{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2074JWFW/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2074JWFW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinC_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 [IGVFDS2074JWFW](/measurement-sets/IGVFDS2074JWFW/) has in progress subobject auxiliary set [IGVFDS2864TOVQ](/auxiliary-sets/IGVFDS2864TOVQ/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS2074JWFW/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM9725CVMG](/in-vitro-systems/IGVFSM9725CVMG/) 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/IGVFSM9725CVMG/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2074JWFW](/measurement-sets/IGVFDS2074JWFW/) 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/IGVFDS2074JWFW/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2864TOVQ](/auxiliary-sets/IGVFDS2864TOVQ/) has sequence file(s): [IGVFFI6641EGJO](/sequence-files/IGVFFI6641EGJO/), [IGVFFI6390KMKF](/sequence-files/IGVFFI6390KMKF/), [IGVFFI3571FKNU](/sequence-files/IGVFFI3571FKNU/), [IGVFFI8365LVRA](/sequence-files/IGVFFI8365LVRA/), [IGVFFI2110CXWO](/sequence-files/IGVFFI2110CXWO/), [IGVFFI3626XNDL](/sequence-files/IGVFFI3626XNDL/), [IGVFFI3171WHRX](/sequence-files/IGVFFI3171WHRX/), [IGVFFI6756DAGQ](/sequence-files/IGVFFI6756DAGQ/), [IGVFFI6323EFQR](/sequence-files/IGVFFI6323EFQR/), [IGVFFI6421BXBI](/sequence-files/IGVFFI6421BXBI/), [IGVFFI3789NRLM](/sequence-files/IGVFFI3789NRLM/), [IGVFFI1524XVVI](/sequence-files/IGVFFI1524XVVI/), [IGVFFI2650AOWQ](/sequence-files/IGVFFI2650AOWQ/), [IGVFFI2826GLZC](/sequence-files/IGVFFI2826GLZC/), [IGVFFI1663XANF](/sequence-files/IGVFFI1663XANF/), [IGVFFI5619NNEW](/sequence-files/IGVFFI5619NNEW/), [IGVFFI1512CDIC](/sequence-files/IGVFFI1512CDIC/), [IGVFFI7162SGVY](/sequence-files/IGVFFI7162SGVY/), [IGVFFI5143RGFD](/sequence-files/IGVFFI5143RGFD/), [IGVFFI3437ZCBU](/sequence-files/IGVFFI3437ZCBU/), [IGVFFI4502VLNC](/sequence-files/IGVFFI4502VLNC/), [IGVFFI5535ICQI](/sequence-files/IGVFFI5535ICQI/), [IGVFFI7004TATT](/sequence-files/IGVFFI7004TATT/), [IGVFFI1306LCJK](/sequence-files/IGVFFI1306LCJK/), [IGVFFI1961ZHUD](/sequence-files/IGVFFI1961ZHUD/), [IGVFFI3455YCKJ](/sequence-files/IGVFFI3455YCKJ/), [IGVFFI9278LVBS](/sequence-files/IGVFFI9278LVBS/), [IGVFFI8961TOUE](/sequence-files/IGVFFI8961TOUE/), [IGVFFI2120LBCS](/sequence-files/IGVFFI2120LBCS/), [IGVFFI3671LTUT](/sequence-files/IGVFFI3671LTUT/), [IGVFFI2848IXCA](/sequence-files/IGVFFI2848IXCA/), [IGVFFI4527QMXS](/sequence-files/IGVFFI4527QMXS/), [IGVFFI4493GILB](/sequence-files/IGVFFI4493GILB/), [IGVFFI5071HYKD](/sequence-files/IGVFFI5071HYKD/), [IGVFFI7724FMWK](/sequence-files/IGVFFI7724FMWK/), [IGVFFI2277SHRL](/sequence-files/IGVFFI2277SHRL/), [IGVFFI9470PXRU](/sequence-files/IGVFFI9470PXRU/), [IGVFFI1688TLKS](/sequence-files/IGVFFI1688TLKS/), [IGVFFI0005GBXS](/sequence-files/IGVFFI0005GBXS/), [IGVFFI1238BOFW](/sequence-files/IGVFFI1238BOFW/), [IGVFFI6386AKLI](/sequence-files/IGVFFI6386AKLI/), [IGVFFI9937TZRF](/sequence-files/IGVFFI9937TZRF/), [IGVFFI5071NCAG](/sequence-files/IGVFFI5071NCAG/), [IGVFFI4052CIEZ](/sequence-files/IGVFFI4052CIEZ/), [IGVFFI4792BZCN](/sequence-files/IGVFFI4792BZCN/), [IGVFFI0018KKLV](/sequence-files/IGVFFI0018KKLV/), [IGVFFI8634LQPV](/sequence-files/IGVFFI8634LQPV/), [IGVFFI1171KOAI](/sequence-files/IGVFFI1171KOAI/) 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/IGVFDS2864TOVQ/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2864TOVQ](/auxiliary-sets/IGVFDS2864TOVQ/) has