{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6710CDSE/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6710CDSE",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep2-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 in vitro system [IGVFSM6665OGEE](/in-vitro-systems/IGVFSM6665OGEE/) has in progress subobject construct library set [IGVFDS2385DHZO](/construct-library-sets/IGVFDS2385DHZO/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM6665OGEE/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS6710CDSE](/measurement-sets/IGVFDS6710CDSE/) has in progress subobject auxiliary set [IGVFDS4002BNAH](/auxiliary-sets/IGVFDS4002BNAH/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS6710CDSE/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6710CDSE](/measurement-sets/IGVFDS6710CDSE/) 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/IGVFDS6710CDSE/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS4002BNAH](/auxiliary-sets/IGVFDS4002BNAH/) has sequence file(s) [IGVFFI6577QZIZ](/sequence-files/IGVFFI6577QZIZ/), [IGVFFI8347ZQYF](/sequence-files/IGVFFI8347ZQYF/), [IGVFFI9101BWRN](/sequence-files/IGVFFI9101BWRN/), [IGVFFI0847GSDH](/sequence-files/IGVFFI0847GSDH/), [IGVFFI4804QRTP](/sequence-files/IGVFFI4804QRTP/), [IGVFFI4524UAQV](/sequence-files/IGVFFI4524UAQV/), [IGVFFI7500YSBE](/sequence-files/IGVFFI7500YSBE/), [IGVFFI0836ZQNB](/sequence-files/IGVFFI0836ZQNB/), [IGVFFI1627LTBS](/sequence-files/IGVFFI1627LTBS/), [IGVFFI3867EYWW](/sequence-files/IGVFFI3867EYWW/), [IGVFFI1981SJLX](/sequence-files/IGVFFI1981SJLX/), [IGVFFI2314MDHT](/sequence-files/IGVFFI2314MDHT/), [IGVFFI7669RPDB](/sequence-files/IGVFFI7669RPDB/), [IGVFFI0814ISRC](/sequence-files/IGVFFI0814ISRC/), [IGVFFI6667PPOF](/sequence-files/IGVFFI6667PPOF/), [IGVFFI6346FZIU](/sequence-files/IGVFFI6346FZIU/), [IGVFFI7737OPBA](/sequence-files/IGVFFI7737OPBA/), [IGVFFI5835KLXS](/sequence-files/IGVFFI5835KLXS/), [IGVFFI2369GRGH](/sequence-files/IGVFFI2369GRGH/), [IGVFFI4498ICCN](/sequence-files/IGVFFI4498ICCN/), [IGVFFI0880ZYUS](/sequence-files/IGVFFI0880ZYUS/), [IGVFFI4714MPUQ](/sequence-files/IGVFFI4714MPUQ/), [IGVFFI6395OKJP](/sequence-files/IGVFFI6395OKJP/), [IGVFFI4880ZBON](/sequence-files/IGVFFI4880ZBON/), [IGVFFI1852THTG](/sequence-files/IGVFFI1852THTG/), [IGVFFI7316RQZP](/sequence-files/IGVFFI7316RQZP/), [IGVFFI5867SZZA](/sequence-files/IGVFFI5867SZZA/), [IGVFFI5883IMXZ](/sequence-files/IGVFFI5883IMXZ/), [IGVFFI6410JSMM](/sequence-files/IGVFFI6410JSMM/), [IGVFFI8275QGRZ](/sequence-files/IGVFFI8275QGRZ/), [IGVFFI2623OFYH](/sequence-files/IGVFFI2623OFYH/), [IGVFFI1287KXUV](/sequence-files/IGVFFI1287KXUV/), [IGVFFI4037UIXE](/sequence-files/IGVFFI4037UIXE/), [IGVFFI0848OKJK](/sequence-files/IGVFFI0848OKJK/), [IGVFFI8251QRFX](/sequence-files/IGVFFI8251QRFX/), [IGVFFI8225QCXA](/sequence-files/IGVFFI8225QCXA/), [IGVFFI5820UTIN](/sequence-files/IGVFFI5820UTIN/), [IGVFFI1970WGTP](/sequence-files/IGVFFI1970WGTP/), [IGVFFI6705UMUB](/sequence-files/IGVFFI6705UMUB/), [IGVFFI1286YIFX](/sequence-files/IGVFFI1286YIFX/), [IGVFFI0765HJEP](/sequence-files/IGVFFI0765HJEP/), [IGVFFI9643DCQI](/sequence-files/IGVFFI9643DCQI/), [IGVFFI0637AJLX](/sequence-files/IGVFFI0637AJLX/), [IGVFFI8589CYVP](/sequence-files/IGVFFI8589CYVP/), [IGVFFI3700DTMV](/sequence-files/IGVFFI3700DTMV/), [IGVFFI1345NBXM](/sequence-files/IGVFFI1345NBXM/), [IGVFFI6415UWQA](/sequence-files/IGVFFI6415UWQA/), [IGVFFI7759KUKS](/sequence-files/IGVFFI7759KUKS/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS4002BNAH/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS4002BNAH](/auxiliary-sets/IGVFDS4002BNAH/) has sequence