{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9179GDAL/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9179GDAL",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-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 [IGVFDS9179GDAL](/measurement-sets/IGVFDS9179GDAL/) has in progress subobject auxiliary set [IGVFDS5738OPBQ](/auxiliary-sets/IGVFDS5738OPBQ/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS9179GDAL/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM5444NCSW](/in-vitro-systems/IGVFSM5444NCSW/) 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/IGVFSM5444NCSW/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS9179GDAL](/measurement-sets/IGVFDS9179GDAL/) 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/IGVFDS9179GDAL/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS5738OPBQ](/auxiliary-sets/IGVFDS5738OPBQ/) has sequence file(s): [IGVFFI7922HVZG](/sequence-files/IGVFFI7922HVZG/), [IGVFFI7074DZYZ](/sequence-files/IGVFFI7074DZYZ/), [IGVFFI3000KQBI](/sequence-files/IGVFFI3000KQBI/), [IGVFFI7442VHHW](/sequence-files/IGVFFI7442VHHW/), [IGVFFI5517GAHE](/sequence-files/IGVFFI5517GAHE/), [IGVFFI6261PITM](/sequence-files/IGVFFI6261PITM/), [IGVFFI0884RFXL](/sequence-files/IGVFFI0884RFXL/), [IGVFFI5128QWQL](/sequence-files/IGVFFI5128QWQL/), [IGVFFI6126VHGM](/sequence-files/IGVFFI6126VHGM/), [IGVFFI2244BTOF](/sequence-files/IGVFFI2244BTOF/), [IGVFFI9558VTNV](/sequence-files/IGVFFI9558VTNV/), [IGVFFI1217KOJK](/sequence-files/IGVFFI1217KOJK/), [IGVFFI4898EWIM](/sequence-files/IGVFFI4898EWIM/), [IGVFFI8371NEKS](/sequence-files/IGVFFI8371NEKS/), [IGVFFI3159AYZU](/sequence-files/IGVFFI3159AYZU/), [IGVFFI4582HLXI](/sequence-files/IGVFFI4582HLXI/), [IGVFFI4103AXFE](/sequence-files/IGVFFI4103AXFE/), [IGVFFI7389AGVT](/sequence-files/IGVFFI7389AGVT/), [IGVFFI5915MEHI](/sequence-files/IGVFFI5915MEHI/), [IGVFFI7361YJHD](/sequence-files/IGVFFI7361YJHD/), [IGVFFI8924MRHN](/sequence-files/IGVFFI8924MRHN/), [IGVFFI3072WPSN](/sequence-files/IGVFFI3072WPSN/), [IGVFFI5385MUIK](/sequence-files/IGVFFI5385MUIK/), [IGVFFI0294QFIC](/sequence-files/IGVFFI0294QFIC/), [IGVFFI9882GMSE](/sequence-files/IGVFFI9882GMSE/), [IGVFFI7576FKWP](/sequence-files/IGVFFI7576FKWP/), [IGVFFI9087XVLR](/sequence-files/IGVFFI9087XVLR/), [IGVFFI1975JPXT](/sequence-files/IGVFFI1975JPXT/), [IGVFFI3271WXET](/sequence-files/IGVFFI3271WXET/), [IGVFFI5065XJWK](/sequence-files/IGVFFI5065XJWK/), [IGVFFI2623NSIA](/sequence-files/IGVFFI2623NSIA/), [IGVFFI6559LLBI](/sequence-files/IGVFFI6559LLBI/), [IGVFFI9236XGTC](/sequence-files/IGVFFI9236XGTC/), [IGVFFI3430BOHP](/sequence-files/IGVFFI3430BOHP/), [IGVFFI6599JKLJ](/sequence-files/IGVFFI6599JKLJ/), [IGVFFI9960ZXAA](/sequence-files/IGVFFI9960ZXAA/), [IGVFFI1171POCR](/sequence-files/IGVFFI1171POCR/), [IGVFFI6704IIUL](/sequence-files/IGVFFI6704IIUL/), [IGVFFI4951SNII](/sequence-files/IGVFFI4951SNII/), [IGVFFI4698YWHD](/sequence-files/IGVFFI4698YWHD/), [IGVFFI4764CXHK](/sequence-files/IGVFFI4764CXHK/), [IGVFFI0980IGCD](/sequence-files/IGVFFI0980IGCD/), [IGVFFI4358DKGC](/sequence-files/IGVFFI4358DKGC/), [IGVFFI0858VWQU](/sequence-files/IGVFFI0858VWQU/), [IGVFFI7673OKXZ](/sequence-files/IGVFFI7673OKXZ/), [IGVFFI7876NPNI](/sequence-files/IGVFFI7876NPNI/), [IGVFFI5357QMIU](/sequence-files/IGVFFI5357QMIU/), [IGVFFI3636UOEP](/sequence-files/IGVFFI3636UOEP/) 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/IGVFDS5738OPBQ/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS5738OPBQ](/auxiliary-sets/IGVFDS5738OPBQ/) has