{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2992ZYJE/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2992ZYJE",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-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 [IGVFDS2992ZYJE](/measurement-sets/IGVFDS2992ZYJE/) has sequence file(s) [IGVFFI5158WENW](/sequence-files/IGVFFI5158WENW/), [IGVFFI6091XEVG](/sequence-files/IGVFFI6091XEVG/), [IGVFFI6312XFTX](/sequence-files/IGVFFI6312XFTX/), [IGVFFI7684VJOE](/sequence-files/IGVFFI7684VJOE/), [IGVFFI5882HZGD](/sequence-files/IGVFFI5882HZGD/), [IGVFFI5748UDPG](/sequence-files/IGVFFI5748UDPG/), [IGVFFI5718IKFV](/sequence-files/IGVFFI5718IKFV/), [IGVFFI7007RKYR](/sequence-files/IGVFFI7007RKYR/), [IGVFFI0962TPFL](/sequence-files/IGVFFI0962TPFL/), [IGVFFI2155OGKD](/sequence-files/IGVFFI2155OGKD/), [IGVFFI4540ACGI](/sequence-files/IGVFFI4540ACGI/), [IGVFFI5804NHKR](/sequence-files/IGVFFI5804NHKR/), [IGVFFI7643SVBR](/sequence-files/IGVFFI7643SVBR/), [IGVFFI1716BJMA](/sequence-files/IGVFFI1716BJMA/), [IGVFFI9344CJZO](/sequence-files/IGVFFI9344CJZO/), [IGVFFI0143SIGA](/sequence-files/IGVFFI0143SIGA/), [IGVFFI2747TDHZ](/sequence-files/IGVFFI2747TDHZ/), [IGVFFI3675PVPY](/sequence-files/IGVFFI3675PVPY/), [IGVFFI5858XJSJ](/sequence-files/IGVFFI5858XJSJ/), [IGVFFI8111ZSUM](/sequence-files/IGVFFI8111ZSUM/), [IGVFFI2671SGZS](/sequence-files/IGVFFI2671SGZS/), [IGVFFI5800IRJK](/sequence-files/IGVFFI5800IRJK/), [IGVFFI4076DKOG](/sequence-files/IGVFFI4076DKOG/), [IGVFFI3665HZWQ](/sequence-files/IGVFFI3665HZWQ/), [IGVFFI1727JGUG](/sequence-files/IGVFFI1727JGUG/), [IGVFFI2860SPFC](/sequence-files/IGVFFI2860SPFC/), [IGVFFI9746AWSX](/sequence-files/IGVFFI9746AWSX/), [IGVFFI9958LTCL](/sequence-files/IGVFFI9958LTCL/), [IGVFFI6356WTUR](/sequence-files/IGVFFI6356WTUR/), [IGVFFI9822JHMY](/sequence-files/IGVFFI9822JHMY/), [IGVFFI1386CKHM](/sequence-files/IGVFFI1386CKHM/), [IGVFFI7488ORWF](/sequence-files/IGVFFI7488ORWF/), [IGVFFI9946OHNJ](/sequence-files/IGVFFI9946OHNJ/), [IGVFFI2073RXYM](/sequence-files/IGVFFI2073RXYM/), [IGVFFI9550HSUI](/sequence-files/IGVFFI9550HSUI/), [IGVFFI1269WYEF](/sequence-files/IGVFFI1269WYEF/), [IGVFFI5961MGOJ](/sequence-files/IGVFFI5961MGOJ/), [IGVFFI9391QDHD](/sequence-files/IGVFFI9391QDHD/), [IGVFFI6294ZNIN](/sequence-files/IGVFFI6294ZNIN/), [IGVFFI6256JNXO](/sequence-files/IGVFFI6256JNXO/), [IGVFFI2143RDEJ](/sequence-files/IGVFFI2143RDEJ/), [IGVFFI5081HCQN](/sequence-files/IGVFFI5081HCQN/), [IGVFFI6873FIHK](/sequence-files/IGVFFI6873FIHK/), [IGVFFI3545IFGL](/sequence-files/IGVFFI3545IFGL/), [IGVFFI5399GQNC](/sequence-files/IGVFFI5399GQNC/), [IGVFFI5157KASC](/sequence-files/IGVFFI5157KASC/), [IGVFFI6627YPTH](/sequence-files/IGVFFI6627YPTH/), [IGVFFI4048ZSOP](/sequence-files/IGVFFI4048ZSOP/) 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/IGVFDS2992ZYJE/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2992ZYJE](/measurement-sets/IGVFDS2992ZYJE/) has sequence