{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7802HNSL/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7802HNSL",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-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 [IGVFDS7802HNSL](/measurement-sets/IGVFDS7802HNSL/) has sequence file(s) [IGVFFI7299KWPR](/sequence-files/IGVFFI7299KWPR/), [IGVFFI6406JBAQ](/sequence-files/IGVFFI6406JBAQ/), [IGVFFI7586KPPH](/sequence-files/IGVFFI7586KPPH/), [IGVFFI5711RZFA](/sequence-files/IGVFFI5711RZFA/), [IGVFFI1971MRCX](/sequence-files/IGVFFI1971MRCX/), [IGVFFI0411FLCB](/sequence-files/IGVFFI0411FLCB/), [IGVFFI9888SLOH](/sequence-files/IGVFFI9888SLOH/), [IGVFFI5103QKRP](/sequence-files/IGVFFI5103QKRP/), [IGVFFI3758PEJM](/sequence-files/IGVFFI3758PEJM/), [IGVFFI1911LTEB](/sequence-files/IGVFFI1911LTEB/), [IGVFFI0013RDKW](/sequence-files/IGVFFI0013RDKW/), [IGVFFI7077EDPB](/sequence-files/IGVFFI7077EDPB/), [IGVFFI4456CKFH](/sequence-files/IGVFFI4456CKFH/), [IGVFFI0737MCMY](/sequence-files/IGVFFI0737MCMY/), [IGVFFI9881CHIH](/sequence-files/IGVFFI9881CHIH/), [IGVFFI9302YHRV](/sequence-files/IGVFFI9302YHRV/), [IGVFFI4626ZGKL](/sequence-files/IGVFFI4626ZGKL/), [IGVFFI7816KGGY](/sequence-files/IGVFFI7816KGGY/), [IGVFFI7567IUIR](/sequence-files/IGVFFI7567IUIR/), [IGVFFI7317GOFB](/sequence-files/IGVFFI7317GOFB/), [IGVFFI2988OZUW](/sequence-files/IGVFFI2988OZUW/), [IGVFFI7318GYMU](/sequence-files/IGVFFI7318GYMU/), [IGVFFI8533FBMG](/sequence-files/IGVFFI8533FBMG/), [IGVFFI4283AATM](/sequence-files/IGVFFI4283AATM/), [IGVFFI9506GQJB](/sequence-files/IGVFFI9506GQJB/), [IGVFFI5564WCSP](/sequence-files/IGVFFI5564WCSP/), [IGVFFI5166XYMD](/sequence-files/IGVFFI5166XYMD/), [IGVFFI8658IZYS](/sequence-files/IGVFFI8658IZYS/), [IGVFFI3456NAHU](/sequence-files/IGVFFI3456NAHU/), [IGVFFI1536JJLB](/sequence-files/IGVFFI1536JJLB/), [IGVFFI1714XTTB](/sequence-files/IGVFFI1714XTTB/), [IGVFFI1722BGRM](/sequence-files/IGVFFI1722BGRM/), [IGVFFI1770MFRD](/sequence-files/IGVFFI1770MFRD/), [IGVFFI1313IOYF](/sequence-files/IGVFFI1313IOYF/), [IGVFFI0414VEIS](/sequence-files/IGVFFI0414VEIS/), [IGVFFI7283EXSI](/sequence-files/IGVFFI7283EXSI/), [IGVFFI4480IJGV](/sequence-files/IGVFFI4480IJGV/), [IGVFFI2624XOEL](/sequence-files/IGVFFI2624XOEL/), [IGVFFI5972YVTM](/sequence-files/IGVFFI5972YVTM/), [IGVFFI8156XGKE](/sequence-files/IGVFFI8156XGKE/), [IGVFFI3385CEHF](/sequence-files/IGVFFI3385CEHF/), [IGVFFI4698SIPL](/sequence-files/IGVFFI4698SIPL/), [IGVFFI1181DAEX](/sequence-files/IGVFFI1181DAEX/), [IGVFFI8014GSGY](/sequence-files/IGVFFI8014GSGY/), [IGVFFI8544HANM](/sequence-files/IGVFFI8544HANM/), [IGVFFI4092JZVE](/sequence-files/IGVFFI4092JZVE/), [IGVFFI2136HHLB](/sequence-files/IGVFFI2136HHLB/), [IGVFFI8367QWEO](/sequence-files/IGVFFI8367QWEO/) 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/IGVFDS7802HNSL/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7802HNSL](/measurement-sets/IGVFDS7802HNSL/) has sequence