{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7312BCBZ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7312BCBZ",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep3-BinC_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 [IGVFDS7312BCBZ](/measurement-sets/IGVFDS7312BCBZ/) has sequence file(s) [IGVFFI7241XKKE](/sequence-files/IGVFFI7241XKKE/), [IGVFFI2087UMAQ](/sequence-files/IGVFFI2087UMAQ/), [IGVFFI9557VBNH](/sequence-files/IGVFFI9557VBNH/), [IGVFFI1419ZYLP](/sequence-files/IGVFFI1419ZYLP/), [IGVFFI3023IADG](/sequence-files/IGVFFI3023IADG/), [IGVFFI5028NMRQ](/sequence-files/IGVFFI5028NMRQ/), [IGVFFI8407ITWC](/sequence-files/IGVFFI8407ITWC/), [IGVFFI9645XCVK](/sequence-files/IGVFFI9645XCVK/), [IGVFFI8274RCDL](/sequence-files/IGVFFI8274RCDL/), [IGVFFI9218PNOW](/sequence-files/IGVFFI9218PNOW/), [IGVFFI2005BVXR](/sequence-files/IGVFFI2005BVXR/), [IGVFFI0336YUDX](/sequence-files/IGVFFI0336YUDX/), [IGVFFI9556RRAS](/sequence-files/IGVFFI9556RRAS/), [IGVFFI8109GRTZ](/sequence-files/IGVFFI8109GRTZ/), [IGVFFI3787SUKX](/sequence-files/IGVFFI3787SUKX/), [IGVFFI0298UZTN](/sequence-files/IGVFFI0298UZTN/), [IGVFFI2967HIMC](/sequence-files/IGVFFI2967HIMC/), [IGVFFI7814NTRF](/sequence-files/IGVFFI7814NTRF/), [IGVFFI8135RFIM](/sequence-files/IGVFFI8135RFIM/), [IGVFFI3507AKOR](/sequence-files/IGVFFI3507AKOR/), [IGVFFI7361RQNM](/sequence-files/IGVFFI7361RQNM/), [IGVFFI7320UZZR](/sequence-files/IGVFFI7320UZZR/), [IGVFFI4954PDLZ](/sequence-files/IGVFFI4954PDLZ/), [IGVFFI5733QAYX](/sequence-files/IGVFFI5733QAYX/), [IGVFFI0272CSIG](/sequence-files/IGVFFI0272CSIG/), [IGVFFI6376WPOX](/sequence-files/IGVFFI6376WPOX/), [IGVFFI0490BKQH](/sequence-files/IGVFFI0490BKQH/), [IGVFFI3330RGOP](/sequence-files/IGVFFI3330RGOP/), [IGVFFI2402DALV](/sequence-files/IGVFFI2402DALV/), [IGVFFI8436BPDB](/sequence-files/IGVFFI8436BPDB/), [IGVFFI6635RIMN](/sequence-files/IGVFFI6635RIMN/), [IGVFFI0471IVPR](/sequence-files/IGVFFI0471IVPR/), [IGVFFI4940IMMC](/sequence-files/IGVFFI4940IMMC/), [IGVFFI2882JCQF](/sequence-files/IGVFFI2882JCQF/), [IGVFFI2899VBFQ](/sequence-files/IGVFFI2899VBFQ/), [IGVFFI8605YTKP](/sequence-files/IGVFFI8605YTKP/), [IGVFFI8333OEQM](/sequence-files/IGVFFI8333OEQM/), [IGVFFI8714DXDX](/sequence-files/IGVFFI8714DXDX/), [IGVFFI3403QFJI](/sequence-files/IGVFFI3403QFJI/), [IGVFFI5202WMUP](/sequence-files/IGVFFI5202WMUP/), [IGVFFI3520AKLX](/sequence-files/IGVFFI3520AKLX/), [IGVFFI1185UUCQ](/sequence-files/IGVFFI1185UUCQ/), [IGVFFI9622KZUG](/sequence-files/IGVFFI9622KZUG/), [IGVFFI4672DBLB](/sequence-files/IGVFFI4672DBLB/), [IGVFFI2416RFQR](/sequence-files/IGVFFI2416RFQR/), [IGVFFI8156KCLN](/sequence-files/IGVFFI8156KCLN/), [IGVFFI4593MEQL](/sequence-files/IGVFFI4593MEQL/), [IGVFFI4617QJIC](/sequence-files/IGVFFI4617QJIC/) 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/IGVFDS7312BCBZ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7312BCBZ](/measurement-sets/IGVFDS7312BCBZ/) has sequence