{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7805IFYA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7805IFYA",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-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 in vitro system [IGVFSM2020MZIU](/in-vitro-systems/IGVFSM2020MZIU/) 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/IGVFSM2020MZIU/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS7805IFYA](/measurement-sets/IGVFDS7805IFYA/) has in progress subobject auxiliary set [IGVFDS3269WTSW](/auxiliary-sets/IGVFDS3269WTSW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS7805IFYA/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7805IFYA](/measurement-sets/IGVFDS7805IFYA/) 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/IGVFDS7805IFYA/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3269WTSW](/auxiliary-sets/IGVFDS3269WTSW/) has sequence file(s): [IGVFFI9770LOSW](/sequence-files/IGVFFI9770LOSW/), [IGVFFI9663GBJK](/sequence-files/IGVFFI9663GBJK/), [IGVFFI4163ZOYS](/sequence-files/IGVFFI4163ZOYS/), [IGVFFI0617AESR](/sequence-files/IGVFFI0617AESR/), [IGVFFI4481TJJI](/sequence-files/IGVFFI4481TJJI/), [IGVFFI7244HWRQ](/sequence-files/IGVFFI7244HWRQ/), [IGVFFI1737OYVO](/sequence-files/IGVFFI1737OYVO/), [IGVFFI5341YAEM](/sequence-files/IGVFFI5341YAEM/), [IGVFFI4299JEXY](/sequence-files/IGVFFI4299JEXY/), [IGVFFI8016ZOUX](/sequence-files/IGVFFI8016ZOUX/), [IGVFFI8210CJFT](/sequence-files/IGVFFI8210CJFT/), [IGVFFI2034LUWC](/sequence-files/IGVFFI2034LUWC/), [IGVFFI4822BWAB](/sequence-files/IGVFFI4822BWAB/), [IGVFFI6187DPIW](/sequence-files/IGVFFI6187DPIW/), [IGVFFI8642KJPG](/sequence-files/IGVFFI8642KJPG/), [IGVFFI4801VINU](/sequence-files/IGVFFI4801VINU/), [IGVFFI5976YOTZ](/sequence-files/IGVFFI5976YOTZ/), [IGVFFI2388ZKNG](/sequence-files/IGVFFI2388ZKNG/), [IGVFFI4736PJVJ](/sequence-files/IGVFFI4736PJVJ/), [IGVFFI9140DFZS](/sequence-files/IGVFFI9140DFZS/), [IGVFFI2173SKAU](/sequence-files/IGVFFI2173SKAU/), [IGVFFI8690EEQL](/sequence-files/IGVFFI8690EEQL/), [IGVFFI4662JLUR](/sequence-files/IGVFFI4662JLUR/), [IGVFFI0498HDGM](/sequence-files/IGVFFI0498HDGM/), [IGVFFI2823EUIF](/sequence-files/IGVFFI2823EUIF/), [IGVFFI6229GGKZ](/sequence-files/IGVFFI6229GGKZ/), [IGVFFI5941XHOH](/sequence-files/IGVFFI5941XHOH/), [IGVFFI7908KEPW](/sequence-files/IGVFFI7908KEPW/), [IGVFFI0555DKSM](/sequence-files/IGVFFI0555DKSM/), [IGVFFI3909WMDL](/sequence-files/IGVFFI3909WMDL/), [IGVFFI7683BUAS](/sequence-files/IGVFFI7683BUAS/), [IGVFFI6020LABT](/sequence-files/IGVFFI6020LABT/), [IGVFFI3521YTED](/sequence-files/IGVFFI3521YTED/), [IGVFFI8564JFCX](/sequence-files/IGVFFI8564JFCX/), [IGVFFI0202HSDH](/sequence-files/IGVFFI0202HSDH/), [IGVFFI8533PWYY](/sequence-files/IGVFFI8533PWYY/), [IGVFFI2892TYRD](/sequence-files/IGVFFI2892TYRD/), [IGVFFI1441SVRB](/sequence-files/IGVFFI1441SVRB/), [IGVFFI4784RHYA](/sequence-files/IGVFFI4784RHYA/), [IGVFFI3102GULY](/sequence-files/IGVFFI3102GULY/), [IGVFFI1469XEEH](/sequence-files/IGVFFI1469XEEH/), [IGVFFI4516NTPX](/sequence-files/IGVFFI4516NTPX/), [IGVFFI6661EKTM](/sequence-files/IGVFFI6661EKTM/), [IGVFFI9825YNUM](/sequence-files/IGVFFI9825YNUM/), [IGVFFI8926KANW](/sequence-files/IGVFFI8926KANW/), [IGVFFI8527CXRF](/sequence-files/IGVFFI8527CXRF/), [IGVFFI3970YDJI](/sequence-files/IGVFFI3970YDJI/), [IGVFFI3366RDDP](/sequence-files/IGVFFI3366RDDP/) 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/IGVFDS3269WTSW/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS3269WTSW](/auxiliary-sets/IGVFDS3269WTSW/) has