{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1285SAVV/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1285SAVV",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-BinC_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 [IGVFDS1285SAVV](/measurement-sets/IGVFDS1285SAVV/) has in progress subobject auxiliary set [IGVFDS3049DSIE](/auxiliary-sets/IGVFDS3049DSIE/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS1285SAVV/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM3275SABA](/in-vitro-systems/IGVFSM3275SABA/) 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/IGVFSM3275SABA/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3049DSIE](/auxiliary-sets/IGVFDS3049DSIE/) has sequence file(s): [IGVFFI0402TMSY](/sequence-files/IGVFFI0402TMSY/), [IGVFFI4532AJXD](/sequence-files/IGVFFI4532AJXD/), [IGVFFI0355DPZS](/sequence-files/IGVFFI0355DPZS/), [IGVFFI6774ICGQ](/sequence-files/IGVFFI6774ICGQ/), [IGVFFI4478UABJ](/sequence-files/IGVFFI4478UABJ/), [IGVFFI8209ZGKG](/sequence-files/IGVFFI8209ZGKG/), [IGVFFI7042MSRD](/sequence-files/IGVFFI7042MSRD/), [IGVFFI6166IYEH](/sequence-files/IGVFFI6166IYEH/), [IGVFFI7927FPTK](/sequence-files/IGVFFI7927FPTK/), [IGVFFI2486NSVI](/sequence-files/IGVFFI2486NSVI/), [IGVFFI8112ZVPB](/sequence-files/IGVFFI8112ZVPB/), [IGVFFI0506DBQH](/sequence-files/IGVFFI0506DBQH/), [IGVFFI9264ISJO](/sequence-files/IGVFFI9264ISJO/), [IGVFFI7089VBHS](/sequence-files/IGVFFI7089VBHS/), [IGVFFI5087WSGS](/sequence-files/IGVFFI5087WSGS/), [IGVFFI6463WXTK](/sequence-files/IGVFFI6463WXTK/), [IGVFFI6997SLOZ](/sequence-files/IGVFFI6997SLOZ/), [IGVFFI5880IRXW](/sequence-files/IGVFFI5880IRXW/), [IGVFFI2277YKXE](/sequence-files/IGVFFI2277YKXE/), [IGVFFI9677YSWT](/sequence-files/IGVFFI9677YSWT/), [IGVFFI7752HDLQ](/sequence-files/IGVFFI7752HDLQ/), [IGVFFI9208IUMP](/sequence-files/IGVFFI9208IUMP/), [IGVFFI8879PJJY](/sequence-files/IGVFFI8879PJJY/), [IGVFFI2475CDEA](/sequence-files/IGVFFI2475CDEA/), [IGVFFI5783LPLC](/sequence-files/IGVFFI5783LPLC/), [IGVFFI7556UYRP](/sequence-files/IGVFFI7556UYRP/), [IGVFFI8943RRZF](/sequence-files/IGVFFI8943RRZF/), [IGVFFI2684KLGM](/sequence-files/IGVFFI2684KLGM/), [IGVFFI0603ZMUW](/sequence-files/IGVFFI0603ZMUW/), [IGVFFI9133SAYI](/sequence-files/IGVFFI9133SAYI/), [IGVFFI3170BSNL](/sequence-files/IGVFFI3170BSNL/), [IGVFFI0359GSBR](/sequence-files/IGVFFI0359GSBR/), [IGVFFI0437BRJM](/sequence-files/IGVFFI0437BRJM/), [IGVFFI6415IIIS](/sequence-files/IGVFFI6415IIIS/), [IGVFFI5530DPTO](/sequence-files/IGVFFI5530DPTO/), [IGVFFI2319ZODY](/sequence-files/IGVFFI2319ZODY/), [IGVFFI5988PPUW](/sequence-files/IGVFFI5988PPUW/), [IGVFFI4780QQPC](/sequence-files/IGVFFI4780QQPC/), [IGVFFI2244FSQQ](/sequence-files/IGVFFI2244FSQQ/), [IGVFFI1625GPWF](/sequence-files/IGVFFI1625GPWF/), [IGVFFI4078JPHG](/sequence-files/IGVFFI4078JPHG/), [IGVFFI8888RUXR](/sequence-files/IGVFFI8888RUXR/), [IGVFFI5891EUZO](/sequence-files/IGVFFI5891EUZO/), [IGVFFI8677XRNK](/sequence-files/IGVFFI8677XRNK/), [IGVFFI5120KWVL](/sequence-files/IGVFFI5120KWVL/), [IGVFFI5135ZACM](/sequence-files/IGVFFI5135ZACM/), [IGVFFI6583JLOB](/sequence-files/IGVFFI6583JLOB/), [IGVFFI0135BHPL](/sequence-files/IGVFFI0135BHPL/) 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/IGVFDS3049DSIE/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1285SAVV](/measurement-sets/IGVFDS1285SAVV/) 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/IGVFDS1285SAVV/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS3049DSIE](/auxiliary-sets/IGVFDS3049DSIE/) has