI3192PEAI/), [IGVFFI2819LADT](/sequence-files/IGVFFI2819LADT/), [IGVFFI4478CKNH](/sequence-files/IGVFFI4478CKNH/), [IGVFFI7803ZWBI](/sequence-files/IGVFFI7803ZWBI/), [IGVFFI6947MQUA](/sequence-files/IGVFFI6947MQUA/), [IGVFFI5878DIXY](/sequence-files/IGVFFI5878DIXY/), [IGVFFI6583SCYG](/sequence-files/IGVFFI6583SCYG/), [IGVFFI6264GZYB](/sequence-files/IGVFFI6264GZYB/), [IGVFFI7872JJXW](/sequence-files/IGVFFI7872JJXW/), [IGVFFI6264ZXYN](/sequence-files/IGVFFI6264ZXYN/), [IGVFFI4399VKTK](/sequence-files/IGVFFI4399VKTK/), [IGVFFI8852RUYH](/sequence-files/IGVFFI8852RUYH/), [IGVFFI3826UXIU](/sequence-files/IGVFFI3826UXIU/), [IGVFFI0315HTTZ](/sequence-files/IGVFFI0315HTTZ/), [IGVFFI6136XCBP](/sequence-files/IGVFFI6136XCBP/), [IGVFFI4305TSAX](/sequence-files/IGVFFI4305TSAX/), [IGVFFI4788UQIC](/sequence-files/IGVFFI4788UQIC/), [IGVFFI6758ZUXB](/sequence-files/IGVFFI6758ZUXB/), [IGVFFI2998IQUG](/sequence-files/IGVFFI2998IQUG/) 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/IGVFDS6967UVNI/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS6967UVNI](/measurement-sets/IGVFDS6967UVNI/) has sequence file(s): [IGVFFI1821ZCUE](/sequence-files/IGVFFI1821ZCUE/), [IGVFFI5431HRCO](/sequence-files/IGVFFI5431HRCO/), [IGVFFI0736JJDC](/sequence-files/IGVFFI0736JJDC/), [IGVFFI2899FICN](/sequence-files/IGVFFI2899FICN/), [IGVFFI4008WEEF](/sequence-files/IGVFFI4008WEEF/), [IGVFFI7395ASXQ](/sequence-files/IGVFFI7395ASXQ/), [IGVFFI6123MSQD](/sequence-files/IGVFFI6123MSQD/), [IGVFFI3338GVBN](/sequence-files/IGVFFI3338GVBN/), [IGVFFI4171GVTP](/sequence-files/IGVFFI4171GVTP/), [IGVFFI8603OFKJ](/sequence-files/IGVFFI8603OFKJ/), [IGVFFI4428UHFM](/sequence-files/IGVFFI4428UHFM/), [IGVFFI9760HACC](/sequence-files/IGVFFI9760HACC/), [IGVFFI8727TUOH](/sequence-files/IGVFFI8727TUOH/), [IGVFFI3192PEAI](/sequence-files/IGVFFI3192PEAI/), [IGVFFI2819LADT](/sequence-files/IGVFFI2819LADT/), [IGVFFI4478CKNH](/sequence-files/IGVFFI4478CKNH/), [IGVFFI7803ZWBI](/sequence-files/IGVFFI7803ZWBI/), [IGVFFI6947MQUA](/sequence-files/IGVFFI6947MQUA/), [IGVFFI5878DIXY](/sequence-files/IGVFFI5878DIXY/), [IGVFFI6583SCYG](/sequence-files/IGVFFI6583SCYG/), [IGVFFI6264GZYB](/sequence-files/IGVFFI6264GZYB/), [IGVFFI7872JJXW](/sequence-files/IGVFFI7872JJXW/), [IGVFFI6264ZXYN](/sequence-files/IGVFFI6264ZXYN/), [IGVFFI4399VKTK](/sequence-files/IGVFFI4399VKTK/), [IGVFFI8852RUYH](/sequence-files/IGVFFI8852RUYH/), [IGVFFI3826UXIU](/sequence-files/IGVFFI3826UXIU/), [IGVFFI0315HTTZ](/sequence-files/IGVFFI0315HTTZ/), [IGVFFI6136XCBP](/sequence-files/IGVFFI6136XCBP/), [IGVFFI4305TSAX](/sequence-files/IGVFFI4305TSAX/), [IGVFFI4788UQIC](/sequence-files/IGVFFI4788UQIC/), [IGVFFI6758ZUXB](/sequence-files/IGVFFI6758ZUXB/), [IGVFFI2998IQUG](/sequence-files/IGVFFI2998IQUG/) 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/IGVFDS6967UVNI/"
},
{
"category": "mismatched status",
"detail": "Preview in vitro system [IGVFSM9297KXBW](/in-vitro-systems/IGVFSM9297KXBW/) 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/IGVFSM9297KXBW/"
},
{
"category": "mismatched status",
"detail": "Preview in vitro system [IGVFSM9297KXBW](/in-vitro-systems/IGVFSM9297KXBW/) 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/IGVFSM9297KXBW/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6967UVNI](/measurement-sets/IGVFDS6967UVNI/) 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/IGVFDS6967UVNI/"
}
]
},
"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": "2024-11-22T00:46:51.905972+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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"accession": "IGVFFI1821ZCUE",
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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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},
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"status": "preview",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2024-11-22T02:17:07.118048+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": "2a7b2fd3-0870-4ee3-ad51-fb830168d63a"
}