{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2890JPBI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2890JPBI",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinD_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS2890JPBI](/measurement-sets/IGVFDS2890JPBI/) has in progress subobject auxiliary set [IGVFDS3649FIXG](/auxiliary-sets/IGVFDS3649FIXG/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS2890JPBI/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM9682FICS](/in-vitro-systems/IGVFSM9682FICS/) has in progress subobject construct library set [IGVFDS2374NXLW](/construct-library-sets/IGVFDS2374NXLW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM9682FICS/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3649FIXG](/auxiliary-sets/IGVFDS3649FIXG/) has sequence file(s): [IGVFFI6743NNPF](/sequence-files/IGVFFI6743NNPF/), [IGVFFI4344VWNK](/sequence-files/IGVFFI4344VWNK/), [IGVFFI4016LPKF](/sequence-files/IGVFFI4016LPKF/), [IGVFFI8079IBFY](/sequence-files/IGVFFI8079IBFY/), [IGVFFI5998KOKY](/sequence-files/IGVFFI5998KOKY/), [IGVFFI0700XOKO](/sequence-files/IGVFFI0700XOKO/), [IGVFFI2345KMLH](/sequence-files/IGVFFI2345KMLH/), [IGVFFI0800JMWS](/sequence-files/IGVFFI0800JMWS/), [IGVFFI8989NGLO](/sequence-files/IGVFFI8989NGLO/), [IGVFFI0314KWEU](/sequence-files/IGVFFI0314KWEU/), [IGVFFI0697XWAD](/sequence-files/IGVFFI0697XWAD/), [IGVFFI6567OYIP](/sequence-files/IGVFFI6567OYIP/), [IGVFFI5319NFSX](/sequence-files/IGVFFI5319NFSX/), [IGVFFI7362QOBW](/sequence-files/IGVFFI7362QOBW/), [IGVFFI7340AZGM](/sequence-files/IGVFFI7340AZGM/), [IGVFFI7481XZXZ](/sequence-files/IGVFFI7481XZXZ/), [IGVFFI7326EMMV](/sequence-files/IGVFFI7326EMMV/), [IGVFFI5811OAMN](/sequence-files/IGVFFI5811OAMN/), [IGVFFI9473RNFO](/sequence-files/IGVFFI9473RNFO/), [IGVFFI8373HBBT](/sequence-files/IGVFFI8373HBBT/), [IGVFFI1850DDYJ](/sequence-files/IGVFFI1850DDYJ/), [IGVFFI5063KUKT](/sequence-files/IGVFFI5063KUKT/), [IGVFFI6520WBXG](/sequence-files/IGVFFI6520WBXG/), [IGVFFI3373OIXF](/sequence-files/IGVFFI3373OIXF/), [IGVFFI7110ATXK](/sequence-files/IGVFFI7110ATXK/), [IGVFFI5239RHET](/sequence-files/IGVFFI5239RHET/), [IGVFFI1321BNMB](/sequence-files/IGVFFI1321BNMB/), [IGVFFI0548AADC](/sequence-files/IGVFFI0548AADC/), [IGVFFI4188KJCD](/sequence-files/IGVFFI4188KJCD/), [IGVFFI6925OHTT](/sequence-files/IGVFFI6925OHTT/), [IGVFFI1812EKNF](/sequence-files/IGVFFI1812EKNF/), [IGVFFI4767NVZD](/sequence-files/IGVFFI4767NVZD/), [IGVFFI8385GMLW](/sequence-files/IGVFFI8385GMLW/), [IGVFFI7740IMWI](/sequence-files/IGVFFI7740IMWI/), [IGVFFI7487UDEI](/sequence-files/IGVFFI7487UDEI/), [IGVFFI5191TUWS](/sequence-files/IGVFFI5191TUWS/), [IGVFFI2812SIWG](/sequence-files/IGVFFI2812SIWG/), [IGVFFI9706GXXS](/sequence-files/IGVFFI9706GXXS/), [IGVFFI0718OXAW](/sequence-files/IGVFFI0718OXAW/), [IGVFFI0523FNVT](/sequence-files/IGVFFI0523FNVT/), [IGVFFI0493CTCY](/sequence-files/IGVFFI0493CTCY/), [IGVFFI3996SLQD](/sequence-files/IGVFFI3996SLQD/), [IGVFFI7335RLWX](/sequence-files/IGVFFI7335RLWX/), [IGVFFI4470TDLX](/sequence-files/IGVFFI4470TDLX/), [IGVFFI0308TTZY](/sequence-files/IGVFFI0308TTZY/), [IGVFFI3830CXZX](/sequence-files/IGVFFI3830CXZX/), [IGVFFI4381FEBA](/sequence-files/IGVFFI4381FEBA/), [IGVFFI8067ITSQ](/sequence-files/IGVFFI8067ITSQ/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS3649FIXG/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2890JPBI](/measurement-sets/IGVFDS2890JPBI/) 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": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS2890JPBI/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS3649FIXG](/auxiliary-sets/IGVFDS3649FIXG/) has sequence