sequence file(s) [IGVFFI0402TMSY](/sequence-files/IGVFFI0402TMSY/), [IGVFFI4532AJXD](/sequence-files/IGVFFI4532AJXD/), [IGVFFI0355DPZS](/sequence-files/IGVFFI0355DPZS/), [IGVFFI6774ICGQ](/sequence-files/IGVFFI6774ICGQ/), [IGVFFI4478UABJ](/sequence-files/IGVFFI4478UABJ/), [IGVFFI8209ZGKG](/sequence-files/IGVFFI8209ZGKG/), [IGVFFI7042MSRD](/sequence-files/IGVFFI7042MSRD/), [IGVFFI6166IYEH](/sequence-files/IGVFFI6166IYEH/), [IGVFFI7927FPTK](/sequence-files/IGVFFI7927FPTK/), [IGVFFI2486NSVI](/sequence-files/IGVFFI2486NSVI/), [IGVFFI8112ZVPB](/sequence-files/IGVFFI8112ZVPB/), [IGVFFI0506DBQH](/sequence-files/IGVFFI0506DBQH/), [IGVFFI9264ISJO](/sequence-files/IGVFFI9264ISJO/), [IGVFFI7089VBHS](/sequence-files/IGVFFI7089VBHS/), [IGVFFI5087WSGS](/sequence-files/IGVFFI5087WSGS/), [IGVFFI6463WXTK](/sequence-files/IGVFFI6463WXTK/), [IGVFFI6997SLOZ](/sequence-files/IGVFFI6997SLOZ/), [IGVFFI5880IRXW](/sequence-files/IGVFFI5880IRXW/), [IGVFFI2277YKXE](/sequence-files/IGVFFI2277YKXE/), [IGVFFI9677YSWT](/sequence-files/IGVFFI9677YSWT/), [IGVFFI7752HDLQ](/sequence-files/IGVFFI7752HDLQ/), [IGVFFI9208IUMP](/sequence-files/IGVFFI9208IUMP/), [IGVFFI8879PJJY](/sequence-files/IGVFFI8879PJJY/), [IGVFFI2475CDEA](/sequence-files/IGVFFI2475CDEA/), [IGVFFI5783LPLC](/sequence-files/IGVFFI5783LPLC/), [IGVFFI7556UYRP](/sequence-files/IGVFFI7556UYRP/), [IGVFFI8943RRZF](/sequence-files/IGVFFI8943RRZF/), [IGVFFI2684KLGM](/sequence-files/IGVFFI2684KLGM/), [IGVFFI0603ZMUW](/sequence-files/IGVFFI0603ZMUW/), [IGVFFI9133SAYI](/sequence-files/IGVFFI9133SAYI/), [IGVFFI3170BSNL](/sequence-files/IGVFFI3170BSNL/), [IGVFFI0359GSBR](/sequence-files/IGVFFI0359GSBR/), [IGVFFI0437BRJM](/sequence-files/IGVFFI0437BRJM/), [IGVFFI6415IIIS](/sequence-files/IGVFFI6415IIIS/), [IGVFFI5530DPTO](/sequence-files/IGVFFI5530DPTO/), [IGVFFI2319ZODY](/sequence-files/IGVFFI2319ZODY/), [IGVFFI5988PPUW](/sequence-files/IGVFFI5988PPUW/), [IGVFFI4780QQPC](/sequence-files/IGVFFI4780QQPC/), [IGVFFI2244FSQQ](/sequence-files/IGVFFI2244FSQQ/), [IGVFFI1625GPWF](/sequence-files/IGVFFI1625GPWF/), [IGVFFI4078JPHG](/sequence-files/IGVFFI4078JPHG/), [IGVFFI8888RUXR](/sequence-files/IGVFFI8888RUXR/), [IGVFFI5891EUZO](/sequence-files/IGVFFI5891EUZO/), [IGVFFI8677XRNK](/sequence-files/IGVFFI8677XRNK/), [IGVFFI5120KWVL](/sequence-files/IGVFFI5120KWVL/), [IGVFFI5135ZACM](/sequence-files/IGVFFI5135ZACM/), [IGVFFI6583JLOB](/sequence-files/IGVFFI6583JLOB/), [IGVFFI0135BHPL](/sequence-files/IGVFFI0135BHPL/) 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/IGVFDS3049DSIE/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS3049DSIE](/auxiliary-sets/IGVFDS3049DSIE/) 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/IGVFDS3049DSIE/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS3049DSIE/",
"accession": "IGVFDS3049DSIE",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-BinC_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": "2023-11-30T22:49:00.632408+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": "2023-12-20T23:07:09.479362+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3275SABA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3275SABA",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-BinC"
],
"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 51-75% 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": "2023-12-05T20:30:34.526345+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": "9e03f5d5-8539-4eb2-bbef-81f030d785ff"
}