{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8230NTUC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8230NTUC",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-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 [IGVFDS8230NTUC](/measurement-sets/IGVFDS8230NTUC/) has sequence file(s) [IGVFFI1638QNHU](/sequence-files/IGVFFI1638QNHU/), [IGVFFI8172TTYS](/sequence-files/IGVFFI8172TTYS/), [IGVFFI0061YGQF](/sequence-files/IGVFFI0061YGQF/), [IGVFFI3686ZRQS](/sequence-files/IGVFFI3686ZRQS/), [IGVFFI6949GTER](/sequence-files/IGVFFI6949GTER/), [IGVFFI3279TAQE](/sequence-files/IGVFFI3279TAQE/), [IGVFFI8727IKUM](/sequence-files/IGVFFI8727IKUM/), [IGVFFI7827ZTZF](/sequence-files/IGVFFI7827ZTZF/), [IGVFFI6144MQEY](/sequence-files/IGVFFI6144MQEY/), [IGVFFI4281XRDL](/sequence-files/IGVFFI4281XRDL/), [IGVFFI2270TQZD](/sequence-files/IGVFFI2270TQZD/), [IGVFFI2208XXCI](/sequence-files/IGVFFI2208XXCI/), [IGVFFI5200YQBH](/sequence-files/IGVFFI5200YQBH/), [IGVFFI8366PMMG](/sequence-files/IGVFFI8366PMMG/), [IGVFFI7627ZADE](/sequence-files/IGVFFI7627ZADE/), [IGVFFI6692FXTI](/sequence-files/IGVFFI6692FXTI/), [IGVFFI9001SWZI](/sequence-files/IGVFFI9001SWZI/), [IGVFFI0822KFZB](/sequence-files/IGVFFI0822KFZB/), [IGVFFI0598DIFH](/sequence-files/IGVFFI0598DIFH/), [IGVFFI1052WTYQ](/sequence-files/IGVFFI1052WTYQ/), [IGVFFI9217FRPG](/sequence-files/IGVFFI9217FRPG/), [IGVFFI9341OMBK](/sequence-files/IGVFFI9341OMBK/), [IGVFFI9733FYOF](/sequence-files/IGVFFI9733FYOF/), [IGVFFI6982IYEP](/sequence-files/IGVFFI6982IYEP/), [IGVFFI8307AIRB](/sequence-files/IGVFFI8307AIRB/), [IGVFFI7017LKDP](/sequence-files/IGVFFI7017LKDP/), [IGVFFI0108HSLI](/sequence-files/IGVFFI0108HSLI/), [IGVFFI7081DOTN](/sequence-files/IGVFFI7081DOTN/), [IGVFFI7866CQDH](/sequence-files/IGVFFI7866CQDH/), [IGVFFI6560YHHV](/sequence-files/IGVFFI6560YHHV/), [IGVFFI9378LDZC](/sequence-files/IGVFFI9378LDZC/), [IGVFFI1538CDMZ](/sequence-files/IGVFFI1538CDMZ/), [IGVFFI5728SDMD](/sequence-files/IGVFFI5728SDMD/), [IGVFFI8518JZNQ](/sequence-files/IGVFFI8518JZNQ/), [IGVFFI9741PXPZ](/sequence-files/IGVFFI9741PXPZ/), [IGVFFI7848COEW](/sequence-files/IGVFFI7848COEW/), [IGVFFI7703LMEB](/sequence-files/IGVFFI7703LMEB/), [IGVFFI2462RXKB](/sequence-files/IGVFFI2462RXKB/), [IGVFFI6712QPAZ](/sequence-files/IGVFFI6712QPAZ/), [IGVFFI0296XPVN](/sequence-files/IGVFFI0296XPVN/), [IGVFFI9092XYMC](/sequence-files/IGVFFI9092XYMC/), [IGVFFI0243XBSC](/sequence-files/IGVFFI0243XBSC/), [IGVFFI6371GIAC](/sequence-files/IGVFFI6371GIAC/), [IGVFFI9636RTHI](/sequence-files/IGVFFI9636RTHI/), [IGVFFI2329MKLK](/sequence-files/IGVFFI2329MKLK/), [IGVFFI6615RUKJ](/sequence-files/IGVFFI6615RUKJ/), [IGVFFI5801AZHS](/sequence-files/IGVFFI5801AZHS/), [IGVFFI3077EWVW](/sequence-files/IGVFFI3077EWVW/) 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/IGVFDS8230NTUC/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8230NTUC](/measurement-sets/IGVFDS8230NTUC/) has sequence