{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6267YRNH/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6267YRNH",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-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 [IGVFDS6267YRNH](/measurement-sets/IGVFDS6267YRNH/) has in progress subobject auxiliary set [IGVFDS6286JOFD](/auxiliary-sets/IGVFDS6286JOFD/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS6267YRNH/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM3394FCPH](/in-vitro-systems/IGVFSM3394FCPH/) has in progress subobject construct library set [IGVFDS6982DESN](/construct-library-sets/IGVFDS6982DESN/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM3394FCPH/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6267YRNH](/measurement-sets/IGVFDS6267YRNH/) 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/IGVFDS6267YRNH/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS6286JOFD](/auxiliary-sets/IGVFDS6286JOFD/) has sequence file(s): [IGVFFI5431QIHK](/sequence-files/IGVFFI5431QIHK/), [IGVFFI1713MUGN](/sequence-files/IGVFFI1713MUGN/), [IGVFFI0996LKFZ](/sequence-files/IGVFFI0996LKFZ/), [IGVFFI8230ERRR](/sequence-files/IGVFFI8230ERRR/), [IGVFFI0646LPXR](/sequence-files/IGVFFI0646LPXR/), [IGVFFI4114CMRD](/sequence-files/IGVFFI4114CMRD/), [IGVFFI8136VPPB](/sequence-files/IGVFFI8136VPPB/), [IGVFFI0676URKU](/sequence-files/IGVFFI0676URKU/), [IGVFFI8900YUVW](/sequence-files/IGVFFI8900YUVW/), [IGVFFI6210YESJ](/sequence-files/IGVFFI6210YESJ/), [IGVFFI0737WUQP](/sequence-files/IGVFFI0737WUQP/), [IGVFFI2588AXXW](/sequence-files/IGVFFI2588AXXW/), [IGVFFI4827WISX](/sequence-files/IGVFFI4827WISX/), [IGVFFI8230PQJJ](/sequence-files/IGVFFI8230PQJJ/), [IGVFFI0348MCPO](/sequence-files/IGVFFI0348MCPO/), [IGVFFI7174FPNE](/sequence-files/IGVFFI7174FPNE/), [IGVFFI4488UJSM](/sequence-files/IGVFFI4488UJSM/), [IGVFFI4684KBXY](/sequence-files/IGVFFI4684KBXY/), [IGVFFI0273KKME](/sequence-files/IGVFFI0273KKME/), [IGVFFI0338PYWL](/sequence-files/IGVFFI0338PYWL/), [IGVFFI5195WRZW](/sequence-files/IGVFFI5195WRZW/), [IGVFFI9722PDEX](/sequence-files/IGVFFI9722PDEX/), [IGVFFI3065KWEP](/sequence-files/IGVFFI3065KWEP/), [IGVFFI9121IGRO](/sequence-files/IGVFFI9121IGRO/), [IGVFFI3684LCNA](/sequence-files/IGVFFI3684LCNA/), [IGVFFI6922KTRA](/sequence-files/IGVFFI6922KTRA/), [IGVFFI3752UGNK](/sequence-files/IGVFFI3752UGNK/), [IGVFFI3906VRIJ](/sequence-files/IGVFFI3906VRIJ/), [IGVFFI4901CITF](/sequence-files/IGVFFI4901CITF/), [IGVFFI3124MVTX](/sequence-files/IGVFFI3124MVTX/), [IGVFFI1013XTPI](/sequence-files/IGVFFI1013XTPI/), [IGVFFI9773KZXY](/sequence-files/IGVFFI9773KZXY/), [IGVFFI8435EMLD](/sequence-files/IGVFFI8435EMLD/), [IGVFFI4067UUSI](/sequence-files/IGVFFI4067UUSI/), [IGVFFI7387ETFG](/sequence-files/IGVFFI7387ETFG/), [IGVFFI2777XJUK](/sequence-files/IGVFFI2777XJUK/), [IGVFFI2824CBDP](/sequence-files/IGVFFI2824CBDP/), [IGVFFI1532LAJW](/sequence-files/IGVFFI1532LAJW/), [IGVFFI3841AJXD](/sequence-files/IGVFFI3841AJXD/), [IGVFFI3953CRLL](/sequence-files/IGVFFI3953CRLL/), [IGVFFI4817ARZB](/sequence-files/IGVFFI4817ARZB/), [IGVFFI0947PEWE](/sequence-files/IGVFFI0947PEWE/), [IGVFFI1375EDJF](/sequence-files/IGVFFI1375EDJF/), [IGVFFI2397OGWW](/sequence-files/IGVFFI2397OGWW/), [IGVFFI3540AZOR](/sequence-files/IGVFFI3540AZOR/), [IGVFFI6475PTNS](/sequence-files/IGVFFI6475PTNS/), [IGVFFI7651WQJW](/sequence-files/IGVFFI7651WQJW/), [IGVFFI2966KRCC](/sequence-files/IGVFFI2966KRCC/) 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/IGVFDS6286JOFD/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS6286JOFD](/auxiliary-sets/IGVFDS6286JOFD/) has sequence