file(s): [IGVFFI7241XKKE](/sequence-files/IGVFFI7241XKKE/), [IGVFFI2087UMAQ](/sequence-files/IGVFFI2087UMAQ/), [IGVFFI9557VBNH](/sequence-files/IGVFFI9557VBNH/), [IGVFFI1419ZYLP](/sequence-files/IGVFFI1419ZYLP/), [IGVFFI3023IADG](/sequence-files/IGVFFI3023IADG/), [IGVFFI5028NMRQ](/sequence-files/IGVFFI5028NMRQ/), [IGVFFI8407ITWC](/sequence-files/IGVFFI8407ITWC/), [IGVFFI9645XCVK](/sequence-files/IGVFFI9645XCVK/), [IGVFFI8274RCDL](/sequence-files/IGVFFI8274RCDL/), [IGVFFI9218PNOW](/sequence-files/IGVFFI9218PNOW/), [IGVFFI2005BVXR](/sequence-files/IGVFFI2005BVXR/), [IGVFFI0336YUDX](/sequence-files/IGVFFI0336YUDX/), [IGVFFI9556RRAS](/sequence-files/IGVFFI9556RRAS/), [IGVFFI8109GRTZ](/sequence-files/IGVFFI8109GRTZ/), [IGVFFI3787SUKX](/sequence-files/IGVFFI3787SUKX/), [IGVFFI0298UZTN](/sequence-files/IGVFFI0298UZTN/), [IGVFFI2967HIMC](/sequence-files/IGVFFI2967HIMC/), [IGVFFI7814NTRF](/sequence-files/IGVFFI7814NTRF/), [IGVFFI8135RFIM](/sequence-files/IGVFFI8135RFIM/), [IGVFFI3507AKOR](/sequence-files/IGVFFI3507AKOR/), [IGVFFI7361RQNM](/sequence-files/IGVFFI7361RQNM/), [IGVFFI7320UZZR](/sequence-files/IGVFFI7320UZZR/), [IGVFFI4954PDLZ](/sequence-files/IGVFFI4954PDLZ/), [IGVFFI5733QAYX](/sequence-files/IGVFFI5733QAYX/), [IGVFFI0272CSIG](/sequence-files/IGVFFI0272CSIG/), [IGVFFI6376WPOX](/sequence-files/IGVFFI6376WPOX/), [IGVFFI0490BKQH](/sequence-files/IGVFFI0490BKQH/), [IGVFFI3330RGOP](/sequence-files/IGVFFI3330RGOP/), [IGVFFI2402DALV](/sequence-files/IGVFFI2402DALV/), [IGVFFI8436BPDB](/sequence-files/IGVFFI8436BPDB/), [IGVFFI6635RIMN](/sequence-files/IGVFFI6635RIMN/), [IGVFFI0471IVPR](/sequence-files/IGVFFI0471IVPR/), [IGVFFI4940IMMC](/sequence-files/IGVFFI4940IMMC/), [IGVFFI2882JCQF](/sequence-files/IGVFFI2882JCQF/), [IGVFFI2899VBFQ](/sequence-files/IGVFFI2899VBFQ/), [IGVFFI8605YTKP](/sequence-files/IGVFFI8605YTKP/), [IGVFFI8333OEQM](/sequence-files/IGVFFI8333OEQM/), [IGVFFI8714DXDX](/sequence-files/IGVFFI8714DXDX/), [IGVFFI3403QFJI](/sequence-files/IGVFFI3403QFJI/), [IGVFFI5202WMUP](/sequence-files/IGVFFI5202WMUP/), [IGVFFI3520AKLX](/sequence-files/IGVFFI3520AKLX/), [IGVFFI1185UUCQ](/sequence-files/IGVFFI1185UUCQ/), [IGVFFI9622KZUG](/sequence-files/IGVFFI9622KZUG/), [IGVFFI4672DBLB](/sequence-files/IGVFFI4672DBLB/), [IGVFFI2416RFQR](/sequence-files/IGVFFI2416RFQR/), [IGVFFI8156KCLN](/sequence-files/IGVFFI8156KCLN/), [IGVFFI4593MEQL](/sequence-files/IGVFFI4593MEQL/), [IGVFFI4617QJIC](/sequence-files/IGVFFI4617QJIC/) 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/IGVFDS7312BCBZ/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7312BCBZ](/measurement-sets/IGVFDS7312BCBZ/) 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/IGVFDS7312BCBZ/"
}
]
},
"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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{
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"accession": "IGVFDS4103BJLT",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
],
"status": "preview"
}
],
"control_for": [],
"creation_timestamp": "2024-11-25T23:54:17.881691+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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"@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 51-75% 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": "2024-11-26T07:41:34.825314+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": "58087f62-a479-49f2-9b3a-46e2ab3fc0f8"
}