{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4823GFCR/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4823GFCR",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinA_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 [IGVFDS4823GFCR](/measurement-sets/IGVFDS4823GFCR/) has in progress subobject auxiliary set [IGVFDS9299YWEV](/auxiliary-sets/IGVFDS9299YWEV/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS4823GFCR/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM7460SNVF](/in-vitro-systems/IGVFSM7460SNVF/) 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/IGVFSM7460SNVF/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4823GFCR](/measurement-sets/IGVFDS4823GFCR/) 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/IGVFDS4823GFCR/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS9299YWEV](/auxiliary-sets/IGVFDS9299YWEV/) has sequence file(s): [IGVFFI7494MIKK](/sequence-files/IGVFFI7494MIKK/), [IGVFFI6277XNJT](/sequence-files/IGVFFI6277XNJT/), [IGVFFI9246VBTO](/sequence-files/IGVFFI9246VBTO/), [IGVFFI2029XCPF](/sequence-files/IGVFFI2029XCPF/), [IGVFFI3482MXNL](/sequence-files/IGVFFI3482MXNL/), [IGVFFI6920MOMD](/sequence-files/IGVFFI6920MOMD/), [IGVFFI9854VTIE](/sequence-files/IGVFFI9854VTIE/), [IGVFFI7462PTDK](/sequence-files/IGVFFI7462PTDK/), [IGVFFI1507YPOH](/sequence-files/IGVFFI1507YPOH/), [IGVFFI7290QTRZ](/sequence-files/IGVFFI7290QTRZ/), [IGVFFI9576LPOQ](/sequence-files/IGVFFI9576LPOQ/), [IGVFFI3250MYEW](/sequence-files/IGVFFI3250MYEW/), [IGVFFI6203RINE](/sequence-files/IGVFFI6203RINE/), [IGVFFI0748IVBC](/sequence-files/IGVFFI0748IVBC/), [IGVFFI8913FTLL](/sequence-files/IGVFFI8913FTLL/), [IGVFFI6187OFBV](/sequence-files/IGVFFI6187OFBV/), [IGVFFI1814RIWT](/sequence-files/IGVFFI1814RIWT/), [IGVFFI2978XLFR](/sequence-files/IGVFFI2978XLFR/), [IGVFFI4624YRTJ](/sequence-files/IGVFFI4624YRTJ/), [IGVFFI5534YUBB](/sequence-files/IGVFFI5534YUBB/), [IGVFFI6829EFMN](/sequence-files/IGVFFI6829EFMN/), [IGVFFI4660BALK](/sequence-files/IGVFFI4660BALK/), [IGVFFI6580KAQX](/sequence-files/IGVFFI6580KAQX/), [IGVFFI5286KNSP](/sequence-files/IGVFFI5286KNSP/), [IGVFFI4434GJET](/sequence-files/IGVFFI4434GJET/), [IGVFFI2123RKCD](/sequence-files/IGVFFI2123RKCD/), [IGVFFI4035XOZM](/sequence-files/IGVFFI4035XOZM/), [IGVFFI6968ADID](/sequence-files/IGVFFI6968ADID/), [IGVFFI2188JIXY](/sequence-files/IGVFFI2188JIXY/), [IGVFFI9431CBDE](/sequence-files/IGVFFI9431CBDE/), [IGVFFI0509HQBW](/sequence-files/IGVFFI0509HQBW/), [IGVFFI8287CDRW](/sequence-files/IGVFFI8287CDRW/), [IGVFFI9325QTXR](/sequence-files/IGVFFI9325QTXR/), [IGVFFI1894YMEP](/sequence-files/IGVFFI1894YMEP/), [IGVFFI0997AGXW](/sequence-files/IGVFFI0997AGXW/), [IGVFFI1714XREB](/sequence-files/IGVFFI1714XREB/), [IGVFFI9066CJDM](/sequence-files/IGVFFI9066CJDM/), [IGVFFI4590EFMQ](/sequence-files/IGVFFI4590EFMQ/), [IGVFFI7617SZUX](/sequence-files/IGVFFI7617SZUX/), [IGVFFI3097SQMH](/sequence-files/IGVFFI3097SQMH/), [IGVFFI3960ZWGZ](/sequence-files/IGVFFI3960ZWGZ/), [IGVFFI6733KTID](/sequence-files/IGVFFI6733KTID/), [IGVFFI9356PWMQ](/sequence-files/IGVFFI9356PWMQ/), [IGVFFI9062HXWI](/sequence-files/IGVFFI9062HXWI/), [IGVFFI2188PISQ](/sequence-files/IGVFFI2188PISQ/), [IGVFFI9133DXTR](/sequence-files/IGVFFI9133DXTR/), [IGVFFI4905TRRM](/sequence-files/IGVFFI4905TRRM/), [IGVFFI8452QJHH](/sequence-files/IGVFFI8452QJHH/) 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/IGVFDS9299YWEV/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS9299YWEV](/auxiliary-sets/IGVFDS9299YWEV/) has