{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8140CVHC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8140CVHC",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-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 [IGVFDS8140CVHC](/measurement-sets/IGVFDS8140CVHC/) has sequence file(s) [IGVFFI6428ASMD](/sequence-files/IGVFFI6428ASMD/), [IGVFFI8157OULG](/sequence-files/IGVFFI8157OULG/), [IGVFFI6809JRGD](/sequence-files/IGVFFI6809JRGD/), [IGVFFI9362HYLG](/sequence-files/IGVFFI9362HYLG/), [IGVFFI7313JVVE](/sequence-files/IGVFFI7313JVVE/), [IGVFFI9016VPZQ](/sequence-files/IGVFFI9016VPZQ/), [IGVFFI5540IZAL](/sequence-files/IGVFFI5540IZAL/), [IGVFFI5821PYWA](/sequence-files/IGVFFI5821PYWA/), [IGVFFI5613KGYN](/sequence-files/IGVFFI5613KGYN/), [IGVFFI6458IOHE](/sequence-files/IGVFFI6458IOHE/), [IGVFFI0227XYOF](/sequence-files/IGVFFI0227XYOF/), [IGVFFI8353YRSQ](/sequence-files/IGVFFI8353YRSQ/), [IGVFFI0260WMST](/sequence-files/IGVFFI0260WMST/), [IGVFFI0990LGVI](/sequence-files/IGVFFI0990LGVI/), [IGVFFI4020BZOP](/sequence-files/IGVFFI4020BZOP/), [IGVFFI6407EHEO](/sequence-files/IGVFFI6407EHEO/), [IGVFFI6002MOYI](/sequence-files/IGVFFI6002MOYI/), [IGVFFI9068IBQZ](/sequence-files/IGVFFI9068IBQZ/), [IGVFFI8694OBZP](/sequence-files/IGVFFI8694OBZP/), [IGVFFI7015MDGE](/sequence-files/IGVFFI7015MDGE/), [IGVFFI4590NONZ](/sequence-files/IGVFFI4590NONZ/), [IGVFFI3300DKXY](/sequence-files/IGVFFI3300DKXY/), [IGVFFI1071MHIA](/sequence-files/IGVFFI1071MHIA/), [IGVFFI2192CMAY](/sequence-files/IGVFFI2192CMAY/), [IGVFFI9691XGXE](/sequence-files/IGVFFI9691XGXE/), [IGVFFI1382MLGP](/sequence-files/IGVFFI1382MLGP/), [IGVFFI3336EEZE](/sequence-files/IGVFFI3336EEZE/), [IGVFFI4306IFAM](/sequence-files/IGVFFI4306IFAM/), [IGVFFI5828XVUW](/sequence-files/IGVFFI5828XVUW/), [IGVFFI2834HNMV](/sequence-files/IGVFFI2834HNMV/), [IGVFFI3277PJPD](/sequence-files/IGVFFI3277PJPD/), [IGVFFI5652HUDO](/sequence-files/IGVFFI5652HUDO/), [IGVFFI9859VMOM](/sequence-files/IGVFFI9859VMOM/), [IGVFFI4737TJFJ](/sequence-files/IGVFFI4737TJFJ/), [IGVFFI7338UFMM](/sequence-files/IGVFFI7338UFMM/), [IGVFFI1818WLHH](/sequence-files/IGVFFI1818WLHH/), [IGVFFI5823HKTU](/sequence-files/IGVFFI5823HKTU/), [IGVFFI4148HHRK](/sequence-files/IGVFFI4148HHRK/), [IGVFFI4038NFBR](/sequence-files/IGVFFI4038NFBR/), [IGVFFI9591KMKC](/sequence-files/IGVFFI9591KMKC/), [IGVFFI7600XPBY](/sequence-files/IGVFFI7600XPBY/), [IGVFFI2027RAHP](/sequence-files/IGVFFI2027RAHP/), [IGVFFI6009TZZD](/sequence-files/IGVFFI6009TZZD/), [IGVFFI1108QODX](/sequence-files/IGVFFI1108QODX/), [IGVFFI1807TBXX](/sequence-files/IGVFFI1807TBXX/), [IGVFFI0843MQMI](/sequence-files/IGVFFI0843MQMI/), [IGVFFI1363RKHE](/sequence-files/IGVFFI1363RKHE/), [IGVFFI7103IFTR](/sequence-files/IGVFFI7103IFTR/) 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/IGVFDS8140CVHC/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8140CVHC](/measurement-sets/IGVFDS8140CVHC/) has sequence