{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7922GOJN/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7922GOJN",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-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 [IGVFDS7922GOJN](/measurement-sets/IGVFDS7922GOJN/) has sequence file(s) [IGVFFI3884VKJY](/sequence-files/IGVFFI3884VKJY/), [IGVFFI6616URFB](/sequence-files/IGVFFI6616URFB/), [IGVFFI3675TRGV](/sequence-files/IGVFFI3675TRGV/), [IGVFFI5212QTJC](/sequence-files/IGVFFI5212QTJC/), [IGVFFI1081UWXC](/sequence-files/IGVFFI1081UWXC/), [IGVFFI2088IHPS](/sequence-files/IGVFFI2088IHPS/), [IGVFFI4662LPKS](/sequence-files/IGVFFI4662LPKS/), [IGVFFI2792SFIX](/sequence-files/IGVFFI2792SFIX/), [IGVFFI3388SHWD](/sequence-files/IGVFFI3388SHWD/), [IGVFFI7619LWUP](/sequence-files/IGVFFI7619LWUP/), [IGVFFI4828NUOF](/sequence-files/IGVFFI4828NUOF/), [IGVFFI2359VNIR](/sequence-files/IGVFFI2359VNIR/), [IGVFFI6993RQZR](/sequence-files/IGVFFI6993RQZR/), [IGVFFI7995ZGCY](/sequence-files/IGVFFI7995ZGCY/), [IGVFFI7266JUQJ](/sequence-files/IGVFFI7266JUQJ/), [IGVFFI6007CWKZ](/sequence-files/IGVFFI6007CWKZ/), [IGVFFI6833RYGN](/sequence-files/IGVFFI6833RYGN/), [IGVFFI8646RSLC](/sequence-files/IGVFFI8646RSLC/), [IGVFFI6421JFNJ](/sequence-files/IGVFFI6421JFNJ/), [IGVFFI1080UTNQ](/sequence-files/IGVFFI1080UTNQ/), [IGVFFI9631XMYK](/sequence-files/IGVFFI9631XMYK/), [IGVFFI3467RXLL](/sequence-files/IGVFFI3467RXLL/), [IGVFFI7582QSBM](/sequence-files/IGVFFI7582QSBM/), [IGVFFI6634VNZM](/sequence-files/IGVFFI6634VNZM/), [IGVFFI4848XCTI](/sequence-files/IGVFFI4848XCTI/), [IGVFFI3508RWIS](/sequence-files/IGVFFI3508RWIS/), [IGVFFI1727OCYX](/sequence-files/IGVFFI1727OCYX/), [IGVFFI3353ZUZQ](/sequence-files/IGVFFI3353ZUZQ/), [IGVFFI7177BMVS](/sequence-files/IGVFFI7177BMVS/), [IGVFFI2106YXXX](/sequence-files/IGVFFI2106YXXX/), [IGVFFI1121VRJL](/sequence-files/IGVFFI1121VRJL/), [IGVFFI1709KIOC](/sequence-files/IGVFFI1709KIOC/), [IGVFFI5133UGOQ](/sequence-files/IGVFFI5133UGOQ/), [IGVFFI0683GBMF](/sequence-files/IGVFFI0683GBMF/), [IGVFFI7260ASDS](/sequence-files/IGVFFI7260ASDS/), [IGVFFI6313EOQX](/sequence-files/IGVFFI6313EOQX/), [IGVFFI3111LPQN](/sequence-files/IGVFFI3111LPQN/), [IGVFFI9106HHMX](/sequence-files/IGVFFI9106HHMX/), [IGVFFI2370WLFM](/sequence-files/IGVFFI2370WLFM/), [IGVFFI3566JJHR](/sequence-files/IGVFFI3566JJHR/), [IGVFFI9977IIYW](/sequence-files/IGVFFI9977IIYW/), [IGVFFI1664RHGH](/sequence-files/IGVFFI1664RHGH/), [IGVFFI2943FJIL](/sequence-files/IGVFFI2943FJIL/), [IGVFFI9888SFVC](/sequence-files/IGVFFI9888SFVC/), [IGVFFI3159EFTG](/sequence-files/IGVFFI3159EFTG/), [IGVFFI2437EVQG](/sequence-files/IGVFFI2437EVQG/), [IGVFFI7434RLXW](/sequence-files/IGVFFI7434RLXW/), [IGVFFI2154OEKZ](/sequence-files/IGVFFI2154OEKZ/) 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/IGVFDS7922GOJN/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7922GOJN](/measurement-sets/IGVFDS7922GOJN/) has sequence