{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5030BFVD/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5030BFVD",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-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 [IGVFDS5030BFVD](/measurement-sets/IGVFDS5030BFVD/) has sequence file(s) [IGVFFI9290WKPF](/sequence-files/IGVFFI9290WKPF/), [IGVFFI5555YFSA](/sequence-files/IGVFFI5555YFSA/), [IGVFFI7470XGQR](/sequence-files/IGVFFI7470XGQR/), [IGVFFI8016OQXD](/sequence-files/IGVFFI8016OQXD/), [IGVFFI6656RRTV](/sequence-files/IGVFFI6656RRTV/), [IGVFFI6334JMKD](/sequence-files/IGVFFI6334JMKD/), [IGVFFI4557FVUP](/sequence-files/IGVFFI4557FVUP/), [IGVFFI3577AOVS](/sequence-files/IGVFFI3577AOVS/), [IGVFFI1941CISV](/sequence-files/IGVFFI1941CISV/), [IGVFFI1100OAWK](/sequence-files/IGVFFI1100OAWK/), [IGVFFI2121WHPB](/sequence-files/IGVFFI2121WHPB/), [IGVFFI7886NUJW](/sequence-files/IGVFFI7886NUJW/), [IGVFFI2418OOXC](/sequence-files/IGVFFI2418OOXC/), [IGVFFI6313GOKF](/sequence-files/IGVFFI6313GOKF/), [IGVFFI5231YNBK](/sequence-files/IGVFFI5231YNBK/), [IGVFFI5853CTQO](/sequence-files/IGVFFI5853CTQO/), [IGVFFI0348TBPT](/sequence-files/IGVFFI0348TBPT/), [IGVFFI4768VZDM](/sequence-files/IGVFFI4768VZDM/), [IGVFFI6943GJJU](/sequence-files/IGVFFI6943GJJU/), [IGVFFI6075XHOQ](/sequence-files/IGVFFI6075XHOQ/), [IGVFFI1215VFEK](/sequence-files/IGVFFI1215VFEK/), [IGVFFI9207WCMM](/sequence-files/IGVFFI9207WCMM/), [IGVFFI6487XTKL](/sequence-files/IGVFFI6487XTKL/), [IGVFFI3107PTQG](/sequence-files/IGVFFI3107PTQG/), [IGVFFI7795YIVM](/sequence-files/IGVFFI7795YIVM/), [IGVFFI1242YYXC](/sequence-files/IGVFFI1242YYXC/), [IGVFFI3891FEWF](/sequence-files/IGVFFI3891FEWF/), [IGVFFI1275XZCE](/sequence-files/IGVFFI1275XZCE/), [IGVFFI6446LVFA](/sequence-files/IGVFFI6446LVFA/), [IGVFFI9021FYDO](/sequence-files/IGVFFI9021FYDO/), [IGVFFI3758GZVO](/sequence-files/IGVFFI3758GZVO/), [IGVFFI4142UUWV](/sequence-files/IGVFFI4142UUWV/), [IGVFFI8830OFKG](/sequence-files/IGVFFI8830OFKG/), [IGVFFI7653ORSL](/sequence-files/IGVFFI7653ORSL/), [IGVFFI8974XRNU](/sequence-files/IGVFFI8974XRNU/), [IGVFFI1954UBWL](/sequence-files/IGVFFI1954UBWL/), [IGVFFI0214EYUU](/sequence-files/IGVFFI0214EYUU/), [IGVFFI1210KRMB](/sequence-files/IGVFFI1210KRMB/), [IGVFFI6374WPSN](/sequence-files/IGVFFI6374WPSN/), [IGVFFI2446EKSA](/sequence-files/IGVFFI2446EKSA/), [IGVFFI8389RLWN](/sequence-files/IGVFFI8389RLWN/), [IGVFFI4211WSIN](/sequence-files/IGVFFI4211WSIN/), [IGVFFI4720ILLC](/sequence-files/IGVFFI4720ILLC/), [IGVFFI1491EMCM](/sequence-files/IGVFFI1491EMCM/), [IGVFFI2809DCKZ](/sequence-files/IGVFFI2809DCKZ/), [IGVFFI6037YNJB](/sequence-files/IGVFFI6037YNJB/), [IGVFFI7851TPKE](/sequence-files/IGVFFI7851TPKE/), [IGVFFI9494ITNK](/sequence-files/IGVFFI9494ITNK/) 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/IGVFDS5030BFVD/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5030BFVD](/measurement-sets/IGVFDS5030BFVD/) has sequence