file(s): [IGVFFI6428ASMD](/sequence-files/IGVFFI6428ASMD/), [IGVFFI8157OULG](/sequence-files/IGVFFI8157OULG/), [IGVFFI6809JRGD](/sequence-files/IGVFFI6809JRGD/), [IGVFFI9362HYLG](/sequence-files/IGVFFI9362HYLG/), [IGVFFI7313JVVE](/sequence-files/IGVFFI7313JVVE/), [IGVFFI9016VPZQ](/sequence-files/IGVFFI9016VPZQ/), [IGVFFI5540IZAL](/sequence-files/IGVFFI5540IZAL/), [IGVFFI5821PYWA](/sequence-files/IGVFFI5821PYWA/), [IGVFFI5613KGYN](/sequence-files/IGVFFI5613KGYN/), [IGVFFI6458IOHE](/sequence-files/IGVFFI6458IOHE/), [IGVFFI0227XYOF](/sequence-files/IGVFFI0227XYOF/), [IGVFFI8353YRSQ](/sequence-files/IGVFFI8353YRSQ/), [IGVFFI0260WMST](/sequence-files/IGVFFI0260WMST/), [IGVFFI0990LGVI](/sequence-files/IGVFFI0990LGVI/), [IGVFFI4020BZOP](/sequence-files/IGVFFI4020BZOP/), [IGVFFI6407EHEO](/sequence-files/IGVFFI6407EHEO/), [IGVFFI6002MOYI](/sequence-files/IGVFFI6002MOYI/), [IGVFFI9068IBQZ](/sequence-files/IGVFFI9068IBQZ/), [IGVFFI8694OBZP](/sequence-files/IGVFFI8694OBZP/), [IGVFFI7015MDGE](/sequence-files/IGVFFI7015MDGE/), [IGVFFI4590NONZ](/sequence-files/IGVFFI4590NONZ/), [IGVFFI3300DKXY](/sequence-files/IGVFFI3300DKXY/), [IGVFFI1071MHIA](/sequence-files/IGVFFI1071MHIA/), [IGVFFI2192CMAY](/sequence-files/IGVFFI2192CMAY/), [IGVFFI9691XGXE](/sequence-files/IGVFFI9691XGXE/), [IGVFFI1382MLGP](/sequence-files/IGVFFI1382MLGP/), [IGVFFI3336EEZE](/sequence-files/IGVFFI3336EEZE/), [IGVFFI4306IFAM](/sequence-files/IGVFFI4306IFAM/), [IGVFFI5828XVUW](/sequence-files/IGVFFI5828XVUW/), [IGVFFI2834HNMV](/sequence-files/IGVFFI2834HNMV/), [IGVFFI3277PJPD](/sequence-files/IGVFFI3277PJPD/), [IGVFFI5652HUDO](/sequence-files/IGVFFI5652HUDO/), [IGVFFI9859VMOM](/sequence-files/IGVFFI9859VMOM/), [IGVFFI4737TJFJ](/sequence-files/IGVFFI4737TJFJ/), [IGVFFI7338UFMM](/sequence-files/IGVFFI7338UFMM/), [IGVFFI1818WLHH](/sequence-files/IGVFFI1818WLHH/), [IGVFFI5823HKTU](/sequence-files/IGVFFI5823HKTU/), [IGVFFI4148HHRK](/sequence-files/IGVFFI4148HHRK/), [IGVFFI4038NFBR](/sequence-files/IGVFFI4038NFBR/), [IGVFFI9591KMKC](/sequence-files/IGVFFI9591KMKC/), [IGVFFI7600XPBY](/sequence-files/IGVFFI7600XPBY/), [IGVFFI2027RAHP](/sequence-files/IGVFFI2027RAHP/), [IGVFFI6009TZZD](/sequence-files/IGVFFI6009TZZD/), [IGVFFI1108QODX](/sequence-files/IGVFFI1108QODX/), [IGVFFI1807TBXX](/sequence-files/IGVFFI1807TBXX/), [IGVFFI0843MQMI](/sequence-files/IGVFFI0843MQMI/), [IGVFFI1363RKHE](/sequence-files/IGVFFI1363RKHE/), [IGVFFI7103IFTR](/sequence-files/IGVFFI7103IFTR/) 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/IGVFDS8140CVHC/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS8140CVHC](/measurement-sets/IGVFDS8140CVHC/) 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/IGVFDS8140CVHC/"
}
]
},
"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_file_sets": [
{
"@id": "/measurement-sets/IGVFDS4103BJLT/",
"accession": "IGVFDS4103BJLT",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
],
"status": "preview"
}
],
"control_for": [],
"creation_timestamp": "2024-11-25T23:53:57.891939+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": "IGVFFI6428ASMD",
"aliases": [
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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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"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": "2024-11-26T07:26:20.075029+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": "6c7e99d3-3130-47c4-bac2-785e4183fbd1"
}