{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5968XLTS/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5968XLTS",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep1-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 [IGVFDS5968XLTS](/measurement-sets/IGVFDS5968XLTS/) has sequence file(s) [IGVFFI3606PQOG](/sequence-files/IGVFFI3606PQOG/), [IGVFFI8691OSKK](/sequence-files/IGVFFI8691OSKK/), [IGVFFI7216LEUX](/sequence-files/IGVFFI7216LEUX/), [IGVFFI9142FUJS](/sequence-files/IGVFFI9142FUJS/), [IGVFFI9391RJYG](/sequence-files/IGVFFI9391RJYG/), [IGVFFI1551CAFY](/sequence-files/IGVFFI1551CAFY/), [IGVFFI9379BCCN](/sequence-files/IGVFFI9379BCCN/), [IGVFFI2502NDGQ](/sequence-files/IGVFFI2502NDGQ/), [IGVFFI7005YBFR](/sequence-files/IGVFFI7005YBFR/), [IGVFFI4592VFMQ](/sequence-files/IGVFFI4592VFMQ/), [IGVFFI3608ZSPA](/sequence-files/IGVFFI3608ZSPA/), [IGVFFI2281QVOV](/sequence-files/IGVFFI2281QVOV/), [IGVFFI3740LHSG](/sequence-files/IGVFFI3740LHSG/), [IGVFFI8485ZSUJ](/sequence-files/IGVFFI8485ZSUJ/), [IGVFFI0214CIMV](/sequence-files/IGVFFI0214CIMV/), [IGVFFI1630BVRW](/sequence-files/IGVFFI1630BVRW/), [IGVFFI0784OUCV](/sequence-files/IGVFFI0784OUCV/), [IGVFFI9217GRFO](/sequence-files/IGVFFI9217GRFO/), [IGVFFI1976TDEI](/sequence-files/IGVFFI1976TDEI/), [IGVFFI9864GLIW](/sequence-files/IGVFFI9864GLIW/), [IGVFFI5780NWBP](/sequence-files/IGVFFI5780NWBP/), [IGVFFI4395LOMM](/sequence-files/IGVFFI4395LOMM/), [IGVFFI1419VMPA](/sequence-files/IGVFFI1419VMPA/), [IGVFFI3870QYDM](/sequence-files/IGVFFI3870QYDM/), [IGVFFI6977WRGC](/sequence-files/IGVFFI6977WRGC/), [IGVFFI8890TDOH](/sequence-files/IGVFFI8890TDOH/), [IGVFFI0739HZTB](/sequence-files/IGVFFI0739HZTB/), [IGVFFI0890VMPK](/sequence-files/IGVFFI0890VMPK/), [IGVFFI3309QIBU](/sequence-files/IGVFFI3309QIBU/), [IGVFFI3105DFFF](/sequence-files/IGVFFI3105DFFF/), [IGVFFI8779NFOH](/sequence-files/IGVFFI8779NFOH/), [IGVFFI6277EFQI](/sequence-files/IGVFFI6277EFQI/), [IGVFFI9714IOFQ](/sequence-files/IGVFFI9714IOFQ/), [IGVFFI1329ISEO](/sequence-files/IGVFFI1329ISEO/), [IGVFFI5109XPFP](/sequence-files/IGVFFI5109XPFP/), [IGVFFI0648MNVO](/sequence-files/IGVFFI0648MNVO/), [IGVFFI8526XLDG](/sequence-files/IGVFFI8526XLDG/), [IGVFFI1509RKGA](/sequence-files/IGVFFI1509RKGA/), [IGVFFI1991WHBJ](/sequence-files/IGVFFI1991WHBJ/), [IGVFFI3570QTQM](/sequence-files/IGVFFI3570QTQM/), [IGVFFI6643UJDK](/sequence-files/IGVFFI6643UJDK/), [IGVFFI0091GSBQ](/sequence-files/IGVFFI0091GSBQ/), [IGVFFI2151LYSM](/sequence-files/IGVFFI2151LYSM/), [IGVFFI3626SWUI](/sequence-files/IGVFFI3626SWUI/), [IGVFFI7157VPZK](/sequence-files/IGVFFI7157VPZK/), [IGVFFI3809PXKH](/sequence-files/IGVFFI3809PXKH/), [IGVFFI0179GRAT](/sequence-files/IGVFFI0179GRAT/), [IGVFFI5457MPPV](/sequence-files/IGVFFI5457MPPV/) 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/IGVFDS5968XLTS/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5968XLTS](/measurement-sets/IGVFDS5968XLTS/) has sequence