file(s) [IGVFFI5431QIHK](/sequence-files/IGVFFI5431QIHK/), [IGVFFI1713MUGN](/sequence-files/IGVFFI1713MUGN/), [IGVFFI0996LKFZ](/sequence-files/IGVFFI0996LKFZ/), [IGVFFI8230ERRR](/sequence-files/IGVFFI8230ERRR/), [IGVFFI0646LPXR](/sequence-files/IGVFFI0646LPXR/), [IGVFFI4114CMRD](/sequence-files/IGVFFI4114CMRD/), [IGVFFI8136VPPB](/sequence-files/IGVFFI8136VPPB/), [IGVFFI0676URKU](/sequence-files/IGVFFI0676URKU/), [IGVFFI8900YUVW](/sequence-files/IGVFFI8900YUVW/), [IGVFFI6210YESJ](/sequence-files/IGVFFI6210YESJ/), [IGVFFI0737WUQP](/sequence-files/IGVFFI0737WUQP/), [IGVFFI2588AXXW](/sequence-files/IGVFFI2588AXXW/), [IGVFFI4827WISX](/sequence-files/IGVFFI4827WISX/), [IGVFFI8230PQJJ](/sequence-files/IGVFFI8230PQJJ/), [IGVFFI0348MCPO](/sequence-files/IGVFFI0348MCPO/), [IGVFFI7174FPNE](/sequence-files/IGVFFI7174FPNE/), [IGVFFI4488UJSM](/sequence-files/IGVFFI4488UJSM/), [IGVFFI4684KBXY](/sequence-files/IGVFFI4684KBXY/), [IGVFFI0273KKME](/sequence-files/IGVFFI0273KKME/), [IGVFFI0338PYWL](/sequence-files/IGVFFI0338PYWL/), [IGVFFI5195WRZW](/sequence-files/IGVFFI5195WRZW/), [IGVFFI9722PDEX](/sequence-files/IGVFFI9722PDEX/), [IGVFFI3065KWEP](/sequence-files/IGVFFI3065KWEP/), [IGVFFI9121IGRO](/sequence-files/IGVFFI9121IGRO/), [IGVFFI3684LCNA](/sequence-files/IGVFFI3684LCNA/), [IGVFFI6922KTRA](/sequence-files/IGVFFI6922KTRA/), [IGVFFI3752UGNK](/sequence-files/IGVFFI3752UGNK/), [IGVFFI3906VRIJ](/sequence-files/IGVFFI3906VRIJ/), [IGVFFI4901CITF](/sequence-files/IGVFFI4901CITF/), [IGVFFI3124MVTX](/sequence-files/IGVFFI3124MVTX/), [IGVFFI1013XTPI](/sequence-files/IGVFFI1013XTPI/), [IGVFFI9773KZXY](/sequence-files/IGVFFI9773KZXY/), [IGVFFI8435EMLD](/sequence-files/IGVFFI8435EMLD/), [IGVFFI4067UUSI](/sequence-files/IGVFFI4067UUSI/), [IGVFFI7387ETFG](/sequence-files/IGVFFI7387ETFG/), [IGVFFI2777XJUK](/sequence-files/IGVFFI2777XJUK/), [IGVFFI2824CBDP](/sequence-files/IGVFFI2824CBDP/), [IGVFFI1532LAJW](/sequence-files/IGVFFI1532LAJW/), [IGVFFI3841AJXD](/sequence-files/IGVFFI3841AJXD/), [IGVFFI3953CRLL](/sequence-files/IGVFFI3953CRLL/), [IGVFFI4817ARZB](/sequence-files/IGVFFI4817ARZB/), [IGVFFI0947PEWE](/sequence-files/IGVFFI0947PEWE/), [IGVFFI1375EDJF](/sequence-files/IGVFFI1375EDJF/), [IGVFFI2397OGWW](/sequence-files/IGVFFI2397OGWW/), [IGVFFI3540AZOR](/sequence-files/IGVFFI3540AZOR/), [IGVFFI6475PTNS](/sequence-files/IGVFFI6475PTNS/), [IGVFFI7651WQJW](/sequence-files/IGVFFI7651WQJW/), [IGVFFI2966KRCC](/sequence-files/IGVFFI2966KRCC/) 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/IGVFDS6286JOFD/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS6286JOFD](/auxiliary-sets/IGVFDS6286JOFD/) 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/IGVFDS6286JOFD/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS6286JOFD/",
"accession": "IGVFDS6286JOFD",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-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/IGVFDS5864UGFT/",
"accession": "IGVFDS5864UGFT",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:50:07.148810+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/IGVFDS3423PSID/"
],
"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": "2023-12-20T23:06:24.757600+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3394FCPH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3394FCPH",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinD"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6982DESN/",
"accession": "IGVFDS6982DESN",
"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": "2023-12-05T22:50:46.233083+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": "bced11bd-f79f-4dbe-be46-346aaddffe0f"
}