{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7957LQTQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7957LQTQ",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-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 [IGVFDS7957LQTQ](/measurement-sets/IGVFDS7957LQTQ/) has in progress subobject auxiliary set [IGVFDS7512GSQC](/auxiliary-sets/IGVFDS7512GSQC/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS7957LQTQ/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM4346QVBF](/in-vitro-systems/IGVFSM4346QVBF/) 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/IGVFSM4346QVBF/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS7512GSQC](/auxiliary-sets/IGVFDS7512GSQC/) has sequence file(s): [IGVFFI2676SQNH](/sequence-files/IGVFFI2676SQNH/), [IGVFFI4780FERQ](/sequence-files/IGVFFI4780FERQ/), [IGVFFI1383FMEI](/sequence-files/IGVFFI1383FMEI/), [IGVFFI6432MAAU](/sequence-files/IGVFFI6432MAAU/), [IGVFFI2825HXWK](/sequence-files/IGVFFI2825HXWK/), [IGVFFI3682NHGF](/sequence-files/IGVFFI3682NHGF/), [IGVFFI5441BUOJ](/sequence-files/IGVFFI5441BUOJ/), [IGVFFI5454DRRS](/sequence-files/IGVFFI5454DRRS/), [IGVFFI2477UQSJ](/sequence-files/IGVFFI2477UQSJ/), [IGVFFI3081LWKM](/sequence-files/IGVFFI3081LWKM/), [IGVFFI6730SZUZ](/sequence-files/IGVFFI6730SZUZ/), [IGVFFI2001PIIL](/sequence-files/IGVFFI2001PIIL/), [IGVFFI8167UAGG](/sequence-files/IGVFFI8167UAGG/), [IGVFFI5250XHZV](/sequence-files/IGVFFI5250XHZV/), [IGVFFI3538BZDC](/sequence-files/IGVFFI3538BZDC/), [IGVFFI2964YVSZ](/sequence-files/IGVFFI2964YVSZ/), [IGVFFI3459RDVI](/sequence-files/IGVFFI3459RDVI/), [IGVFFI4464SXAX](/sequence-files/IGVFFI4464SXAX/), [IGVFFI5399PTVY](/sequence-files/IGVFFI5399PTVY/), [IGVFFI1736DMZU](/sequence-files/IGVFFI1736DMZU/), [IGVFFI0381NDTC](/sequence-files/IGVFFI0381NDTC/), [IGVFFI0621SJTS](/sequence-files/IGVFFI0621SJTS/), [IGVFFI4514IYSU](/sequence-files/IGVFFI4514IYSU/), [IGVFFI1692QETB](/sequence-files/IGVFFI1692QETB/), [IGVFFI1291CVRA](/sequence-files/IGVFFI1291CVRA/), [IGVFFI8016HGSP](/sequence-files/IGVFFI8016HGSP/), [IGVFFI5236MDXH](/sequence-files/IGVFFI5236MDXH/), [IGVFFI5256DTNJ](/sequence-files/IGVFFI5256DTNJ/), [IGVFFI9568UXQZ](/sequence-files/IGVFFI9568UXQZ/), [IGVFFI9985CTHV](/sequence-files/IGVFFI9985CTHV/), [IGVFFI8426MXRP](/sequence-files/IGVFFI8426MXRP/), [IGVFFI8851IIIR](/sequence-files/IGVFFI8851IIIR/), [IGVFFI7365ZWLN](/sequence-files/IGVFFI7365ZWLN/), [IGVFFI6472RNEZ](/sequence-files/IGVFFI6472RNEZ/), [IGVFFI4493DGXX](/sequence-files/IGVFFI4493DGXX/), [IGVFFI5210HAXA](/sequence-files/IGVFFI5210HAXA/), [IGVFFI6445IWYZ](/sequence-files/IGVFFI6445IWYZ/), [IGVFFI1343UKOE](/sequence-files/IGVFFI1343UKOE/), [IGVFFI6829LQBW](/sequence-files/IGVFFI6829LQBW/), [IGVFFI6525DCFK](/sequence-files/IGVFFI6525DCFK/), [IGVFFI1625ULVT](/sequence-files/IGVFFI1625ULVT/), [IGVFFI9916DGNB](/sequence-files/IGVFFI9916DGNB/), [IGVFFI1629KRVQ](/sequence-files/IGVFFI1629KRVQ/), [IGVFFI0365XTNS](/sequence-files/IGVFFI0365XTNS/), [IGVFFI8051WWDF](/sequence-files/IGVFFI8051WWDF/), [IGVFFI6813RMTV](/sequence-files/IGVFFI6813RMTV/), [IGVFFI8395UIDC](/sequence-files/IGVFFI8395UIDC/), [IGVFFI7103JDWM](/sequence-files/IGVFFI7103JDWM/) 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/IGVFDS7512GSQC/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7957LQTQ](/measurement-sets/IGVFDS7957LQTQ/) 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/IGVFDS7957LQTQ/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS7512GSQC](/auxiliary-sets/IGVFDS7512GSQC/) has sequence