{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7482HPXK/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7482HPXK",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep4-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 [IGVFDS7482HPXK](/measurement-sets/IGVFDS7482HPXK/) has sequence file(s) [IGVFFI6053LVWL](/sequence-files/IGVFFI6053LVWL/), [IGVFFI5223QHPE](/sequence-files/IGVFFI5223QHPE/), [IGVFFI1743SIGF](/sequence-files/IGVFFI1743SIGF/), [IGVFFI7899PLGE](/sequence-files/IGVFFI7899PLGE/), [IGVFFI8746YLWQ](/sequence-files/IGVFFI8746YLWQ/), [IGVFFI6116ENHQ](/sequence-files/IGVFFI6116ENHQ/), [IGVFFI4641GQAG](/sequence-files/IGVFFI4641GQAG/), [IGVFFI0747SAAH](/sequence-files/IGVFFI0747SAAH/), [IGVFFI0235EYBH](/sequence-files/IGVFFI0235EYBH/), [IGVFFI5707BPBC](/sequence-files/IGVFFI5707BPBC/), [IGVFFI8150RCHU](/sequence-files/IGVFFI8150RCHU/), [IGVFFI1605SSYP](/sequence-files/IGVFFI1605SSYP/), [IGVFFI5882AAFQ](/sequence-files/IGVFFI5882AAFQ/), [IGVFFI6045KPCD](/sequence-files/IGVFFI6045KPCD/), [IGVFFI8717QAZJ](/sequence-files/IGVFFI8717QAZJ/), [IGVFFI8947ZUFP](/sequence-files/IGVFFI8947ZUFP/), [IGVFFI5915MMUW](/sequence-files/IGVFFI5915MMUW/), [IGVFFI7758ETRJ](/sequence-files/IGVFFI7758ETRJ/), [IGVFFI3057YAJX](/sequence-files/IGVFFI3057YAJX/), [IGVFFI2423DDFU](/sequence-files/IGVFFI2423DDFU/), [IGVFFI8499IBTC](/sequence-files/IGVFFI8499IBTC/), [IGVFFI7938FXXY](/sequence-files/IGVFFI7938FXXY/), [IGVFFI3801FKWF](/sequence-files/IGVFFI3801FKWF/), [IGVFFI7956APIC](/sequence-files/IGVFFI7956APIC/), [IGVFFI3329THNO](/sequence-files/IGVFFI3329THNO/), [IGVFFI0882BUNU](/sequence-files/IGVFFI0882BUNU/), [IGVFFI4597LSJS](/sequence-files/IGVFFI4597LSJS/), [IGVFFI4002DINJ](/sequence-files/IGVFFI4002DINJ/), [IGVFFI6611EJQM](/sequence-files/IGVFFI6611EJQM/), [IGVFFI1099JNSA](/sequence-files/IGVFFI1099JNSA/), [IGVFFI2699UXIS](/sequence-files/IGVFFI2699UXIS/), [IGVFFI7863YKKH](/sequence-files/IGVFFI7863YKKH/), [IGVFFI2513EOMV](/sequence-files/IGVFFI2513EOMV/), [IGVFFI0358RKKW](/sequence-files/IGVFFI0358RKKW/), [IGVFFI3165XTXL](/sequence-files/IGVFFI3165XTXL/), [IGVFFI6761VKGI](/sequence-files/IGVFFI6761VKGI/), [IGVFFI2028NGKW](/sequence-files/IGVFFI2028NGKW/), [IGVFFI4070PIWT](/sequence-files/IGVFFI4070PIWT/), [IGVFFI8065HMQG](/sequence-files/IGVFFI8065HMQG/), [IGVFFI4532AIST](/sequence-files/IGVFFI4532AIST/), [IGVFFI5296QFVL](/sequence-files/IGVFFI5296QFVL/), [IGVFFI9434GLYH](/sequence-files/IGVFFI9434GLYH/), [IGVFFI2528ZCJQ](/sequence-files/IGVFFI2528ZCJQ/), [IGVFFI6620EYSV](/sequence-files/IGVFFI6620EYSV/), [IGVFFI5328KDUX](/sequence-files/IGVFFI5328KDUX/), [IGVFFI7133CVYY](/sequence-files/IGVFFI7133CVYY/), [IGVFFI5644CUEB](/sequence-files/IGVFFI5644CUEB/), [IGVFFI1658VVEI](/sequence-files/IGVFFI1658VVEI/), [IGVFFI5313XWTJ](/sequence-files/IGVFFI5313XWTJ/) 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/IGVFDS7482HPXK/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7482HPXK](/measurement-sets/IGVFDS7482HPXK/) has sequence file(s): [IGVFFI6053LVWL](/sequence-files/IGVFFI6053LVWL/), [IGVFFI5223QHPE](/sequence-files/IGVFFI5223QHPE/), [IGVFFI1743SIGF](/sequence-files/IGVFFI1743SIGF/), [IGVFFI7899PLGE](/sequence-files/IGVFFI7899PLGE/), [IGVFFI8746YLWQ](/sequence-files/IGVFFI8746YLWQ/), [IGVFFI6116ENHQ](/sequence-files/IGVFFI6116ENHQ/), [IGVFFI4641GQAG](/sequence-files/IGVFFI4641GQAG/), [IGVFFI0747SAAH](/sequence-files/IGVFFI0747SAAH/), [IGVFFI0235EYBH](/sequence-files/IGVFFI0235EYBH/), [IGVFFI5707BPBC](/sequence-files/IGVFFI5707BPBC/), [IGVFFI8150RCHU](/sequence-files/IGVFFI8150RCHU/), [IGVFFI1605SSYP](/sequence-files/IGVFFI1605SSYP/), [IGVFFI5882AAFQ](/sequence-files/IGVFFI5882AAFQ/), [IGVFFI6045KPCD](/sequence-files/IGVFFI6045KPCD/), [IGVFFI8717QAZJ](/sequence-files/IGVFFI8717QAZJ/), [IGVFFI8947ZUFP](/sequence-files/IGVFFI8947ZUFP/), [IGVFFI5915MMUW](/sequence-files/IGVFFI5915MMUW/), [IGVFFI7758ETRJ](/sequence-files/IGVFFI7758ETRJ/), [IGVFFI3057YAJX](/sequence-files/IGVFFI3057YAJX/), [IGVFFI2423DDFU](/sequence-files/IGVFFI2423DDFU/), [IGVFFI8499IBTC](/sequence-files/IGVFFI8499IBTC/), [IGVFFI7938FXXY](/sequence-files/IGVFFI7938FXXY/), [IGVFFI3801FKWF](/sequence-files/IGVFFI3801FKWF/), [IGVFFI7956APIC](/sequence-files/IGVFFI7956APIC/), [IGVFFI3329THNO](/sequence-files/IGVFFI3329THNO/), [IGVFFI0882BUNU](/sequence-files/IGVFFI0882BUNU/), [IGVFFI4597LSJS](/sequence-files/IGVFFI4597LSJS/), [IGVFFI4002DINJ](/sequence-files/IGVFFI4002DINJ/), [IGVFFI6611EJQM](/sequence-files/IGVFFI6611EJQM/), [IGVFFI1099JNSA](/sequence-files/IGVFFI1099JNSA/), [IGVFFI2699UXIS](/sequence-files/IGVFFI2699UXIS/), [IGVFFI7863YKKH](/sequence-files/IGVFFI7863YKKH/), [IGVFFI2513EOMV](/sequence-files/IGVFFI2513EOMV/), [IGVFFI0358RKKW](/sequence-files/IGVFFI0358RKKW/), [IGVFFI3165XTXL](/sequence-files/IGVFFI3165XTXL/), [IGVFFI6761VKGI](/sequence-files/IGVFFI6761VKGI/), [IGVFFI2028NGKW](/sequence-files/IGVFFI2028NGKW/), [IGVFFI4070PIWT](/sequence-files/IGVFFI4070PIWT/), [IGVFFI8065HMQG](/sequence-files/IGVFFI8065HMQG/), [IGVFFI4532AIST](/sequence-files/IGVFFI4532AIST/), [IGVFFI5296QFVL](/sequence-files/IGVFFI5296QFVL/), [IGVFFI9434GLYH](/sequence-files/IGVFFI9434GLYH/), [IGVFFI2528ZCJQ](/sequence-files/IGVFFI2528ZCJQ/), [IGVFFI6620EYSV](/sequence-files/IGVFFI6620EYSV/), [IGVFFI5328KDUX](/sequence-files/IGVFFI5328KDUX/), [IGVFFI7133CVYY](/sequence-files/IGVFFI7133CVYY/), [IGVFFI5644CUEB](/sequence-files/IGVFFI5644CUEB/), [IGVFFI1658VVEI](/sequence-files/IGVFFI1658VVEI/), [IGVFFI5313XWTJ](/sequence-files/IGVFFI5313XWTJ/) 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/IGVFDS7482HPXK/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM4123NEIH](/in-vitro-systems/IGVFSM4123NEIH/) has in progress subobject construct library set [IGVFDS2385DHZO](/construct-library-sets/IGVFDS2385DHZO/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM4123NEIH/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7482HPXK](/measurement-sets/IGVFDS7482HPXK/) 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/IGVFDS7482HPXK/"
}
]
},
"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": "IGVFDS4869FXYY",
"aliases": [
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],
"status": "released"
}
],
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"creation_timestamp": "2023-12-13T08:48:15.166437+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1080XFGV/",
"accession": "IGVFDO1080XFGV",
"aliases": [
"igvf:donor_of_Jurkat"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
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},
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"summary": "guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002796/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:Jurkat"
],
"status": "released",
"summary": "Jurkat",
"term_name": "Jurkat"
}
],
"status": "released",
"summary": "Jurkat cell line, male, Homo sapiens (sorting details: FACS bin for 26-50% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-13T10:24:36.845406+00:00",
"summary": "CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"targeted_genes": [
{
"@id": "/genes/ENSG00000108179/",
"geneid": "ENSG00000108179",
"name": "peptidylprolyl isomerase F",
"status": "released",
"symbol": "PPIF",
"synonyms": [
"rotamase F",
"CYP3",
"cyclophilin F",
"mitochondrial cyclophilin",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"CypD",
"Cyp-D",
"cyclophilin 3",
"cyclophilin D",
"CyP-M",
"peptidyl-prolyl cis-trans isomerase F, mitochondrial",
"PPIase F"
]
}
],
"uuid": "20e646b8-fe22-4940-9dcd-69241ee4e47f"
}