file(s): [IGVFFI9290WKPF](/sequence-files/IGVFFI9290WKPF/), [IGVFFI5555YFSA](/sequence-files/IGVFFI5555YFSA/), [IGVFFI7470XGQR](/sequence-files/IGVFFI7470XGQR/), [IGVFFI8016OQXD](/sequence-files/IGVFFI8016OQXD/), [IGVFFI6656RRTV](/sequence-files/IGVFFI6656RRTV/), [IGVFFI6334JMKD](/sequence-files/IGVFFI6334JMKD/), [IGVFFI4557FVUP](/sequence-files/IGVFFI4557FVUP/), [IGVFFI3577AOVS](/sequence-files/IGVFFI3577AOVS/), [IGVFFI1941CISV](/sequence-files/IGVFFI1941CISV/), [IGVFFI1100OAWK](/sequence-files/IGVFFI1100OAWK/), [IGVFFI2121WHPB](/sequence-files/IGVFFI2121WHPB/), [IGVFFI7886NUJW](/sequence-files/IGVFFI7886NUJW/), [IGVFFI2418OOXC](/sequence-files/IGVFFI2418OOXC/), [IGVFFI6313GOKF](/sequence-files/IGVFFI6313GOKF/), [IGVFFI5231YNBK](/sequence-files/IGVFFI5231YNBK/), [IGVFFI5853CTQO](/sequence-files/IGVFFI5853CTQO/), [IGVFFI0348TBPT](/sequence-files/IGVFFI0348TBPT/), [IGVFFI4768VZDM](/sequence-files/IGVFFI4768VZDM/), [IGVFFI6943GJJU](/sequence-files/IGVFFI6943GJJU/), [IGVFFI6075XHOQ](/sequence-files/IGVFFI6075XHOQ/), [IGVFFI1215VFEK](/sequence-files/IGVFFI1215VFEK/), [IGVFFI9207WCMM](/sequence-files/IGVFFI9207WCMM/), [IGVFFI6487XTKL](/sequence-files/IGVFFI6487XTKL/), [IGVFFI3107PTQG](/sequence-files/IGVFFI3107PTQG/), [IGVFFI7795YIVM](/sequence-files/IGVFFI7795YIVM/), [IGVFFI1242YYXC](/sequence-files/IGVFFI1242YYXC/), [IGVFFI3891FEWF](/sequence-files/IGVFFI3891FEWF/), [IGVFFI1275XZCE](/sequence-files/IGVFFI1275XZCE/), [IGVFFI6446LVFA](/sequence-files/IGVFFI6446LVFA/), [IGVFFI9021FYDO](/sequence-files/IGVFFI9021FYDO/), [IGVFFI3758GZVO](/sequence-files/IGVFFI3758GZVO/), [IGVFFI4142UUWV](/sequence-files/IGVFFI4142UUWV/), [IGVFFI8830OFKG](/sequence-files/IGVFFI8830OFKG/), [IGVFFI7653ORSL](/sequence-files/IGVFFI7653ORSL/), [IGVFFI8974XRNU](/sequence-files/IGVFFI8974XRNU/), [IGVFFI1954UBWL](/sequence-files/IGVFFI1954UBWL/), [IGVFFI0214EYUU](/sequence-files/IGVFFI0214EYUU/), [IGVFFI1210KRMB](/sequence-files/IGVFFI1210KRMB/), [IGVFFI6374WPSN](/sequence-files/IGVFFI6374WPSN/), [IGVFFI2446EKSA](/sequence-files/IGVFFI2446EKSA/), [IGVFFI8389RLWN](/sequence-files/IGVFFI8389RLWN/), [IGVFFI4211WSIN](/sequence-files/IGVFFI4211WSIN/), [IGVFFI4720ILLC](/sequence-files/IGVFFI4720ILLC/), [IGVFFI1491EMCM](/sequence-files/IGVFFI1491EMCM/), [IGVFFI2809DCKZ](/sequence-files/IGVFFI2809DCKZ/), [IGVFFI6037YNJB](/sequence-files/IGVFFI6037YNJB/), [IGVFFI7851TPKE](/sequence-files/IGVFFI7851TPKE/), [IGVFFI9494ITNK](/sequence-files/IGVFFI9494ITNK/) 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/IGVFDS5030BFVD/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5030BFVD](/measurement-sets/IGVFDS5030BFVD/) 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/IGVFDS5030BFVD/"
}
]
},
"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": "2024-11-25T23:53:16.043518+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": "IGVFFI9290WKPF",
"aliases": [
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},
{
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},
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},
{
"@id": "/sequence-files/IGVFFI2121WHPB/",
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],
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"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": "2024-11-26T06:56:02.318582+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": "55229b94-0eda-473c-b2be-c3a386cf55c0"
}