file(s): [IGVFFI5158WENW](/sequence-files/IGVFFI5158WENW/), [IGVFFI6091XEVG](/sequence-files/IGVFFI6091XEVG/), [IGVFFI6312XFTX](/sequence-files/IGVFFI6312XFTX/), [IGVFFI7684VJOE](/sequence-files/IGVFFI7684VJOE/), [IGVFFI5882HZGD](/sequence-files/IGVFFI5882HZGD/), [IGVFFI5748UDPG](/sequence-files/IGVFFI5748UDPG/), [IGVFFI5718IKFV](/sequence-files/IGVFFI5718IKFV/), [IGVFFI7007RKYR](/sequence-files/IGVFFI7007RKYR/), [IGVFFI0962TPFL](/sequence-files/IGVFFI0962TPFL/), [IGVFFI2155OGKD](/sequence-files/IGVFFI2155OGKD/), [IGVFFI4540ACGI](/sequence-files/IGVFFI4540ACGI/), [IGVFFI5804NHKR](/sequence-files/IGVFFI5804NHKR/), [IGVFFI7643SVBR](/sequence-files/IGVFFI7643SVBR/), [IGVFFI1716BJMA](/sequence-files/IGVFFI1716BJMA/), [IGVFFI9344CJZO](/sequence-files/IGVFFI9344CJZO/), [IGVFFI0143SIGA](/sequence-files/IGVFFI0143SIGA/), [IGVFFI2747TDHZ](/sequence-files/IGVFFI2747TDHZ/), [IGVFFI3675PVPY](/sequence-files/IGVFFI3675PVPY/), [IGVFFI5858XJSJ](/sequence-files/IGVFFI5858XJSJ/), [IGVFFI8111ZSUM](/sequence-files/IGVFFI8111ZSUM/), [IGVFFI2671SGZS](/sequence-files/IGVFFI2671SGZS/), [IGVFFI5800IRJK](/sequence-files/IGVFFI5800IRJK/), [IGVFFI4076DKOG](/sequence-files/IGVFFI4076DKOG/), [IGVFFI3665HZWQ](/sequence-files/IGVFFI3665HZWQ/), [IGVFFI1727JGUG](/sequence-files/IGVFFI1727JGUG/), [IGVFFI2860SPFC](/sequence-files/IGVFFI2860SPFC/), [IGVFFI9746AWSX](/sequence-files/IGVFFI9746AWSX/), [IGVFFI9958LTCL](/sequence-files/IGVFFI9958LTCL/), [IGVFFI6356WTUR](/sequence-files/IGVFFI6356WTUR/), [IGVFFI9822JHMY](/sequence-files/IGVFFI9822JHMY/), [IGVFFI1386CKHM](/sequence-files/IGVFFI1386CKHM/), [IGVFFI7488ORWF](/sequence-files/IGVFFI7488ORWF/), [IGVFFI9946OHNJ](/sequence-files/IGVFFI9946OHNJ/), [IGVFFI2073RXYM](/sequence-files/IGVFFI2073RXYM/), [IGVFFI9550HSUI](/sequence-files/IGVFFI9550HSUI/), [IGVFFI1269WYEF](/sequence-files/IGVFFI1269WYEF/), [IGVFFI5961MGOJ](/sequence-files/IGVFFI5961MGOJ/), [IGVFFI9391QDHD](/sequence-files/IGVFFI9391QDHD/), [IGVFFI6294ZNIN](/sequence-files/IGVFFI6294ZNIN/), [IGVFFI6256JNXO](/sequence-files/IGVFFI6256JNXO/), [IGVFFI2143RDEJ](/sequence-files/IGVFFI2143RDEJ/), [IGVFFI5081HCQN](/sequence-files/IGVFFI5081HCQN/), [IGVFFI6873FIHK](/sequence-files/IGVFFI6873FIHK/), [IGVFFI3545IFGL](/sequence-files/IGVFFI3545IFGL/), [IGVFFI5399GQNC](/sequence-files/IGVFFI5399GQNC/), [IGVFFI5157KASC](/sequence-files/IGVFFI5157KASC/), [IGVFFI6627YPTH](/sequence-files/IGVFFI6627YPTH/), [IGVFFI4048ZSOP](/sequence-files/IGVFFI4048ZSOP/) 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/IGVFDS2992ZYJE/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2992ZYJE](/measurement-sets/IGVFDS2992ZYJE/) 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/IGVFDS2992ZYJE/"
}
]
},
"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": "2024-11-25T23:54:21.615834+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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"accession": "IGVFFI5158WENW",
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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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"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 76-100% 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": "2024-11-26T07:41:52.081499+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": "ada81a01-804f-40ad-8de7-bd7285fc16ab"
}