sequence file(s) [IGVFFI7922HVZG](/sequence-files/IGVFFI7922HVZG/), [IGVFFI7074DZYZ](/sequence-files/IGVFFI7074DZYZ/), [IGVFFI3000KQBI](/sequence-files/IGVFFI3000KQBI/), [IGVFFI7442VHHW](/sequence-files/IGVFFI7442VHHW/), [IGVFFI5517GAHE](/sequence-files/IGVFFI5517GAHE/), [IGVFFI6261PITM](/sequence-files/IGVFFI6261PITM/), [IGVFFI0884RFXL](/sequence-files/IGVFFI0884RFXL/), [IGVFFI5128QWQL](/sequence-files/IGVFFI5128QWQL/), [IGVFFI6126VHGM](/sequence-files/IGVFFI6126VHGM/), [IGVFFI2244BTOF](/sequence-files/IGVFFI2244BTOF/), [IGVFFI9558VTNV](/sequence-files/IGVFFI9558VTNV/), [IGVFFI1217KOJK](/sequence-files/IGVFFI1217KOJK/), [IGVFFI4898EWIM](/sequence-files/IGVFFI4898EWIM/), [IGVFFI8371NEKS](/sequence-files/IGVFFI8371NEKS/), [IGVFFI3159AYZU](/sequence-files/IGVFFI3159AYZU/), [IGVFFI4582HLXI](/sequence-files/IGVFFI4582HLXI/), [IGVFFI4103AXFE](/sequence-files/IGVFFI4103AXFE/), [IGVFFI7389AGVT](/sequence-files/IGVFFI7389AGVT/), [IGVFFI5915MEHI](/sequence-files/IGVFFI5915MEHI/), [IGVFFI7361YJHD](/sequence-files/IGVFFI7361YJHD/), [IGVFFI8924MRHN](/sequence-files/IGVFFI8924MRHN/), [IGVFFI3072WPSN](/sequence-files/IGVFFI3072WPSN/), [IGVFFI5385MUIK](/sequence-files/IGVFFI5385MUIK/), [IGVFFI0294QFIC](/sequence-files/IGVFFI0294QFIC/), [IGVFFI9882GMSE](/sequence-files/IGVFFI9882GMSE/), [IGVFFI7576FKWP](/sequence-files/IGVFFI7576FKWP/), [IGVFFI9087XVLR](/sequence-files/IGVFFI9087XVLR/), [IGVFFI1975JPXT](/sequence-files/IGVFFI1975JPXT/), [IGVFFI3271WXET](/sequence-files/IGVFFI3271WXET/), [IGVFFI5065XJWK](/sequence-files/IGVFFI5065XJWK/), [IGVFFI2623NSIA](/sequence-files/IGVFFI2623NSIA/), [IGVFFI6559LLBI](/sequence-files/IGVFFI6559LLBI/), [IGVFFI9236XGTC](/sequence-files/IGVFFI9236XGTC/), [IGVFFI3430BOHP](/sequence-files/IGVFFI3430BOHP/), [IGVFFI6599JKLJ](/sequence-files/IGVFFI6599JKLJ/), [IGVFFI9960ZXAA](/sequence-files/IGVFFI9960ZXAA/), [IGVFFI1171POCR](/sequence-files/IGVFFI1171POCR/), [IGVFFI6704IIUL](/sequence-files/IGVFFI6704IIUL/), [IGVFFI4951SNII](/sequence-files/IGVFFI4951SNII/), [IGVFFI4698YWHD](/sequence-files/IGVFFI4698YWHD/), [IGVFFI4764CXHK](/sequence-files/IGVFFI4764CXHK/), [IGVFFI0980IGCD](/sequence-files/IGVFFI0980IGCD/), [IGVFFI4358DKGC](/sequence-files/IGVFFI4358DKGC/), [IGVFFI0858VWQU](/sequence-files/IGVFFI0858VWQU/), [IGVFFI7673OKXZ](/sequence-files/IGVFFI7673OKXZ/), [IGVFFI7876NPNI](/sequence-files/IGVFFI7876NPNI/), [IGVFFI5357QMIU](/sequence-files/IGVFFI5357QMIU/), [IGVFFI3636UOEP](/sequence-files/IGVFFI3636UOEP/) 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/IGVFDS5738OPBQ/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS5738OPBQ](/auxiliary-sets/IGVFDS5738OPBQ/) 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/IGVFDS5738OPBQ/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS5738OPBQ/",
"accession": "IGVFDS5738OPBQ",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-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": "2023-11-30T22:49:07.499923+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": "2023-12-20T23:07:04.445437+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5444NCSW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5444NCSW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-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": "2023-12-05T21:09:01.360375+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": "631d271c-f17e-4e5b-ae29-e9723134ac13"
}