file(s): [IGVFFI3606PQOG](/sequence-files/IGVFFI3606PQOG/), [IGVFFI8691OSKK](/sequence-files/IGVFFI8691OSKK/), [IGVFFI7216LEUX](/sequence-files/IGVFFI7216LEUX/), [IGVFFI9142FUJS](/sequence-files/IGVFFI9142FUJS/), [IGVFFI9391RJYG](/sequence-files/IGVFFI9391RJYG/), [IGVFFI1551CAFY](/sequence-files/IGVFFI1551CAFY/), [IGVFFI9379BCCN](/sequence-files/IGVFFI9379BCCN/), [IGVFFI2502NDGQ](/sequence-files/IGVFFI2502NDGQ/), [IGVFFI7005YBFR](/sequence-files/IGVFFI7005YBFR/), [IGVFFI4592VFMQ](/sequence-files/IGVFFI4592VFMQ/), [IGVFFI3608ZSPA](/sequence-files/IGVFFI3608ZSPA/), [IGVFFI2281QVOV](/sequence-files/IGVFFI2281QVOV/), [IGVFFI3740LHSG](/sequence-files/IGVFFI3740LHSG/), [IGVFFI8485ZSUJ](/sequence-files/IGVFFI8485ZSUJ/), [IGVFFI0214CIMV](/sequence-files/IGVFFI0214CIMV/), [IGVFFI1630BVRW](/sequence-files/IGVFFI1630BVRW/), [IGVFFI0784OUCV](/sequence-files/IGVFFI0784OUCV/), [IGVFFI9217GRFO](/sequence-files/IGVFFI9217GRFO/), [IGVFFI1976TDEI](/sequence-files/IGVFFI1976TDEI/), [IGVFFI9864GLIW](/sequence-files/IGVFFI9864GLIW/), [IGVFFI5780NWBP](/sequence-files/IGVFFI5780NWBP/), [IGVFFI4395LOMM](/sequence-files/IGVFFI4395LOMM/), [IGVFFI1419VMPA](/sequence-files/IGVFFI1419VMPA/), [IGVFFI3870QYDM](/sequence-files/IGVFFI3870QYDM/), [IGVFFI6977WRGC](/sequence-files/IGVFFI6977WRGC/), [IGVFFI8890TDOH](/sequence-files/IGVFFI8890TDOH/), [IGVFFI0739HZTB](/sequence-files/IGVFFI0739HZTB/), [IGVFFI0890VMPK](/sequence-files/IGVFFI0890VMPK/), [IGVFFI3309QIBU](/sequence-files/IGVFFI3309QIBU/), [IGVFFI3105DFFF](/sequence-files/IGVFFI3105DFFF/), [IGVFFI8779NFOH](/sequence-files/IGVFFI8779NFOH/), [IGVFFI6277EFQI](/sequence-files/IGVFFI6277EFQI/), [IGVFFI9714IOFQ](/sequence-files/IGVFFI9714IOFQ/), [IGVFFI1329ISEO](/sequence-files/IGVFFI1329ISEO/), [IGVFFI5109XPFP](/sequence-files/IGVFFI5109XPFP/), [IGVFFI0648MNVO](/sequence-files/IGVFFI0648MNVO/), [IGVFFI8526XLDG](/sequence-files/IGVFFI8526XLDG/), [IGVFFI1509RKGA](/sequence-files/IGVFFI1509RKGA/), [IGVFFI1991WHBJ](/sequence-files/IGVFFI1991WHBJ/), [IGVFFI3570QTQM](/sequence-files/IGVFFI3570QTQM/), [IGVFFI6643UJDK](/sequence-files/IGVFFI6643UJDK/), [IGVFFI0091GSBQ](/sequence-files/IGVFFI0091GSBQ/), [IGVFFI2151LYSM](/sequence-files/IGVFFI2151LYSM/), [IGVFFI3626SWUI](/sequence-files/IGVFFI3626SWUI/), [IGVFFI7157VPZK](/sequence-files/IGVFFI7157VPZK/), [IGVFFI3809PXKH](/sequence-files/IGVFFI3809PXKH/), [IGVFFI0179GRAT](/sequence-files/IGVFFI0179GRAT/), [IGVFFI5457MPPV](/sequence-files/IGVFFI5457MPPV/) 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/IGVFDS5968XLTS/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5968XLTS](/measurement-sets/IGVFDS5968XLTS/) 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/IGVFDS5968XLTS/"
}
]
},
"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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{
"@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": "2024-11-25T23:53:27.602755+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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},
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},
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},
{
"@id": "/sequence-files/IGVFFI3608ZSPA/",
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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 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": "preview",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2024-11-26T07:11:12.186640+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": "e21237d0-88bb-45ce-b034-5a65eed83f32"
}