sequence file(s) [IGVFFI6641EGJO](/sequence-files/IGVFFI6641EGJO/), [IGVFFI6390KMKF](/sequence-files/IGVFFI6390KMKF/), [IGVFFI3571FKNU](/sequence-files/IGVFFI3571FKNU/), [IGVFFI8365LVRA](/sequence-files/IGVFFI8365LVRA/), [IGVFFI2110CXWO](/sequence-files/IGVFFI2110CXWO/), [IGVFFI3626XNDL](/sequence-files/IGVFFI3626XNDL/), [IGVFFI3171WHRX](/sequence-files/IGVFFI3171WHRX/), [IGVFFI6756DAGQ](/sequence-files/IGVFFI6756DAGQ/), [IGVFFI6323EFQR](/sequence-files/IGVFFI6323EFQR/), [IGVFFI6421BXBI](/sequence-files/IGVFFI6421BXBI/), [IGVFFI3789NRLM](/sequence-files/IGVFFI3789NRLM/), [IGVFFI1524XVVI](/sequence-files/IGVFFI1524XVVI/), [IGVFFI2650AOWQ](/sequence-files/IGVFFI2650AOWQ/), [IGVFFI2826GLZC](/sequence-files/IGVFFI2826GLZC/), [IGVFFI1663XANF](/sequence-files/IGVFFI1663XANF/), [IGVFFI5619NNEW](/sequence-files/IGVFFI5619NNEW/), [IGVFFI1512CDIC](/sequence-files/IGVFFI1512CDIC/), [IGVFFI7162SGVY](/sequence-files/IGVFFI7162SGVY/), [IGVFFI5143RGFD](/sequence-files/IGVFFI5143RGFD/), [IGVFFI3437ZCBU](/sequence-files/IGVFFI3437ZCBU/), [IGVFFI4502VLNC](/sequence-files/IGVFFI4502VLNC/), [IGVFFI5535ICQI](/sequence-files/IGVFFI5535ICQI/), [IGVFFI7004TATT](/sequence-files/IGVFFI7004TATT/), [IGVFFI1306LCJK](/sequence-files/IGVFFI1306LCJK/), [IGVFFI1961ZHUD](/sequence-files/IGVFFI1961ZHUD/), [IGVFFI3455YCKJ](/sequence-files/IGVFFI3455YCKJ/), [IGVFFI9278LVBS](/sequence-files/IGVFFI9278LVBS/), [IGVFFI8961TOUE](/sequence-files/IGVFFI8961TOUE/), [IGVFFI2120LBCS](/sequence-files/IGVFFI2120LBCS/), [IGVFFI3671LTUT](/sequence-files/IGVFFI3671LTUT/), [IGVFFI2848IXCA](/sequence-files/IGVFFI2848IXCA/), [IGVFFI4527QMXS](/sequence-files/IGVFFI4527QMXS/), [IGVFFI4493GILB](/sequence-files/IGVFFI4493GILB/), [IGVFFI5071HYKD](/sequence-files/IGVFFI5071HYKD/), [IGVFFI7724FMWK](/sequence-files/IGVFFI7724FMWK/), [IGVFFI2277SHRL](/sequence-files/IGVFFI2277SHRL/), [IGVFFI9470PXRU](/sequence-files/IGVFFI9470PXRU/), [IGVFFI1688TLKS](/sequence-files/IGVFFI1688TLKS/), [IGVFFI0005GBXS](/sequence-files/IGVFFI0005GBXS/), [IGVFFI1238BOFW](/sequence-files/IGVFFI1238BOFW/), [IGVFFI6386AKLI](/sequence-files/IGVFFI6386AKLI/), [IGVFFI9937TZRF](/sequence-files/IGVFFI9937TZRF/), [IGVFFI5071NCAG](/sequence-files/IGVFFI5071NCAG/), [IGVFFI4052CIEZ](/sequence-files/IGVFFI4052CIEZ/), [IGVFFI4792BZCN](/sequence-files/IGVFFI4792BZCN/), [IGVFFI0018KKLV](/sequence-files/IGVFFI0018KKLV/), [IGVFFI8634LQPV](/sequence-files/IGVFFI8634LQPV/), [IGVFFI1171KOAI](/sequence-files/IGVFFI1171KOAI/) 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/IGVFDS2864TOVQ/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS2864TOVQ](/auxiliary-sets/IGVFDS2864TOVQ/) 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/IGVFDS2864TOVQ/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS2864TOVQ/",
"accession": "IGVFDS2864TOVQ",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinC_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": "2023-11-30T22:49:16.680571+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": "2023-12-20T23:05:21.751381+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9725CVMG/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9725CVMG",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinC"
],
"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 51-75% 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": "2023-12-05T22:37:12.561708+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": "88718d19-7aa0-4ed7-8b52-8252474c0090"
}