file(s): [IGVFFI7299KWPR](/sequence-files/IGVFFI7299KWPR/), [IGVFFI6406JBAQ](/sequence-files/IGVFFI6406JBAQ/), [IGVFFI7586KPPH](/sequence-files/IGVFFI7586KPPH/), [IGVFFI5711RZFA](/sequence-files/IGVFFI5711RZFA/), [IGVFFI1971MRCX](/sequence-files/IGVFFI1971MRCX/), [IGVFFI0411FLCB](/sequence-files/IGVFFI0411FLCB/), [IGVFFI9888SLOH](/sequence-files/IGVFFI9888SLOH/), [IGVFFI5103QKRP](/sequence-files/IGVFFI5103QKRP/), [IGVFFI3758PEJM](/sequence-files/IGVFFI3758PEJM/), [IGVFFI1911LTEB](/sequence-files/IGVFFI1911LTEB/), [IGVFFI0013RDKW](/sequence-files/IGVFFI0013RDKW/), [IGVFFI7077EDPB](/sequence-files/IGVFFI7077EDPB/), [IGVFFI4456CKFH](/sequence-files/IGVFFI4456CKFH/), [IGVFFI0737MCMY](/sequence-files/IGVFFI0737MCMY/), [IGVFFI9881CHIH](/sequence-files/IGVFFI9881CHIH/), [IGVFFI9302YHRV](/sequence-files/IGVFFI9302YHRV/), [IGVFFI4626ZGKL](/sequence-files/IGVFFI4626ZGKL/), [IGVFFI7816KGGY](/sequence-files/IGVFFI7816KGGY/), [IGVFFI7567IUIR](/sequence-files/IGVFFI7567IUIR/), [IGVFFI7317GOFB](/sequence-files/IGVFFI7317GOFB/), [IGVFFI2988OZUW](/sequence-files/IGVFFI2988OZUW/), [IGVFFI7318GYMU](/sequence-files/IGVFFI7318GYMU/), [IGVFFI8533FBMG](/sequence-files/IGVFFI8533FBMG/), [IGVFFI4283AATM](/sequence-files/IGVFFI4283AATM/), [IGVFFI9506GQJB](/sequence-files/IGVFFI9506GQJB/), [IGVFFI5564WCSP](/sequence-files/IGVFFI5564WCSP/), [IGVFFI5166XYMD](/sequence-files/IGVFFI5166XYMD/), [IGVFFI8658IZYS](/sequence-files/IGVFFI8658IZYS/), [IGVFFI3456NAHU](/sequence-files/IGVFFI3456NAHU/), [IGVFFI1536JJLB](/sequence-files/IGVFFI1536JJLB/), [IGVFFI1714XTTB](/sequence-files/IGVFFI1714XTTB/), [IGVFFI1722BGRM](/sequence-files/IGVFFI1722BGRM/), [IGVFFI1770MFRD](/sequence-files/IGVFFI1770MFRD/), [IGVFFI1313IOYF](/sequence-files/IGVFFI1313IOYF/), [IGVFFI0414VEIS](/sequence-files/IGVFFI0414VEIS/), [IGVFFI7283EXSI](/sequence-files/IGVFFI7283EXSI/), [IGVFFI4480IJGV](/sequence-files/IGVFFI4480IJGV/), [IGVFFI2624XOEL](/sequence-files/IGVFFI2624XOEL/), [IGVFFI5972YVTM](/sequence-files/IGVFFI5972YVTM/), [IGVFFI8156XGKE](/sequence-files/IGVFFI8156XGKE/), [IGVFFI3385CEHF](/sequence-files/IGVFFI3385CEHF/), [IGVFFI4698SIPL](/sequence-files/IGVFFI4698SIPL/), [IGVFFI1181DAEX](/sequence-files/IGVFFI1181DAEX/), [IGVFFI8014GSGY](/sequence-files/IGVFFI8014GSGY/), [IGVFFI8544HANM](/sequence-files/IGVFFI8544HANM/), [IGVFFI4092JZVE](/sequence-files/IGVFFI4092JZVE/), [IGVFFI2136HHLB](/sequence-files/IGVFFI2136HHLB/), [IGVFFI8367QWEO](/sequence-files/IGVFFI8367QWEO/) 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/IGVFDS7802HNSL/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7802HNSL](/measurement-sets/IGVFDS7802HNSL/) 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/IGVFDS7802HNSL/"
}
]
},
"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": "2024-11-25T23:54:41.648135+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": "IGVFFI7299KWPR",
"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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"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": "2024-11-26T07:57:26.406807+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": "9cf0a997-0282-4b5f-bf33-a29f44ef615f"
}