{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8633UBLT/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8633UBLT",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep3-BinA_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 [IGVFDS8633UBLT](/measurement-sets/IGVFDS8633UBLT/) has in progress subobject auxiliary set [IGVFDS6990VKUH](/auxiliary-sets/IGVFDS6990VKUH/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS8633UBLT/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM5076ZJCL](/in-vitro-systems/IGVFSM5076ZJCL/) 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/IGVFSM5076ZJCL/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS8633UBLT](/measurement-sets/IGVFDS8633UBLT/) 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/IGVFDS8633UBLT/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS6990VKUH](/auxiliary-sets/IGVFDS6990VKUH/) has sequence file(s): [IGVFFI2375PVJJ](/sequence-files/IGVFFI2375PVJJ/), [IGVFFI1626WOXC](/sequence-files/IGVFFI1626WOXC/), [IGVFFI2015DFDA](/sequence-files/IGVFFI2015DFDA/), [IGVFFI3211UXIX](/sequence-files/IGVFFI3211UXIX/), [IGVFFI1398DEIE](/sequence-files/IGVFFI1398DEIE/), [IGVFFI6201AYMN](/sequence-files/IGVFFI6201AYMN/), [IGVFFI2183MXRP](/sequence-files/IGVFFI2183MXRP/), [IGVFFI5198DBSE](/sequence-files/IGVFFI5198DBSE/), [IGVFFI6068XPKX](/sequence-files/IGVFFI6068XPKX/), [IGVFFI8583JMPK](/sequence-files/IGVFFI8583JMPK/), [IGVFFI4773MBAS](/sequence-files/IGVFFI4773MBAS/), [IGVFFI2366AXEG](/sequence-files/IGVFFI2366AXEG/), [IGVFFI1843YDGM](/sequence-files/IGVFFI1843YDGM/), [IGVFFI7616XJSA](/sequence-files/IGVFFI7616XJSA/), [IGVFFI5992DZXS](/sequence-files/IGVFFI5992DZXS/), [IGVFFI9411MDSV](/sequence-files/IGVFFI9411MDSV/), [IGVFFI3582TSPK](/sequence-files/IGVFFI3582TSPK/), [IGVFFI8419EPOK](/sequence-files/IGVFFI8419EPOK/), [IGVFFI8655RNLI](/sequence-files/IGVFFI8655RNLI/), [IGVFFI7057MPOV](/sequence-files/IGVFFI7057MPOV/), [IGVFFI3713FMXW](/sequence-files/IGVFFI3713FMXW/), [IGVFFI8186XJVM](/sequence-files/IGVFFI8186XJVM/), [IGVFFI7104GFEJ](/sequence-files/IGVFFI7104GFEJ/), [IGVFFI9530OWMF](/sequence-files/IGVFFI9530OWMF/), [IGVFFI5084JMAI](/sequence-files/IGVFFI5084JMAI/), [IGVFFI7150KRJO](/sequence-files/IGVFFI7150KRJO/), [IGVFFI9284HVJC](/sequence-files/IGVFFI9284HVJC/), [IGVFFI3867FNIV](/sequence-files/IGVFFI3867FNIV/), [IGVFFI6164WDOQ](/sequence-files/IGVFFI6164WDOQ/), [IGVFFI2857YKFQ](/sequence-files/IGVFFI2857YKFQ/), [IGVFFI0328INQX](/sequence-files/IGVFFI0328INQX/), [IGVFFI8680PWXH](/sequence-files/IGVFFI8680PWXH/), [IGVFFI3501CDRX](/sequence-files/IGVFFI3501CDRX/), [IGVFFI4499YMHI](/sequence-files/IGVFFI4499YMHI/), [IGVFFI2308KOLW](/sequence-files/IGVFFI2308KOLW/), [IGVFFI4282INDL](/sequence-files/IGVFFI4282INDL/), [IGVFFI7751NYXY](/sequence-files/IGVFFI7751NYXY/), [IGVFFI1863BJMZ](/sequence-files/IGVFFI1863BJMZ/), [IGVFFI1276VIBD](/sequence-files/IGVFFI1276VIBD/), [IGVFFI6126LJWP](/sequence-files/IGVFFI6126LJWP/), [IGVFFI7968PITB](/sequence-files/IGVFFI7968PITB/), [IGVFFI8221XJUD](/sequence-files/IGVFFI8221XJUD/), [IGVFFI8730XNIL](/sequence-files/IGVFFI8730XNIL/), [IGVFFI8223MDRM](/sequence-files/IGVFFI8223MDRM/), [IGVFFI8226VCKE](/sequence-files/IGVFFI8226VCKE/), [IGVFFI2167MPPY](/sequence-files/IGVFFI2167MPPY/), [IGVFFI6044RGSL](/sequence-files/IGVFFI6044RGSL/), [IGVFFI6129PWHH](/sequence-files/IGVFFI6129PWHH/) 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/IGVFDS6990VKUH/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS6990VKUH](/auxiliary-sets/IGVFDS6990VKUH/) has sequence