{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5477WNYP/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5477WNYP",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-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 [IGVFDS5477WNYP](/measurement-sets/IGVFDS5477WNYP/) has in progress subobject auxiliary set [IGVFDS3190HKSW](/auxiliary-sets/IGVFDS3190HKSW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS5477WNYP/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM9885ZFLQ](/in-vitro-systems/IGVFSM9885ZFLQ/) 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/IGVFSM9885ZFLQ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5477WNYP](/measurement-sets/IGVFDS5477WNYP/) 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/IGVFDS5477WNYP/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3190HKSW](/auxiliary-sets/IGVFDS3190HKSW/) has sequence file(s): [IGVFFI9516NNFX](/sequence-files/IGVFFI9516NNFX/), [IGVFFI1792RKRX](/sequence-files/IGVFFI1792RKRX/), [IGVFFI2393OTSX](/sequence-files/IGVFFI2393OTSX/), [IGVFFI8003TTWY](/sequence-files/IGVFFI8003TTWY/), [IGVFFI5848YMAZ](/sequence-files/IGVFFI5848YMAZ/), [IGVFFI4151NBWZ](/sequence-files/IGVFFI4151NBWZ/), [IGVFFI5390HCVI](/sequence-files/IGVFFI5390HCVI/), [IGVFFI6736ZEKX](/sequence-files/IGVFFI6736ZEKX/), [IGVFFI4560NNFM](/sequence-files/IGVFFI4560NNFM/), [IGVFFI0991WDRN](/sequence-files/IGVFFI0991WDRN/), [IGVFFI1281VXNX](/sequence-files/IGVFFI1281VXNX/), [IGVFFI3585OFZJ](/sequence-files/IGVFFI3585OFZJ/), [IGVFFI1956RNGN](/sequence-files/IGVFFI1956RNGN/), [IGVFFI4255CFZV](/sequence-files/IGVFFI4255CFZV/), [IGVFFI0374IWLU](/sequence-files/IGVFFI0374IWLU/), [IGVFFI6927GQDY](/sequence-files/IGVFFI6927GQDY/), [IGVFFI0648GPZW](/sequence-files/IGVFFI0648GPZW/), [IGVFFI5309KPDI](/sequence-files/IGVFFI5309KPDI/), [IGVFFI9512FNAC](/sequence-files/IGVFFI9512FNAC/), [IGVFFI5628XVFI](/sequence-files/IGVFFI5628XVFI/), [IGVFFI5144QHLR](/sequence-files/IGVFFI5144QHLR/), [IGVFFI5171BCDJ](/sequence-files/IGVFFI5171BCDJ/), [IGVFFI9099SLBG](/sequence-files/IGVFFI9099SLBG/), [IGVFFI2797ANPA](/sequence-files/IGVFFI2797ANPA/), [IGVFFI2110KAHF](/sequence-files/IGVFFI2110KAHF/), [IGVFFI8551UDTB](/sequence-files/IGVFFI8551UDTB/), [IGVFFI7223VMRP](/sequence-files/IGVFFI7223VMRP/), [IGVFFI7910CVXJ](/sequence-files/IGVFFI7910CVXJ/), [IGVFFI8539GMBL](/sequence-files/IGVFFI8539GMBL/), [IGVFFI8177EEPG](/sequence-files/IGVFFI8177EEPG/), [IGVFFI1178XOXU](/sequence-files/IGVFFI1178XOXU/), [IGVFFI3566YLHM](/sequence-files/IGVFFI3566YLHM/), [IGVFFI2054TDYJ](/sequence-files/IGVFFI2054TDYJ/), [IGVFFI3264LXAW](/sequence-files/IGVFFI3264LXAW/), [IGVFFI1912LVJT](/sequence-files/IGVFFI1912LVJT/), [IGVFFI6169EWXA](/sequence-files/IGVFFI6169EWXA/), [IGVFFI5949EOUJ](/sequence-files/IGVFFI5949EOUJ/), [IGVFFI5800FGLP](/sequence-files/IGVFFI5800FGLP/), [IGVFFI5785QLPT](/sequence-files/IGVFFI5785QLPT/), [IGVFFI5610EVMF](/sequence-files/IGVFFI5610EVMF/), [IGVFFI3940WJXI](/sequence-files/IGVFFI3940WJXI/), [IGVFFI6487NWKX](/sequence-files/IGVFFI6487NWKX/), [IGVFFI0042NSBU](/sequence-files/IGVFFI0042NSBU/), [IGVFFI2605DQIM](/sequence-files/IGVFFI2605DQIM/), [IGVFFI9861XHPY](/sequence-files/IGVFFI9861XHPY/), [IGVFFI7883JRKY](/sequence-files/IGVFFI7883JRKY/), [IGVFFI3187QDMT](/sequence-files/IGVFFI3187QDMT/), [IGVFFI9665RFUR](/sequence-files/IGVFFI9665RFUR/) 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/IGVFDS3190HKSW/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS3190HKSW](/auxiliary-sets/IGVFDS3190HKSW/) has