sequence file(s) [IGVFFI9770LOSW](/sequence-files/IGVFFI9770LOSW/), [IGVFFI9663GBJK](/sequence-files/IGVFFI9663GBJK/), [IGVFFI4163ZOYS](/sequence-files/IGVFFI4163ZOYS/), [IGVFFI0617AESR](/sequence-files/IGVFFI0617AESR/), [IGVFFI4481TJJI](/sequence-files/IGVFFI4481TJJI/), [IGVFFI7244HWRQ](/sequence-files/IGVFFI7244HWRQ/), [IGVFFI1737OYVO](/sequence-files/IGVFFI1737OYVO/), [IGVFFI5341YAEM](/sequence-files/IGVFFI5341YAEM/), [IGVFFI4299JEXY](/sequence-files/IGVFFI4299JEXY/), [IGVFFI8016ZOUX](/sequence-files/IGVFFI8016ZOUX/), [IGVFFI8210CJFT](/sequence-files/IGVFFI8210CJFT/), [IGVFFI2034LUWC](/sequence-files/IGVFFI2034LUWC/), [IGVFFI4822BWAB](/sequence-files/IGVFFI4822BWAB/), [IGVFFI6187DPIW](/sequence-files/IGVFFI6187DPIW/), [IGVFFI8642KJPG](/sequence-files/IGVFFI8642KJPG/), [IGVFFI4801VINU](/sequence-files/IGVFFI4801VINU/), [IGVFFI5976YOTZ](/sequence-files/IGVFFI5976YOTZ/), [IGVFFI2388ZKNG](/sequence-files/IGVFFI2388ZKNG/), [IGVFFI4736PJVJ](/sequence-files/IGVFFI4736PJVJ/), [IGVFFI9140DFZS](/sequence-files/IGVFFI9140DFZS/), [IGVFFI2173SKAU](/sequence-files/IGVFFI2173SKAU/), [IGVFFI8690EEQL](/sequence-files/IGVFFI8690EEQL/), [IGVFFI4662JLUR](/sequence-files/IGVFFI4662JLUR/), [IGVFFI0498HDGM](/sequence-files/IGVFFI0498HDGM/), [IGVFFI2823EUIF](/sequence-files/IGVFFI2823EUIF/), [IGVFFI6229GGKZ](/sequence-files/IGVFFI6229GGKZ/), [IGVFFI5941XHOH](/sequence-files/IGVFFI5941XHOH/), [IGVFFI7908KEPW](/sequence-files/IGVFFI7908KEPW/), [IGVFFI0555DKSM](/sequence-files/IGVFFI0555DKSM/), [IGVFFI3909WMDL](/sequence-files/IGVFFI3909WMDL/), [IGVFFI7683BUAS](/sequence-files/IGVFFI7683BUAS/), [IGVFFI6020LABT](/sequence-files/IGVFFI6020LABT/), [IGVFFI3521YTED](/sequence-files/IGVFFI3521YTED/), [IGVFFI8564JFCX](/sequence-files/IGVFFI8564JFCX/), [IGVFFI0202HSDH](/sequence-files/IGVFFI0202HSDH/), [IGVFFI8533PWYY](/sequence-files/IGVFFI8533PWYY/), [IGVFFI2892TYRD](/sequence-files/IGVFFI2892TYRD/), [IGVFFI1441SVRB](/sequence-files/IGVFFI1441SVRB/), [IGVFFI4784RHYA](/sequence-files/IGVFFI4784RHYA/), [IGVFFI3102GULY](/sequence-files/IGVFFI3102GULY/), [IGVFFI1469XEEH](/sequence-files/IGVFFI1469XEEH/), [IGVFFI4516NTPX](/sequence-files/IGVFFI4516NTPX/), [IGVFFI6661EKTM](/sequence-files/IGVFFI6661EKTM/), [IGVFFI9825YNUM](/sequence-files/IGVFFI9825YNUM/), [IGVFFI8926KANW](/sequence-files/IGVFFI8926KANW/), [IGVFFI8527CXRF](/sequence-files/IGVFFI8527CXRF/), [IGVFFI3970YDJI](/sequence-files/IGVFFI3970YDJI/), [IGVFFI3366RDDP](/sequence-files/IGVFFI3366RDDP/) 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/IGVFDS3269WTSW/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS3269WTSW](/auxiliary-sets/IGVFDS3269WTSW/) 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/IGVFDS3269WTSW/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS3269WTSW/",
"accession": "IGVFDS3269WTSW",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-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": "2023-12-13T08:01:39.316121+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": "2023-12-20T23:07:36.799999+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2020MZIU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2020MZIU",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-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": "2023-12-13T08:25:41.912459+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": "266d20d6-b0a0-411c-bf6c-4d4a1d709263"
}