file(s): [IGVFFI1638QNHU](/sequence-files/IGVFFI1638QNHU/), [IGVFFI8172TTYS](/sequence-files/IGVFFI8172TTYS/), [IGVFFI0061YGQF](/sequence-files/IGVFFI0061YGQF/), [IGVFFI3686ZRQS](/sequence-files/IGVFFI3686ZRQS/), [IGVFFI6949GTER](/sequence-files/IGVFFI6949GTER/), [IGVFFI3279TAQE](/sequence-files/IGVFFI3279TAQE/), [IGVFFI8727IKUM](/sequence-files/IGVFFI8727IKUM/), [IGVFFI7827ZTZF](/sequence-files/IGVFFI7827ZTZF/), [IGVFFI6144MQEY](/sequence-files/IGVFFI6144MQEY/), [IGVFFI4281XRDL](/sequence-files/IGVFFI4281XRDL/), [IGVFFI2270TQZD](/sequence-files/IGVFFI2270TQZD/), [IGVFFI2208XXCI](/sequence-files/IGVFFI2208XXCI/), [IGVFFI5200YQBH](/sequence-files/IGVFFI5200YQBH/), [IGVFFI8366PMMG](/sequence-files/IGVFFI8366PMMG/), [IGVFFI7627ZADE](/sequence-files/IGVFFI7627ZADE/), [IGVFFI6692FXTI](/sequence-files/IGVFFI6692FXTI/), [IGVFFI9001SWZI](/sequence-files/IGVFFI9001SWZI/), [IGVFFI0822KFZB](/sequence-files/IGVFFI0822KFZB/), [IGVFFI0598DIFH](/sequence-files/IGVFFI0598DIFH/), [IGVFFI1052WTYQ](/sequence-files/IGVFFI1052WTYQ/), [IGVFFI9217FRPG](/sequence-files/IGVFFI9217FRPG/), [IGVFFI9341OMBK](/sequence-files/IGVFFI9341OMBK/), [IGVFFI9733FYOF](/sequence-files/IGVFFI9733FYOF/), [IGVFFI6982IYEP](/sequence-files/IGVFFI6982IYEP/), [IGVFFI8307AIRB](/sequence-files/IGVFFI8307AIRB/), [IGVFFI7017LKDP](/sequence-files/IGVFFI7017LKDP/), [IGVFFI0108HSLI](/sequence-files/IGVFFI0108HSLI/), [IGVFFI7081DOTN](/sequence-files/IGVFFI7081DOTN/), [IGVFFI7866CQDH](/sequence-files/IGVFFI7866CQDH/), [IGVFFI6560YHHV](/sequence-files/IGVFFI6560YHHV/), [IGVFFI9378LDZC](/sequence-files/IGVFFI9378LDZC/), [IGVFFI1538CDMZ](/sequence-files/IGVFFI1538CDMZ/), [IGVFFI5728SDMD](/sequence-files/IGVFFI5728SDMD/), [IGVFFI8518JZNQ](/sequence-files/IGVFFI8518JZNQ/), [IGVFFI9741PXPZ](/sequence-files/IGVFFI9741PXPZ/), [IGVFFI7848COEW](/sequence-files/IGVFFI7848COEW/), [IGVFFI7703LMEB](/sequence-files/IGVFFI7703LMEB/), [IGVFFI2462RXKB](/sequence-files/IGVFFI2462RXKB/), [IGVFFI6712QPAZ](/sequence-files/IGVFFI6712QPAZ/), [IGVFFI0296XPVN](/sequence-files/IGVFFI0296XPVN/), [IGVFFI9092XYMC](/sequence-files/IGVFFI9092XYMC/), [IGVFFI0243XBSC](/sequence-files/IGVFFI0243XBSC/), [IGVFFI6371GIAC](/sequence-files/IGVFFI6371GIAC/), [IGVFFI9636RTHI](/sequence-files/IGVFFI9636RTHI/), [IGVFFI2329MKLK](/sequence-files/IGVFFI2329MKLK/), [IGVFFI6615RUKJ](/sequence-files/IGVFFI6615RUKJ/), [IGVFFI5801AZHS](/sequence-files/IGVFFI5801AZHS/), [IGVFFI3077EWVW](/sequence-files/IGVFFI3077EWVW/) 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/IGVFDS8230NTUC/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS8230NTUC](/measurement-sets/IGVFDS8230NTUC/) 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/IGVFDS8230NTUC/"
}
]
},
"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": "2024-11-25T23:53:50.386209+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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"accession": "IGVFFI1638QNHU",
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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/IGVFFI2270TQZD/",
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"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS4955GEYO/",
"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": "2024-11-26T07:25:41.829914+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": "5f2e3340-9181-494f-bcec-97da86bb76d8"
}