sequence file(s) [IGVFFI7494MIKK](/sequence-files/IGVFFI7494MIKK/), [IGVFFI6277XNJT](/sequence-files/IGVFFI6277XNJT/), [IGVFFI9246VBTO](/sequence-files/IGVFFI9246VBTO/), [IGVFFI2029XCPF](/sequence-files/IGVFFI2029XCPF/), [IGVFFI3482MXNL](/sequence-files/IGVFFI3482MXNL/), [IGVFFI6920MOMD](/sequence-files/IGVFFI6920MOMD/), [IGVFFI9854VTIE](/sequence-files/IGVFFI9854VTIE/), [IGVFFI7462PTDK](/sequence-files/IGVFFI7462PTDK/), [IGVFFI1507YPOH](/sequence-files/IGVFFI1507YPOH/), [IGVFFI7290QTRZ](/sequence-files/IGVFFI7290QTRZ/), [IGVFFI9576LPOQ](/sequence-files/IGVFFI9576LPOQ/), [IGVFFI3250MYEW](/sequence-files/IGVFFI3250MYEW/), [IGVFFI6203RINE](/sequence-files/IGVFFI6203RINE/), [IGVFFI0748IVBC](/sequence-files/IGVFFI0748IVBC/), [IGVFFI8913FTLL](/sequence-files/IGVFFI8913FTLL/), [IGVFFI6187OFBV](/sequence-files/IGVFFI6187OFBV/), [IGVFFI1814RIWT](/sequence-files/IGVFFI1814RIWT/), [IGVFFI2978XLFR](/sequence-files/IGVFFI2978XLFR/), [IGVFFI4624YRTJ](/sequence-files/IGVFFI4624YRTJ/), [IGVFFI5534YUBB](/sequence-files/IGVFFI5534YUBB/), [IGVFFI6829EFMN](/sequence-files/IGVFFI6829EFMN/), [IGVFFI4660BALK](/sequence-files/IGVFFI4660BALK/), [IGVFFI6580KAQX](/sequence-files/IGVFFI6580KAQX/), [IGVFFI5286KNSP](/sequence-files/IGVFFI5286KNSP/), [IGVFFI4434GJET](/sequence-files/IGVFFI4434GJET/), [IGVFFI2123RKCD](/sequence-files/IGVFFI2123RKCD/), [IGVFFI4035XOZM](/sequence-files/IGVFFI4035XOZM/), [IGVFFI6968ADID](/sequence-files/IGVFFI6968ADID/), [IGVFFI2188JIXY](/sequence-files/IGVFFI2188JIXY/), [IGVFFI9431CBDE](/sequence-files/IGVFFI9431CBDE/), [IGVFFI0509HQBW](/sequence-files/IGVFFI0509HQBW/), [IGVFFI8287CDRW](/sequence-files/IGVFFI8287CDRW/), [IGVFFI9325QTXR](/sequence-files/IGVFFI9325QTXR/), [IGVFFI1894YMEP](/sequence-files/IGVFFI1894YMEP/), [IGVFFI0997AGXW](/sequence-files/IGVFFI0997AGXW/), [IGVFFI1714XREB](/sequence-files/IGVFFI1714XREB/), [IGVFFI9066CJDM](/sequence-files/IGVFFI9066CJDM/), [IGVFFI4590EFMQ](/sequence-files/IGVFFI4590EFMQ/), [IGVFFI7617SZUX](/sequence-files/IGVFFI7617SZUX/), [IGVFFI3097SQMH](/sequence-files/IGVFFI3097SQMH/), [IGVFFI3960ZWGZ](/sequence-files/IGVFFI3960ZWGZ/), [IGVFFI6733KTID](/sequence-files/IGVFFI6733KTID/), [IGVFFI9356PWMQ](/sequence-files/IGVFFI9356PWMQ/), [IGVFFI9062HXWI](/sequence-files/IGVFFI9062HXWI/), [IGVFFI2188PISQ](/sequence-files/IGVFFI2188PISQ/), [IGVFFI9133DXTR](/sequence-files/IGVFFI9133DXTR/), [IGVFFI4905TRRM](/sequence-files/IGVFFI4905TRRM/), [IGVFFI8452QJHH](/sequence-files/IGVFFI8452QJHH/) 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/IGVFDS9299YWEV/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS9299YWEV](/auxiliary-sets/IGVFDS9299YWEV/) 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/IGVFDS9299YWEV/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS9299YWEV/",
"accession": "IGVFDS9299YWEV",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinA_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": "2023-11-30T22:49:24.315429+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": "2023-12-20T23:05:36.982725+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7460SNVF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7460SNVF",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinA"
],
"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 0-25% 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": "2023-12-05T23:23:15.993255+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": "75974895-0210-49d1-8d31-8b7edc7379d4"
}