{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6874YIXA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6874YIXA",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-NegControl_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Preview in vitro system [IGVFSM7816WZNZ](/in-vitro-systems/IGVFSM7816WZNZ/) 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/IGVFSM7816WZNZ/"
},
{
"category": "mismatched status",
"detail": "Preview in vitro system [IGVFSM7816WZNZ](/in-vitro-systems/IGVFSM7816WZNZ/) 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/IGVFSM7816WZNZ/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS6874YIXA](/measurement-sets/IGVFDS6874YIXA/) has sequence file(s) [IGVFFI9172CUNO](/sequence-files/IGVFFI9172CUNO/), [IGVFFI1681PMGU](/sequence-files/IGVFFI1681PMGU/), [IGVFFI0970RCKU](/sequence-files/IGVFFI0970RCKU/), [IGVFFI7049OPYY](/sequence-files/IGVFFI7049OPYY/), [IGVFFI9757VOYK](/sequence-files/IGVFFI9757VOYK/), [IGVFFI0124GUIN](/sequence-files/IGVFFI0124GUIN/), [IGVFFI0249CBTP](/sequence-files/IGVFFI0249CBTP/), [IGVFFI9770QQZB](/sequence-files/IGVFFI9770QQZB/), [IGVFFI9119HFYK](/sequence-files/IGVFFI9119HFYK/), [IGVFFI2507OKEP](/sequence-files/IGVFFI2507OKEP/), [IGVFFI9475XYVX](/sequence-files/IGVFFI9475XYVX/), [IGVFFI2164MOBD](/sequence-files/IGVFFI2164MOBD/), [IGVFFI8179LFTM](/sequence-files/IGVFFI8179LFTM/), [IGVFFI1362WUVK](/sequence-files/IGVFFI1362WUVK/), [IGVFFI5697NKKJ](/sequence-files/IGVFFI5697NKKJ/), [IGVFFI7915YAQK](/sequence-files/IGVFFI7915YAQK/) 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/IGVFDS6874YIXA/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS6874YIXA](/measurement-sets/IGVFDS6874YIXA/) has sequence file(s): [IGVFFI9172CUNO](/sequence-files/IGVFFI9172CUNO/), [IGVFFI1681PMGU](/sequence-files/IGVFFI1681PMGU/), [IGVFFI0970RCKU](/sequence-files/IGVFFI0970RCKU/), [IGVFFI7049OPYY](/sequence-files/IGVFFI7049OPYY/), [IGVFFI9757VOYK](/sequence-files/IGVFFI9757VOYK/), [IGVFFI0124GUIN](/sequence-files/IGVFFI0124GUIN/), [IGVFFI0249CBTP](/sequence-files/IGVFFI0249CBTP/), [IGVFFI9770QQZB](/sequence-files/IGVFFI9770QQZB/), [IGVFFI9119HFYK](/sequence-files/IGVFFI9119HFYK/), [IGVFFI2507OKEP](/sequence-files/IGVFFI2507OKEP/), [IGVFFI9475XYVX](/sequence-files/IGVFFI9475XYVX/), [IGVFFI2164MOBD](/sequence-files/IGVFFI2164MOBD/), [IGVFFI8179LFTM](/sequence-files/IGVFFI8179LFTM/), [IGVFFI1362WUVK](/sequence-files/IGVFFI1362WUVK/), [IGVFFI5697NKKJ](/sequence-files/IGVFFI5697NKKJ/), [IGVFFI7915YAQK](/sequence-files/IGVFFI7915YAQK/) 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/IGVFDS6874YIXA/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6874YIXA](/measurement-sets/IGVFDS6874YIXA/) 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/IGVFDS6874YIXA/"
}
]
},
"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"
},
"control_for": [
{
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"accession": "IGVFDS9252NUTS",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA_AmpliconSequencing"
],
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS9863HSXN/",
"accession": "IGVFDS9863HSXN",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep2-BinA_AmpliconSequencing"
],
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS0414OFOP/",
"accession": "IGVFDS0414OFOP",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinD_AmpliconSequencing"
],
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS6967UVNI/",
"accession": "IGVFDS6967UVNI",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinA_AmpliconSequencing"
],
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS2419JBTK/",
"accession": "IGVFDS2419JBTK",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinB_AmpliconSequencing"
],
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS7995HXFV/",
"accession": "IGVFDS7995HXFV",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC_AmpliconSequencing"
],
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS2408JJSR/",
"accession": "IGVFDS2408JJSR",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep2-BinB_AmpliconSequencing"
],
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS3851BRIR/",
"accession": "IGVFDS3851BRIR",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep2-BinC_AmpliconSequencing"
],
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS1434CFNM/",
"accession": "IGVFDS1434CFNM",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep2-BinD_AmpliconSequencing"
],
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS3202JLFH/",
"accession": "IGVFDS3202JLFH",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinB_AmpliconSequencing"
],
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS7494CPQT/",
"accession": "IGVFDS7494CPQT",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep2-FFRep3-BinD_AmpliconSequencing"
],
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS9847QETL/",
"accession": "IGVFDS9847QETL",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC_AmpliconSequencing"
],
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS9762JBUG/",
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],
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},
{
"@id": "/measurement-sets/IGVFDS2226SPYF/",
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},
{
"@id": "/measurement-sets/IGVFDS9444MPCG/",
"accession": "IGVFDS9444MPCG",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep2-FFRep1-BinA_AmpliconSequencing"
],
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS9743TYOT/",
"accession": "IGVFDS9743TYOT",
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"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep2-FFRep1-BinB_AmpliconSequencing"
],
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},
{
"@id": "/measurement-sets/IGVFDS6953SXZW/",
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},
{
"@id": "/measurement-sets/IGVFDS6913KQLF/",
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},
{
"@id": "/measurement-sets/IGVFDS0065BALX/",
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],
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{
"@id": "/measurement-sets/IGVFDS4537KNTB/",
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},
{
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{
"@id": "/measurement-sets/IGVFDS3270YULL/",
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],
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},
{
"@id": "/measurement-sets/IGVFDS6025ASSH/",
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],
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},
{
"@id": "/measurement-sets/IGVFDS2990MLAQ/",
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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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"title": "Jesse Engreitz, Stanford"
},
"notes": "This measurement set previously used Variant FlowFISH as a preferred_assay_title, but this enum is now removed. So it has been defaulted to Variant-EFFECTS.",
"preferred_assay_title": "Variant-EFFECTS",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
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{
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"Sample",
"Item"
],
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"Item"
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],
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}
],
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},
{
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"summary": "prime editing Variant-EFFECTS",
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{
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"name": "interleukin 2 receptor subunit alpha",
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"IL2R",
"TAC antigen",
"IMD41",
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"CD25",
"IL-2 receptor subunit alpha",
"IDDM10",
"TCGFR",
"p55",
"interleukin 2 receptor, alpha"
]
}
],
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}