sequence file(s) [IGVFFI9516NNFX](/sequence-files/IGVFFI9516NNFX/), [IGVFFI1792RKRX](/sequence-files/IGVFFI1792RKRX/), [IGVFFI2393OTSX](/sequence-files/IGVFFI2393OTSX/), [IGVFFI8003TTWY](/sequence-files/IGVFFI8003TTWY/), [IGVFFI5848YMAZ](/sequence-files/IGVFFI5848YMAZ/), [IGVFFI4151NBWZ](/sequence-files/IGVFFI4151NBWZ/), [IGVFFI5390HCVI](/sequence-files/IGVFFI5390HCVI/), [IGVFFI6736ZEKX](/sequence-files/IGVFFI6736ZEKX/), [IGVFFI4560NNFM](/sequence-files/IGVFFI4560NNFM/), [IGVFFI0991WDRN](/sequence-files/IGVFFI0991WDRN/), [IGVFFI1281VXNX](/sequence-files/IGVFFI1281VXNX/), [IGVFFI3585OFZJ](/sequence-files/IGVFFI3585OFZJ/), [IGVFFI1956RNGN](/sequence-files/IGVFFI1956RNGN/), [IGVFFI4255CFZV](/sequence-files/IGVFFI4255CFZV/), [IGVFFI0374IWLU](/sequence-files/IGVFFI0374IWLU/), [IGVFFI6927GQDY](/sequence-files/IGVFFI6927GQDY/), [IGVFFI0648GPZW](/sequence-files/IGVFFI0648GPZW/), [IGVFFI5309KPDI](/sequence-files/IGVFFI5309KPDI/), [IGVFFI9512FNAC](/sequence-files/IGVFFI9512FNAC/), [IGVFFI5628XVFI](/sequence-files/IGVFFI5628XVFI/), [IGVFFI5144QHLR](/sequence-files/IGVFFI5144QHLR/), [IGVFFI5171BCDJ](/sequence-files/IGVFFI5171BCDJ/), [IGVFFI9099SLBG](/sequence-files/IGVFFI9099SLBG/), [IGVFFI2797ANPA](/sequence-files/IGVFFI2797ANPA/), [IGVFFI2110KAHF](/sequence-files/IGVFFI2110KAHF/), [IGVFFI8551UDTB](/sequence-files/IGVFFI8551UDTB/), [IGVFFI7223VMRP](/sequence-files/IGVFFI7223VMRP/), [IGVFFI7910CVXJ](/sequence-files/IGVFFI7910CVXJ/), [IGVFFI8539GMBL](/sequence-files/IGVFFI8539GMBL/), [IGVFFI8177EEPG](/sequence-files/IGVFFI8177EEPG/), [IGVFFI1178XOXU](/sequence-files/IGVFFI1178XOXU/), [IGVFFI3566YLHM](/sequence-files/IGVFFI3566YLHM/), [IGVFFI2054TDYJ](/sequence-files/IGVFFI2054TDYJ/), [IGVFFI3264LXAW](/sequence-files/IGVFFI3264LXAW/), [IGVFFI1912LVJT](/sequence-files/IGVFFI1912LVJT/), [IGVFFI6169EWXA](/sequence-files/IGVFFI6169EWXA/), [IGVFFI5949EOUJ](/sequence-files/IGVFFI5949EOUJ/), [IGVFFI5800FGLP](/sequence-files/IGVFFI5800FGLP/), [IGVFFI5785QLPT](/sequence-files/IGVFFI5785QLPT/), [IGVFFI5610EVMF](/sequence-files/IGVFFI5610EVMF/), [IGVFFI3940WJXI](/sequence-files/IGVFFI3940WJXI/), [IGVFFI6487NWKX](/sequence-files/IGVFFI6487NWKX/), [IGVFFI0042NSBU](/sequence-files/IGVFFI0042NSBU/), [IGVFFI2605DQIM](/sequence-files/IGVFFI2605DQIM/), [IGVFFI9861XHPY](/sequence-files/IGVFFI9861XHPY/), [IGVFFI7883JRKY](/sequence-files/IGVFFI7883JRKY/), [IGVFFI3187QDMT](/sequence-files/IGVFFI3187QDMT/), [IGVFFI9665RFUR](/sequence-files/IGVFFI9665RFUR/) 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/IGVFDS3190HKSW/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS3190HKSW](/auxiliary-sets/IGVFDS3190HKSW/) 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/IGVFDS3190HKSW/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS3190HKSW/",
"accession": "IGVFDS3190HKSW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-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/IGVFDS4989HPTW/",
"accession": "IGVFDS4989HPTW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:49:01.572913+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": "2023-12-20T23:05:56.203495+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9885ZFLQ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9885ZFLQ",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-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": "20",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T20:37:59.287859+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": "e015db4d-ce0a-439f-a221-9ad813fb9975"
}