{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0934SYRQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0934SYRQ",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep1-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 [IGVFDS0934SYRQ](/measurement-sets/IGVFDS0934SYRQ/) has in progress subobject auxiliary set [IGVFDS0548QQSX](/auxiliary-sets/IGVFDS0548QQSX/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0934SYRQ/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM1176SLYJ](/in-vitro-systems/IGVFSM1176SLYJ/) 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/IGVFSM1176SLYJ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0934SYRQ](/measurement-sets/IGVFDS0934SYRQ/) 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/IGVFDS0934SYRQ/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS0548QQSX](/auxiliary-sets/IGVFDS0548QQSX/) has sequence file(s): [IGVFFI4823HGER](/sequence-files/IGVFFI4823HGER/), [IGVFFI9533KEOA](/sequence-files/IGVFFI9533KEOA/), [IGVFFI9883GWFX](/sequence-files/IGVFFI9883GWFX/), [IGVFFI0170IIJR](/sequence-files/IGVFFI0170IIJR/), [IGVFFI2143FXJB](/sequence-files/IGVFFI2143FXJB/), [IGVFFI5003UCQS](/sequence-files/IGVFFI5003UCQS/), [IGVFFI0076FIBX](/sequence-files/IGVFFI0076FIBX/), [IGVFFI9145JWRO](/sequence-files/IGVFFI9145JWRO/), [IGVFFI0100YQYA](/sequence-files/IGVFFI0100YQYA/), [IGVFFI2679KRUC](/sequence-files/IGVFFI2679KRUC/), [IGVFFI6256ANPJ](/sequence-files/IGVFFI6256ANPJ/), [IGVFFI0574EAGF](/sequence-files/IGVFFI0574EAGF/), [IGVFFI6739SQTK](/sequence-files/IGVFFI6739SQTK/), [IGVFFI9502TRDQ](/sequence-files/IGVFFI9502TRDQ/), [IGVFFI8544WVQG](/sequence-files/IGVFFI8544WVQG/), [IGVFFI1044WEIN](/sequence-files/IGVFFI1044WEIN/), [IGVFFI6158MJIN](/sequence-files/IGVFFI6158MJIN/), [IGVFFI6943HUNA](/sequence-files/IGVFFI6943HUNA/), [IGVFFI3563PTOE](/sequence-files/IGVFFI3563PTOE/), [IGVFFI9558AYHA](/sequence-files/IGVFFI9558AYHA/), [IGVFFI7100QPVK](/sequence-files/IGVFFI7100QPVK/), [IGVFFI1929ZUTI](/sequence-files/IGVFFI1929ZUTI/), [IGVFFI7367KTLU](/sequence-files/IGVFFI7367KTLU/), [IGVFFI0286TBHI](/sequence-files/IGVFFI0286TBHI/), [IGVFFI2557NBLU](/sequence-files/IGVFFI2557NBLU/), [IGVFFI0791CPNC](/sequence-files/IGVFFI0791CPNC/), [IGVFFI9311LLRP](/sequence-files/IGVFFI9311LLRP/), [IGVFFI3723KXEY](/sequence-files/IGVFFI3723KXEY/), [IGVFFI0315TLGN](/sequence-files/IGVFFI0315TLGN/), [IGVFFI2762JLDW](/sequence-files/IGVFFI2762JLDW/), [IGVFFI3903MZBT](/sequence-files/IGVFFI3903MZBT/), [IGVFFI4454MJUH](/sequence-files/IGVFFI4454MJUH/), [IGVFFI0860GIXW](/sequence-files/IGVFFI0860GIXW/), [IGVFFI9464KGND](/sequence-files/IGVFFI9464KGND/), [IGVFFI3113CFJM](/sequence-files/IGVFFI3113CFJM/), [IGVFFI4508NSLN](/sequence-files/IGVFFI4508NSLN/), [IGVFFI9105DOIH](/sequence-files/IGVFFI9105DOIH/), [IGVFFI9452RFBC](/sequence-files/IGVFFI9452RFBC/), [IGVFFI3098AJAP](/sequence-files/IGVFFI3098AJAP/), [IGVFFI5037ULUU](/sequence-files/IGVFFI5037ULUU/), [IGVFFI8126JGXQ](/sequence-files/IGVFFI8126JGXQ/), [IGVFFI4597JJEN](/sequence-files/IGVFFI4597JJEN/), [IGVFFI8650UVHT](/sequence-files/IGVFFI8650UVHT/), [IGVFFI6755EXPU](/sequence-files/IGVFFI6755EXPU/), [IGVFFI5287VSRE](/sequence-files/IGVFFI5287VSRE/), [IGVFFI8577IGPG](/sequence-files/IGVFFI8577IGPG/), [IGVFFI2032BGYI](/sequence-files/IGVFFI2032BGYI/), [IGVFFI4558IXGW](/sequence-files/IGVFFI4558IXGW/) 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/IGVFDS0548QQSX/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS0548QQSX](/auxiliary-sets/IGVFDS0548QQSX/) has