file(s): [IGVFFI3884VKJY](/sequence-files/IGVFFI3884VKJY/), [IGVFFI6616URFB](/sequence-files/IGVFFI6616URFB/), [IGVFFI3675TRGV](/sequence-files/IGVFFI3675TRGV/), [IGVFFI5212QTJC](/sequence-files/IGVFFI5212QTJC/), [IGVFFI1081UWXC](/sequence-files/IGVFFI1081UWXC/), [IGVFFI2088IHPS](/sequence-files/IGVFFI2088IHPS/), [IGVFFI4662LPKS](/sequence-files/IGVFFI4662LPKS/), [IGVFFI2792SFIX](/sequence-files/IGVFFI2792SFIX/), [IGVFFI3388SHWD](/sequence-files/IGVFFI3388SHWD/), [IGVFFI7619LWUP](/sequence-files/IGVFFI7619LWUP/), [IGVFFI4828NUOF](/sequence-files/IGVFFI4828NUOF/), [IGVFFI2359VNIR](/sequence-files/IGVFFI2359VNIR/), [IGVFFI6993RQZR](/sequence-files/IGVFFI6993RQZR/), [IGVFFI7995ZGCY](/sequence-files/IGVFFI7995ZGCY/), [IGVFFI7266JUQJ](/sequence-files/IGVFFI7266JUQJ/), [IGVFFI6007CWKZ](/sequence-files/IGVFFI6007CWKZ/), [IGVFFI6833RYGN](/sequence-files/IGVFFI6833RYGN/), [IGVFFI8646RSLC](/sequence-files/IGVFFI8646RSLC/), [IGVFFI6421JFNJ](/sequence-files/IGVFFI6421JFNJ/), [IGVFFI1080UTNQ](/sequence-files/IGVFFI1080UTNQ/), [IGVFFI9631XMYK](/sequence-files/IGVFFI9631XMYK/), [IGVFFI3467RXLL](/sequence-files/IGVFFI3467RXLL/), [IGVFFI7582QSBM](/sequence-files/IGVFFI7582QSBM/), [IGVFFI6634VNZM](/sequence-files/IGVFFI6634VNZM/), [IGVFFI4848XCTI](/sequence-files/IGVFFI4848XCTI/), [IGVFFI3508RWIS](/sequence-files/IGVFFI3508RWIS/), [IGVFFI1727OCYX](/sequence-files/IGVFFI1727OCYX/), [IGVFFI3353ZUZQ](/sequence-files/IGVFFI3353ZUZQ/), [IGVFFI7177BMVS](/sequence-files/IGVFFI7177BMVS/), [IGVFFI2106YXXX](/sequence-files/IGVFFI2106YXXX/), [IGVFFI1121VRJL](/sequence-files/IGVFFI1121VRJL/), [IGVFFI1709KIOC](/sequence-files/IGVFFI1709KIOC/), [IGVFFI5133UGOQ](/sequence-files/IGVFFI5133UGOQ/), [IGVFFI0683GBMF](/sequence-files/IGVFFI0683GBMF/), [IGVFFI7260ASDS](/sequence-files/IGVFFI7260ASDS/), [IGVFFI6313EOQX](/sequence-files/IGVFFI6313EOQX/), [IGVFFI3111LPQN](/sequence-files/IGVFFI3111LPQN/), [IGVFFI9106HHMX](/sequence-files/IGVFFI9106HHMX/), [IGVFFI2370WLFM](/sequence-files/IGVFFI2370WLFM/), [IGVFFI3566JJHR](/sequence-files/IGVFFI3566JJHR/), [IGVFFI9977IIYW](/sequence-files/IGVFFI9977IIYW/), [IGVFFI1664RHGH](/sequence-files/IGVFFI1664RHGH/), [IGVFFI2943FJIL](/sequence-files/IGVFFI2943FJIL/), [IGVFFI9888SFVC](/sequence-files/IGVFFI9888SFVC/), [IGVFFI3159EFTG](/sequence-files/IGVFFI3159EFTG/), [IGVFFI2437EVQG](/sequence-files/IGVFFI2437EVQG/), [IGVFFI7434RLXW](/sequence-files/IGVFFI7434RLXW/), [IGVFFI2154OEKZ](/sequence-files/IGVFFI2154OEKZ/) 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/IGVFDS7922GOJN/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7922GOJN](/measurement-sets/IGVFDS7922GOJN/) 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/IGVFDS7922GOJN/"
}
]
},
"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": "IGVFDS4103BJLT",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
],
"status": "preview"
}
],
"control_for": [],
"creation_timestamp": "2024-11-25T23:53:23.919072+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"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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"accession": "IGVFDS4955GEYO",
"file_set_type": "guide library",
"status": "preview",
"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_0001253/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "released",
"summary": "THP-1",
"term_name": "THP-1"
}
],
"status": "preview",
"summary": "THP-1 cell line, male, Homo sapiens (sorting details: FACS bin for 0-25% 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": "preview",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2024-11-26T07:10:53.291332+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": "847fe7a1-f3bb-48e8-b390-b36cc71d7b0a"
}