{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2990MLAQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2990MLAQ",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep2-FFRep3-BinB_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 [IGVFDS2990MLAQ](/measurement-sets/IGVFDS2990MLAQ/) has sequence file(s) [IGVFFI0741BZBH](/sequence-files/IGVFFI0741BZBH/), [IGVFFI0493SXAC](/sequence-files/IGVFFI0493SXAC/), [IGVFFI4701OXLK](/sequence-files/IGVFFI4701OXLK/), [IGVFFI5520GNOG](/sequence-files/IGVFFI5520GNOG/), [IGVFFI8112LDZD](/sequence-files/IGVFFI8112LDZD/), [IGVFFI3848JADH](/sequence-files/IGVFFI3848JADH/), [IGVFFI1886FDNR](/sequence-files/IGVFFI1886FDNR/), [IGVFFI1414TYJF](/sequence-files/IGVFFI1414TYJF/), [IGVFFI0848GNQB](/sequence-files/IGVFFI0848GNQB/), [IGVFFI0211GANU](/sequence-files/IGVFFI0211GANU/), [IGVFFI0351FTCS](/sequence-files/IGVFFI0351FTCS/), [IGVFFI0767IFAY](/sequence-files/IGVFFI0767IFAY/), [IGVFFI8839MCHE](/sequence-files/IGVFFI8839MCHE/), [IGVFFI5288WUZO](/sequence-files/IGVFFI5288WUZO/), [IGVFFI4499KZIB](/sequence-files/IGVFFI4499KZIB/), [IGVFFI5444ZLSC](/sequence-files/IGVFFI5444ZLSC/), [IGVFFI4877BJUO](/sequence-files/IGVFFI4877BJUO/), [IGVFFI0882YLIX](/sequence-files/IGVFFI0882YLIX/), [IGVFFI6550FPTW](/sequence-files/IGVFFI6550FPTW/), [IGVFFI9353IFJV](/sequence-files/IGVFFI9353IFJV/), [IGVFFI6311AXHC](/sequence-files/IGVFFI6311AXHC/), [IGVFFI5466DKFO](/sequence-files/IGVFFI5466DKFO/), [IGVFFI4952RBGL](/sequence-files/IGVFFI4952RBGL/), [IGVFFI4607UDHX](/sequence-files/IGVFFI4607UDHX/), [IGVFFI9947OKIN](/sequence-files/IGVFFI9947OKIN/), [IGVFFI8730YRDO](/sequence-files/IGVFFI8730YRDO/), [IGVFFI4649OPAD](/sequence-files/IGVFFI4649OPAD/), [IGVFFI9132QEDK](/sequence-files/IGVFFI9132QEDK/), [IGVFFI2176FIYD](/sequence-files/IGVFFI2176FIYD/), [IGVFFI8293QEXG](/sequence-files/IGVFFI8293QEXG/), [IGVFFI7504DAYL](/sequence-files/IGVFFI7504DAYL/), [IGVFFI3918PACX](/sequence-files/IGVFFI3918PACX/) 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/IGVFDS2990MLAQ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2990MLAQ](/measurement-sets/IGVFDS2990MLAQ/) has sequence file(s): [IGVFFI0741BZBH](/sequence-files/IGVFFI0741BZBH/), [IGVFFI0493SXAC](/sequence-files/IGVFFI0493SXAC/), [IGVFFI4701OXLK](/sequence-files/IGVFFI4701OXLK/), [IGVFFI5520GNOG](/sequence-files/IGVFFI5520GNOG/), [IGVFFI8112LDZD](/sequence-files/IGVFFI8112LDZD/), [IGVFFI3848JADH](/sequence-files/IGVFFI3848JADH/), [IGVFFI1886FDNR](/sequence-files/IGVFFI1886FDNR/), [IGVFFI1414TYJF](/sequence-files/IGVFFI1414TYJF/), [IGVFFI0848GNQB](/sequence-files/IGVFFI0848GNQB/), [IGVFFI0211GANU](/sequence-files/IGVFFI0211GANU/), [IGVFFI0351FTCS](/sequence-files/IGVFFI0351FTCS/), [IGVFFI0767IFAY](/sequence-files/IGVFFI0767IFAY/), [IGVFFI8839MCHE](/sequence-files/IGVFFI8839MCHE/), [IGVFFI5288WUZO](/sequence-files/IGVFFI5288WUZO/), [IGVFFI4499KZIB](/sequence-files/IGVFFI4499KZIB/), [IGVFFI5444ZLSC](/sequence-files/IGVFFI5444ZLSC/), [IGVFFI4877BJUO](/sequence-files/IGVFFI4877BJUO/), [IGVFFI0882YLIX](/sequence-files/IGVFFI0882YLIX/), [IGVFFI6550FPTW](/sequence-files/IGVFFI6550FPTW/), [IGVFFI9353IFJV](/sequence-files/IGVFFI9353IFJV/), [IGVFFI6311AXHC](/sequence-files/IGVFFI6311AXHC/), [IGVFFI5466DKFO](/sequence-files/IGVFFI5466DKFO/), [IGVFFI4952RBGL](/sequence-files/IGVFFI4952RBGL/), [IGVFFI4607UDHX](/sequence-files/IGVFFI4607UDHX/), [IGVFFI9947OKIN](/sequence-files/IGVFFI9947OKIN/), [IGVFFI8730YRDO](/sequence-files/IGVFFI8730YRDO/), [IGVFFI4649OPAD](/sequence-files/IGVFFI4649OPAD/), [IGVFFI9132QEDK](/sequence-files/IGVFFI9132QEDK/), [IGVFFI2176FIYD](/sequence-files/IGVFFI2176FIYD/), [IGVFFI8293QEXG](/sequence-files/IGVFFI8293QEXG/), [IGVFFI7504DAYL](/sequence-files/IGVFFI7504DAYL/), [IGVFFI3918PACX](/sequence-files/IGVFFI3918PACX/) 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/IGVFDS2990MLAQ/"
},
{
"category": "mismatched status",
"detail": "Preview in vitro system [IGVFSM8345LMXC](/in-vitro-systems/IGVFSM8345LMXC/) 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/IGVFSM8345LMXC/"
},
{
"category": "mismatched status",
"detail": "Preview in vitro system [IGVFSM8345LMXC](/in-vitro-systems/IGVFSM8345LMXC/) 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/IGVFSM8345LMXC/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2990MLAQ](/measurement-sets/IGVFDS2990MLAQ/) 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/IGVFDS2990MLAQ/"
}
]
},
"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": "2024-11-22T00:49:01.271136+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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},
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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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"schema_version": "23",
"status": "preview",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2024-11-22T06:51:30.556517+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": "29b220b7-94d8-40aa-91e4-e55f1c49f994"
}