file(s) [IGVFFI2375PVJJ](/sequence-files/IGVFFI2375PVJJ/), [IGVFFI1626WOXC](/sequence-files/IGVFFI1626WOXC/), [IGVFFI2015DFDA](/sequence-files/IGVFFI2015DFDA/), [IGVFFI3211UXIX](/sequence-files/IGVFFI3211UXIX/), [IGVFFI1398DEIE](/sequence-files/IGVFFI1398DEIE/), [IGVFFI6201AYMN](/sequence-files/IGVFFI6201AYMN/), [IGVFFI2183MXRP](/sequence-files/IGVFFI2183MXRP/), [IGVFFI5198DBSE](/sequence-files/IGVFFI5198DBSE/), [IGVFFI6068XPKX](/sequence-files/IGVFFI6068XPKX/), [IGVFFI8583JMPK](/sequence-files/IGVFFI8583JMPK/), [IGVFFI4773MBAS](/sequence-files/IGVFFI4773MBAS/), [IGVFFI2366AXEG](/sequence-files/IGVFFI2366AXEG/), [IGVFFI1843YDGM](/sequence-files/IGVFFI1843YDGM/), [IGVFFI7616XJSA](/sequence-files/IGVFFI7616XJSA/), [IGVFFI5992DZXS](/sequence-files/IGVFFI5992DZXS/), [IGVFFI9411MDSV](/sequence-files/IGVFFI9411MDSV/), [IGVFFI3582TSPK](/sequence-files/IGVFFI3582TSPK/), [IGVFFI8419EPOK](/sequence-files/IGVFFI8419EPOK/), [IGVFFI8655RNLI](/sequence-files/IGVFFI8655RNLI/), [IGVFFI7057MPOV](/sequence-files/IGVFFI7057MPOV/), [IGVFFI3713FMXW](/sequence-files/IGVFFI3713FMXW/), [IGVFFI8186XJVM](/sequence-files/IGVFFI8186XJVM/), [IGVFFI7104GFEJ](/sequence-files/IGVFFI7104GFEJ/), [IGVFFI9530OWMF](/sequence-files/IGVFFI9530OWMF/), [IGVFFI5084JMAI](/sequence-files/IGVFFI5084JMAI/), [IGVFFI7150KRJO](/sequence-files/IGVFFI7150KRJO/), [IGVFFI9284HVJC](/sequence-files/IGVFFI9284HVJC/), [IGVFFI3867FNIV](/sequence-files/IGVFFI3867FNIV/), [IGVFFI6164WDOQ](/sequence-files/IGVFFI6164WDOQ/), [IGVFFI2857YKFQ](/sequence-files/IGVFFI2857YKFQ/), [IGVFFI0328INQX](/sequence-files/IGVFFI0328INQX/), [IGVFFI8680PWXH](/sequence-files/IGVFFI8680PWXH/), [IGVFFI3501CDRX](/sequence-files/IGVFFI3501CDRX/), [IGVFFI4499YMHI](/sequence-files/IGVFFI4499YMHI/), [IGVFFI2308KOLW](/sequence-files/IGVFFI2308KOLW/), [IGVFFI4282INDL](/sequence-files/IGVFFI4282INDL/), [IGVFFI7751NYXY](/sequence-files/IGVFFI7751NYXY/), [IGVFFI1863BJMZ](/sequence-files/IGVFFI1863BJMZ/), [IGVFFI1276VIBD](/sequence-files/IGVFFI1276VIBD/), [IGVFFI6126LJWP](/sequence-files/IGVFFI6126LJWP/), [IGVFFI7968PITB](/sequence-files/IGVFFI7968PITB/), [IGVFFI8221XJUD](/sequence-files/IGVFFI8221XJUD/), [IGVFFI8730XNIL](/sequence-files/IGVFFI8730XNIL/), [IGVFFI8223MDRM](/sequence-files/IGVFFI8223MDRM/), [IGVFFI8226VCKE](/sequence-files/IGVFFI8226VCKE/), [IGVFFI2167MPPY](/sequence-files/IGVFFI2167MPPY/), [IGVFFI6044RGSL](/sequence-files/IGVFFI6044RGSL/), [IGVFFI6129PWHH](/sequence-files/IGVFFI6129PWHH/) 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/IGVFDS6990VKUH/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS6990VKUH](/auxiliary-sets/IGVFDS6990VKUH/) 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/IGVFDS6990VKUH/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS6990VKUH/",
"accession": "IGVFDS6990VKUH",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep3-BinA_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/IGVFDS4869FXYY/",
"accession": "IGVFDS4869FXYY",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-Jurkat-PE2_Exp2_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-12-13T08:48:13.145635+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1080XFGV/",
"accession": "IGVFDO1080XFGV",
"aliases": [
"igvf:donor_of_Jurkat"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "experimental data",
"files": [],
"input_file_set_for": [
"/analysis-sets/IGVFDS6299IJHG/"
],
"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": "2023-12-20T23:08:57.806355+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5076ZJCL/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5076ZJCL",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep3-BinA"
],
"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_0002796/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:Jurkat"
],
"status": "released",
"summary": "Jurkat",
"term_name": "Jurkat"
}
],
"status": "released",
"summary": "Jurkat cell line, male, Homo sapiens (sorting details: FACS bin for 0-25% 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": "2023-12-13T10:16:22.988866+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": "7a4a6201-26c0-4725-8fe7-637b188e91e3"
}