file(s): [IGVFFI6577QZIZ](/sequence-files/IGVFFI6577QZIZ/), [IGVFFI8347ZQYF](/sequence-files/IGVFFI8347ZQYF/), [IGVFFI9101BWRN](/sequence-files/IGVFFI9101BWRN/), [IGVFFI0847GSDH](/sequence-files/IGVFFI0847GSDH/), [IGVFFI4804QRTP](/sequence-files/IGVFFI4804QRTP/), [IGVFFI4524UAQV](/sequence-files/IGVFFI4524UAQV/), [IGVFFI7500YSBE](/sequence-files/IGVFFI7500YSBE/), [IGVFFI0836ZQNB](/sequence-files/IGVFFI0836ZQNB/), [IGVFFI1627LTBS](/sequence-files/IGVFFI1627LTBS/), [IGVFFI3867EYWW](/sequence-files/IGVFFI3867EYWW/), [IGVFFI1981SJLX](/sequence-files/IGVFFI1981SJLX/), [IGVFFI2314MDHT](/sequence-files/IGVFFI2314MDHT/), [IGVFFI7669RPDB](/sequence-files/IGVFFI7669RPDB/), [IGVFFI0814ISRC](/sequence-files/IGVFFI0814ISRC/), [IGVFFI6667PPOF](/sequence-files/IGVFFI6667PPOF/), [IGVFFI6346FZIU](/sequence-files/IGVFFI6346FZIU/), [IGVFFI7737OPBA](/sequence-files/IGVFFI7737OPBA/), [IGVFFI5835KLXS](/sequence-files/IGVFFI5835KLXS/), [IGVFFI2369GRGH](/sequence-files/IGVFFI2369GRGH/), [IGVFFI4498ICCN](/sequence-files/IGVFFI4498ICCN/), [IGVFFI0880ZYUS](/sequence-files/IGVFFI0880ZYUS/), [IGVFFI4714MPUQ](/sequence-files/IGVFFI4714MPUQ/), [IGVFFI6395OKJP](/sequence-files/IGVFFI6395OKJP/), [IGVFFI4880ZBON](/sequence-files/IGVFFI4880ZBON/), [IGVFFI1852THTG](/sequence-files/IGVFFI1852THTG/), [IGVFFI7316RQZP](/sequence-files/IGVFFI7316RQZP/), [IGVFFI5867SZZA](/sequence-files/IGVFFI5867SZZA/), [IGVFFI5883IMXZ](/sequence-files/IGVFFI5883IMXZ/), [IGVFFI6410JSMM](/sequence-files/IGVFFI6410JSMM/), [IGVFFI8275QGRZ](/sequence-files/IGVFFI8275QGRZ/), [IGVFFI2623OFYH](/sequence-files/IGVFFI2623OFYH/), [IGVFFI1287KXUV](/sequence-files/IGVFFI1287KXUV/), [IGVFFI4037UIXE](/sequence-files/IGVFFI4037UIXE/), [IGVFFI0848OKJK](/sequence-files/IGVFFI0848OKJK/), [IGVFFI8251QRFX](/sequence-files/IGVFFI8251QRFX/), [IGVFFI8225QCXA](/sequence-files/IGVFFI8225QCXA/), [IGVFFI5820UTIN](/sequence-files/IGVFFI5820UTIN/), [IGVFFI1970WGTP](/sequence-files/IGVFFI1970WGTP/), [IGVFFI6705UMUB](/sequence-files/IGVFFI6705UMUB/), [IGVFFI1286YIFX](/sequence-files/IGVFFI1286YIFX/), [IGVFFI0765HJEP](/sequence-files/IGVFFI0765HJEP/), [IGVFFI9643DCQI](/sequence-files/IGVFFI9643DCQI/), [IGVFFI0637AJLX](/sequence-files/IGVFFI0637AJLX/), [IGVFFI8589CYVP](/sequence-files/IGVFFI8589CYVP/), [IGVFFI3700DTMV](/sequence-files/IGVFFI3700DTMV/), [IGVFFI1345NBXM](/sequence-files/IGVFFI1345NBXM/), [IGVFFI6415UWQA](/sequence-files/IGVFFI6415UWQA/), [IGVFFI7759KUKS](/sequence-files/IGVFFI7759KUKS/) 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/IGVFDS4002BNAH/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS4002BNAH](/auxiliary-sets/IGVFDS4002BNAH/) 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/IGVFDS4002BNAH/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS4002BNAH/",
"accession": "IGVFDS4002BNAH",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep2-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/IGVFDS4869FXYY/",
"accession": "IGVFDS4869FXYY",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-Jurkat-PE2_Exp2_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-12-13T08:48:05.545766+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1080XFGV/",
"accession": "IGVFDO1080XFGV",
"aliases": [
"igvf:donor_of_Jurkat"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "experimental data",
"files": [],
"input_file_set_for": [
"/analysis-sets/IGVFDS6299IJHG/"
],
"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": "2023-12-20T23:09:06.243754+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6665OGEE/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6665OGEE",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep2-BinD"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2385DHZO/",
"accession": "IGVFDS2385DHZO",
"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_0002796/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:Jurkat"
],
"status": "released",
"summary": "Jurkat",
"term_name": "Jurkat"
}
],
"status": "released",
"summary": "Jurkat 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": "22",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-13T09:36:56.974195+00:00",
"summary": "prime editing 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": "86136a72-bde1-4c6c-b956-cb034652b39e"
}