file(s) [IGVFFI6743NNPF](/sequence-files/IGVFFI6743NNPF/), [IGVFFI4344VWNK](/sequence-files/IGVFFI4344VWNK/), [IGVFFI4016LPKF](/sequence-files/IGVFFI4016LPKF/), [IGVFFI8079IBFY](/sequence-files/IGVFFI8079IBFY/), [IGVFFI5998KOKY](/sequence-files/IGVFFI5998KOKY/), [IGVFFI0700XOKO](/sequence-files/IGVFFI0700XOKO/), [IGVFFI2345KMLH](/sequence-files/IGVFFI2345KMLH/), [IGVFFI0800JMWS](/sequence-files/IGVFFI0800JMWS/), [IGVFFI8989NGLO](/sequence-files/IGVFFI8989NGLO/), [IGVFFI0314KWEU](/sequence-files/IGVFFI0314KWEU/), [IGVFFI0697XWAD](/sequence-files/IGVFFI0697XWAD/), [IGVFFI6567OYIP](/sequence-files/IGVFFI6567OYIP/), [IGVFFI5319NFSX](/sequence-files/IGVFFI5319NFSX/), [IGVFFI7362QOBW](/sequence-files/IGVFFI7362QOBW/), [IGVFFI7340AZGM](/sequence-files/IGVFFI7340AZGM/), [IGVFFI7481XZXZ](/sequence-files/IGVFFI7481XZXZ/), [IGVFFI7326EMMV](/sequence-files/IGVFFI7326EMMV/), [IGVFFI5811OAMN](/sequence-files/IGVFFI5811OAMN/), [IGVFFI9473RNFO](/sequence-files/IGVFFI9473RNFO/), [IGVFFI8373HBBT](/sequence-files/IGVFFI8373HBBT/), [IGVFFI1850DDYJ](/sequence-files/IGVFFI1850DDYJ/), [IGVFFI5063KUKT](/sequence-files/IGVFFI5063KUKT/), [IGVFFI6520WBXG](/sequence-files/IGVFFI6520WBXG/), [IGVFFI3373OIXF](/sequence-files/IGVFFI3373OIXF/), [IGVFFI7110ATXK](/sequence-files/IGVFFI7110ATXK/), [IGVFFI5239RHET](/sequence-files/IGVFFI5239RHET/), [IGVFFI1321BNMB](/sequence-files/IGVFFI1321BNMB/), [IGVFFI0548AADC](/sequence-files/IGVFFI0548AADC/), [IGVFFI4188KJCD](/sequence-files/IGVFFI4188KJCD/), [IGVFFI6925OHTT](/sequence-files/IGVFFI6925OHTT/), [IGVFFI1812EKNF](/sequence-files/IGVFFI1812EKNF/), [IGVFFI4767NVZD](/sequence-files/IGVFFI4767NVZD/), [IGVFFI8385GMLW](/sequence-files/IGVFFI8385GMLW/), [IGVFFI7740IMWI](/sequence-files/IGVFFI7740IMWI/), [IGVFFI7487UDEI](/sequence-files/IGVFFI7487UDEI/), [IGVFFI5191TUWS](/sequence-files/IGVFFI5191TUWS/), [IGVFFI2812SIWG](/sequence-files/IGVFFI2812SIWG/), [IGVFFI9706GXXS](/sequence-files/IGVFFI9706GXXS/), [IGVFFI0718OXAW](/sequence-files/IGVFFI0718OXAW/), [IGVFFI0523FNVT](/sequence-files/IGVFFI0523FNVT/), [IGVFFI0493CTCY](/sequence-files/IGVFFI0493CTCY/), [IGVFFI3996SLQD](/sequence-files/IGVFFI3996SLQD/), [IGVFFI7335RLWX](/sequence-files/IGVFFI7335RLWX/), [IGVFFI4470TDLX](/sequence-files/IGVFFI4470TDLX/), [IGVFFI0308TTZY](/sequence-files/IGVFFI0308TTZY/), [IGVFFI3830CXZX](/sequence-files/IGVFFI3830CXZX/), [IGVFFI4381FEBA](/sequence-files/IGVFFI4381FEBA/), [IGVFFI8067ITSQ](/sequence-files/IGVFFI8067ITSQ/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 40,
"level_name": "WARNING",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS3649FIXG/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS3649FIXG](/auxiliary-sets/IGVFDS3649FIXG/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_file_set_for",
"path": "/auxiliary-sets/IGVFDS3649FIXG/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS3649FIXG/",
"accession": "IGVFDS3649FIXG",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinD_AmpliconSequencing_AuxiliarySet"
],
"file_set_type": "variant sequencing"
}
],
"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/IGVFDS4989HPTW/",
"accession": "IGVFDS4989HPTW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:49:12.579877+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "experimental data",
"files": [],
"input_file_set_for": [
"/analysis-sets/IGVFDS5031MNRR/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set.",
"preferred_assay_title": "Variant FlowFISH",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"release_timestamp": "2023-12-20T23:05:50.155309+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9682FICS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9682FICS",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinD"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2374NXLW/",
"accession": "IGVFDS2374NXLW",
"file_set_type": "guide library",
"summary": "Guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing"
}
],
"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": "released",
"summary": "THP-1 cell line, male, Homo sapiens (sorting details: FACS bin for 76-100% expression of PPIF) modified with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "21",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T22:13:23.923944+00:00",
"summary": "Variant FlowFISH integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"targeted_genes": [
{
"@id": "/genes/ENSG00000108179/",
"geneid": "ENSG00000108179",
"name": "peptidylprolyl isomerase F",
"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": "d81b514b-3109-47c3-a755-bb413738a845"
}