{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2226SPYF/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2226SPYF",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-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 [IGVFDS2226SPYF](/measurement-sets/IGVFDS2226SPYF/) has sequence file(s) [IGVFFI0626BGLQ](/sequence-files/IGVFFI0626BGLQ/), [IGVFFI8681AYRN](/sequence-files/IGVFFI8681AYRN/), [IGVFFI9027IUEG](/sequence-files/IGVFFI9027IUEG/), [IGVFFI8420QXDT](/sequence-files/IGVFFI8420QXDT/), [IGVFFI1266XPEQ](/sequence-files/IGVFFI1266XPEQ/), [IGVFFI6008XUPU](/sequence-files/IGVFFI6008XUPU/), [IGVFFI2151BDTN](/sequence-files/IGVFFI2151BDTN/), [IGVFFI8910RYPU](/sequence-files/IGVFFI8910RYPU/), [IGVFFI1795MDAU](/sequence-files/IGVFFI1795MDAU/), [IGVFFI3674KVZX](/sequence-files/IGVFFI3674KVZX/), [IGVFFI2881JQQB](/sequence-files/IGVFFI2881JQQB/), [IGVFFI3129HQXY](/sequence-files/IGVFFI3129HQXY/), [IGVFFI4696UXEU](/sequence-files/IGVFFI4696UXEU/), [IGVFFI2269HMLY](/sequence-files/IGVFFI2269HMLY/), [IGVFFI4618GSXT](/sequence-files/IGVFFI4618GSXT/), [IGVFFI3347LXMJ](/sequence-files/IGVFFI3347LXMJ/), [IGVFFI6837WCJX](/sequence-files/IGVFFI6837WCJX/), [IGVFFI3821BRQS](/sequence-files/IGVFFI3821BRQS/), [IGVFFI0268YQSF](/sequence-files/IGVFFI0268YQSF/), [IGVFFI9249UUWF](/sequence-files/IGVFFI9249UUWF/), [IGVFFI4978DUYW](/sequence-files/IGVFFI4978DUYW/), [IGVFFI8445YYFS](/sequence-files/IGVFFI8445YYFS/), [IGVFFI8662ICZA](/sequence-files/IGVFFI8662ICZA/), [IGVFFI6338CHKJ](/sequence-files/IGVFFI6338CHKJ/), [IGVFFI0229FWHC](/sequence-files/IGVFFI0229FWHC/), [IGVFFI3619ZVHW](/sequence-files/IGVFFI3619ZVHW/), [IGVFFI7553VASE](/sequence-files/IGVFFI7553VASE/), [IGVFFI7636QZXT](/sequence-files/IGVFFI7636QZXT/), [IGVFFI1839KWJP](/sequence-files/IGVFFI1839KWJP/), [IGVFFI8427EAFE](/sequence-files/IGVFFI8427EAFE/), [IGVFFI3062JPOB](/sequence-files/IGVFFI3062JPOB/), [IGVFFI5773UCDZ](/sequence-files/IGVFFI5773UCDZ/) 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/IGVFDS2226SPYF/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2226SPYF](/measurement-sets/IGVFDS2226SPYF/) has sequence file(s): [IGVFFI0626BGLQ](/sequence-files/IGVFFI0626BGLQ/), [IGVFFI8681AYRN](/sequence-files/IGVFFI8681AYRN/), [IGVFFI9027IUEG](/sequence-files/IGVFFI9027IUEG/), [IGVFFI8420QXDT](/sequence-files/IGVFFI8420QXDT/), [IGVFFI1266XPEQ](/sequence-files/IGVFFI1266XPEQ/), [IGVFFI6008XUPU](/sequence-files/IGVFFI6008XUPU/), [IGVFFI2151BDTN](/sequence-files/IGVFFI2151BDTN/), [IGVFFI8910RYPU](/sequence-files/IGVFFI8910RYPU/), [IGVFFI1795MDAU](/sequence-files/IGVFFI1795MDAU/), [IGVFFI3674KVZX](/sequence-files/IGVFFI3674KVZX/), [IGVFFI2881JQQB](/sequence-files/IGVFFI2881JQQB/), [IGVFFI3129HQXY](/sequence-files/IGVFFI3129HQXY/), [IGVFFI4696UXEU](/sequence-files/IGVFFI4696UXEU/), [IGVFFI2269HMLY](/sequence-files/IGVFFI2269HMLY/), [IGVFFI4618GSXT](/sequence-files/IGVFFI4618GSXT/), [IGVFFI3347LXMJ](/sequence-files/IGVFFI3347LXMJ/), [IGVFFI6837WCJX](/sequence-files/IGVFFI6837WCJX/), [IGVFFI3821BRQS](/sequence-files/IGVFFI3821BRQS/), [IGVFFI0268YQSF](/sequence-files/IGVFFI0268YQSF/), [IGVFFI9249UUWF](/sequence-files/IGVFFI9249UUWF/), [IGVFFI4978DUYW](/sequence-files/IGVFFI4978DUYW/), [IGVFFI8445YYFS](/sequence-files/IGVFFI8445YYFS/), [IGVFFI8662ICZA](/sequence-files/IGVFFI8662ICZA/), [IGVFFI6338CHKJ](/sequence-files/IGVFFI6338CHKJ/), [IGVFFI0229FWHC](/sequence-files/IGVFFI0229FWHC/), [IGVFFI3619ZVHW](/sequence-files/IGVFFI3619ZVHW/), [IGVFFI7553VASE](/sequence-files/IGVFFI7553VASE/), [IGVFFI7636QZXT](/sequence-files/IGVFFI7636QZXT/), [IGVFFI1839KWJP](/sequence-files/IGVFFI1839KWJP/), [IGVFFI8427EAFE](/sequence-files/IGVFFI8427EAFE/), [IGVFFI3062JPOB](/sequence-files/IGVFFI3062JPOB/), [IGVFFI5773UCDZ](/sequence-files/IGVFFI5773UCDZ/) 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/IGVFDS2226SPYF/"
},
{
"category": "mismatched status",
"detail": "Preview in vitro system [IGVFSM5709XAIS](/in-vitro-systems/IGVFSM5709XAIS/) 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/IGVFSM5709XAIS/"
},
{
"category": "mismatched status",
"detail": "Preview in vitro system [IGVFSM5709XAIS](/in-vitro-systems/IGVFSM5709XAIS/) 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/IGVFSM5709XAIS/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2226SPYF](/measurement-sets/IGVFDS2226SPYF/) 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/IGVFDS2226SPYF/"
}
]
},
"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": "2024-11-22T00:47:58.990173+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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},
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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": "2024-11-22T06:04:11.654750+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": "e99c0c89-03a0-4772-b353-41f5a006d712"
}