file(s) [IGVFFI2676SQNH](/sequence-files/IGVFFI2676SQNH/), [IGVFFI4780FERQ](/sequence-files/IGVFFI4780FERQ/), [IGVFFI1383FMEI](/sequence-files/IGVFFI1383FMEI/), [IGVFFI6432MAAU](/sequence-files/IGVFFI6432MAAU/), [IGVFFI2825HXWK](/sequence-files/IGVFFI2825HXWK/), [IGVFFI3682NHGF](/sequence-files/IGVFFI3682NHGF/), [IGVFFI5441BUOJ](/sequence-files/IGVFFI5441BUOJ/), [IGVFFI5454DRRS](/sequence-files/IGVFFI5454DRRS/), [IGVFFI2477UQSJ](/sequence-files/IGVFFI2477UQSJ/), [IGVFFI3081LWKM](/sequence-files/IGVFFI3081LWKM/), [IGVFFI6730SZUZ](/sequence-files/IGVFFI6730SZUZ/), [IGVFFI2001PIIL](/sequence-files/IGVFFI2001PIIL/), [IGVFFI8167UAGG](/sequence-files/IGVFFI8167UAGG/), [IGVFFI5250XHZV](/sequence-files/IGVFFI5250XHZV/), [IGVFFI3538BZDC](/sequence-files/IGVFFI3538BZDC/), [IGVFFI2964YVSZ](/sequence-files/IGVFFI2964YVSZ/), [IGVFFI3459RDVI](/sequence-files/IGVFFI3459RDVI/), [IGVFFI4464SXAX](/sequence-files/IGVFFI4464SXAX/), [IGVFFI5399PTVY](/sequence-files/IGVFFI5399PTVY/), [IGVFFI1736DMZU](/sequence-files/IGVFFI1736DMZU/), [IGVFFI0381NDTC](/sequence-files/IGVFFI0381NDTC/), [IGVFFI0621SJTS](/sequence-files/IGVFFI0621SJTS/), [IGVFFI4514IYSU](/sequence-files/IGVFFI4514IYSU/), [IGVFFI1692QETB](/sequence-files/IGVFFI1692QETB/), [IGVFFI1291CVRA](/sequence-files/IGVFFI1291CVRA/), [IGVFFI8016HGSP](/sequence-files/IGVFFI8016HGSP/), [IGVFFI5236MDXH](/sequence-files/IGVFFI5236MDXH/), [IGVFFI5256DTNJ](/sequence-files/IGVFFI5256DTNJ/), [IGVFFI9568UXQZ](/sequence-files/IGVFFI9568UXQZ/), [IGVFFI9985CTHV](/sequence-files/IGVFFI9985CTHV/), [IGVFFI8426MXRP](/sequence-files/IGVFFI8426MXRP/), [IGVFFI8851IIIR](/sequence-files/IGVFFI8851IIIR/), [IGVFFI7365ZWLN](/sequence-files/IGVFFI7365ZWLN/), [IGVFFI6472RNEZ](/sequence-files/IGVFFI6472RNEZ/), [IGVFFI4493DGXX](/sequence-files/IGVFFI4493DGXX/), [IGVFFI5210HAXA](/sequence-files/IGVFFI5210HAXA/), [IGVFFI6445IWYZ](/sequence-files/IGVFFI6445IWYZ/), [IGVFFI1343UKOE](/sequence-files/IGVFFI1343UKOE/), [IGVFFI6829LQBW](/sequence-files/IGVFFI6829LQBW/), [IGVFFI6525DCFK](/sequence-files/IGVFFI6525DCFK/), [IGVFFI1625ULVT](/sequence-files/IGVFFI1625ULVT/), [IGVFFI9916DGNB](/sequence-files/IGVFFI9916DGNB/), [IGVFFI1629KRVQ](/sequence-files/IGVFFI1629KRVQ/), [IGVFFI0365XTNS](/sequence-files/IGVFFI0365XTNS/), [IGVFFI8051WWDF](/sequence-files/IGVFFI8051WWDF/), [IGVFFI6813RMTV](/sequence-files/IGVFFI6813RMTV/), [IGVFFI8395UIDC](/sequence-files/IGVFFI8395UIDC/), [IGVFFI7103JDWM](/sequence-files/IGVFFI7103JDWM/) 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/IGVFDS7512GSQC/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS7512GSQC](/auxiliary-sets/IGVFDS7512GSQC/) 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/IGVFDS7512GSQC/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS7512GSQC/",
"accession": "IGVFDS7512GSQC",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-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/IGVFDS5128CXIS/",
"accession": "IGVFDS5128CXIS",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-12-13T08:01:48.783922+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/IGVFDS4359OODY/"
],
"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": "2023-12-20T23:07:58.020953+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4346QVBF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4346QVBF",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep4-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_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": "2023-12-13T09:16:01.377007+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": "05ec0cfe-be74-4644-a933-d6fb77f5f559"
}