sequence file(s) [IGVFFI4823HGER](/sequence-files/IGVFFI4823HGER/), [IGVFFI9533KEOA](/sequence-files/IGVFFI9533KEOA/), [IGVFFI9883GWFX](/sequence-files/IGVFFI9883GWFX/), [IGVFFI0170IIJR](/sequence-files/IGVFFI0170IIJR/), [IGVFFI2143FXJB](/sequence-files/IGVFFI2143FXJB/), [IGVFFI5003UCQS](/sequence-files/IGVFFI5003UCQS/), [IGVFFI0076FIBX](/sequence-files/IGVFFI0076FIBX/), [IGVFFI9145JWRO](/sequence-files/IGVFFI9145JWRO/), [IGVFFI0100YQYA](/sequence-files/IGVFFI0100YQYA/), [IGVFFI2679KRUC](/sequence-files/IGVFFI2679KRUC/), [IGVFFI6256ANPJ](/sequence-files/IGVFFI6256ANPJ/), [IGVFFI0574EAGF](/sequence-files/IGVFFI0574EAGF/), [IGVFFI6739SQTK](/sequence-files/IGVFFI6739SQTK/), [IGVFFI9502TRDQ](/sequence-files/IGVFFI9502TRDQ/), [IGVFFI8544WVQG](/sequence-files/IGVFFI8544WVQG/), [IGVFFI1044WEIN](/sequence-files/IGVFFI1044WEIN/), [IGVFFI6158MJIN](/sequence-files/IGVFFI6158MJIN/), [IGVFFI6943HUNA](/sequence-files/IGVFFI6943HUNA/), [IGVFFI3563PTOE](/sequence-files/IGVFFI3563PTOE/), [IGVFFI9558AYHA](/sequence-files/IGVFFI9558AYHA/), [IGVFFI7100QPVK](/sequence-files/IGVFFI7100QPVK/), [IGVFFI1929ZUTI](/sequence-files/IGVFFI1929ZUTI/), [IGVFFI7367KTLU](/sequence-files/IGVFFI7367KTLU/), [IGVFFI0286TBHI](/sequence-files/IGVFFI0286TBHI/), [IGVFFI2557NBLU](/sequence-files/IGVFFI2557NBLU/), [IGVFFI0791CPNC](/sequence-files/IGVFFI0791CPNC/), [IGVFFI9311LLRP](/sequence-files/IGVFFI9311LLRP/), [IGVFFI3723KXEY](/sequence-files/IGVFFI3723KXEY/), [IGVFFI0315TLGN](/sequence-files/IGVFFI0315TLGN/), [IGVFFI2762JLDW](/sequence-files/IGVFFI2762JLDW/), [IGVFFI3903MZBT](/sequence-files/IGVFFI3903MZBT/), [IGVFFI4454MJUH](/sequence-files/IGVFFI4454MJUH/), [IGVFFI0860GIXW](/sequence-files/IGVFFI0860GIXW/), [IGVFFI9464KGND](/sequence-files/IGVFFI9464KGND/), [IGVFFI3113CFJM](/sequence-files/IGVFFI3113CFJM/), [IGVFFI4508NSLN](/sequence-files/IGVFFI4508NSLN/), [IGVFFI9105DOIH](/sequence-files/IGVFFI9105DOIH/), [IGVFFI9452RFBC](/sequence-files/IGVFFI9452RFBC/), [IGVFFI3098AJAP](/sequence-files/IGVFFI3098AJAP/), [IGVFFI5037ULUU](/sequence-files/IGVFFI5037ULUU/), [IGVFFI8126JGXQ](/sequence-files/IGVFFI8126JGXQ/), [IGVFFI4597JJEN](/sequence-files/IGVFFI4597JJEN/), [IGVFFI8650UVHT](/sequence-files/IGVFFI8650UVHT/), [IGVFFI6755EXPU](/sequence-files/IGVFFI6755EXPU/), [IGVFFI5287VSRE](/sequence-files/IGVFFI5287VSRE/), [IGVFFI8577IGPG](/sequence-files/IGVFFI8577IGPG/), [IGVFFI2032BGYI](/sequence-files/IGVFFI2032BGYI/), [IGVFFI4558IXGW](/sequence-files/IGVFFI4558IXGW/) 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/IGVFDS0548QQSX/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS0548QQSX](/auxiliary-sets/IGVFDS0548QQSX/) 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/IGVFDS0548QQSX/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0548QQSX/",
"accession": "IGVFDS0548QQSX",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep1-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": "2023-12-13T08:48:09.888597+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": "2023-12-20T23:08:48.897838+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1176SLYJ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1176SLYJ",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep1-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": "2023-12-13T10:00:25.360792+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": "5d35da39-bc37-42ed-9aba-28ac4f2b6e43"
}