{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2609BGAI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2609BGAI",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep1-BinB_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 [IGVFDS2609BGAI](/measurement-sets/IGVFDS2609BGAI/) has in progress subobject auxiliary set [IGVFDS0637GXZD](/auxiliary-sets/IGVFDS0637GXZD/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS2609BGAI/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM9828HZOI](/in-vitro-systems/IGVFSM9828HZOI/) 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/IGVFSM9828HZOI/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2609BGAI](/measurement-sets/IGVFDS2609BGAI/) 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/IGVFDS2609BGAI/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS0637GXZD](/auxiliary-sets/IGVFDS0637GXZD/) has sequence file(s) [IGVFFI6765PTHE](/sequence-files/IGVFFI6765PTHE/), [IGVFFI9919AMNA](/sequence-files/IGVFFI9919AMNA/), [IGVFFI2585OIQW](/sequence-files/IGVFFI2585OIQW/), [IGVFFI9306GYYW](/sequence-files/IGVFFI9306GYYW/), [IGVFFI3283PIAQ](/sequence-files/IGVFFI3283PIAQ/), [IGVFFI4896HIGG](/sequence-files/IGVFFI4896HIGG/), [IGVFFI2840YUGH](/sequence-files/IGVFFI2840YUGH/), [IGVFFI1620CPGV](/sequence-files/IGVFFI1620CPGV/), [IGVFFI3062KFNS](/sequence-files/IGVFFI3062KFNS/), [IGVFFI0092CNKX](/sequence-files/IGVFFI0092CNKX/), [IGVFFI9186LZHM](/sequence-files/IGVFFI9186LZHM/), [IGVFFI6327FKCG](/sequence-files/IGVFFI6327FKCG/), [IGVFFI0328DJZB](/sequence-files/IGVFFI0328DJZB/), [IGVFFI4104RRQF](/sequence-files/IGVFFI4104RRQF/), [IGVFFI4609BQLQ](/sequence-files/IGVFFI4609BQLQ/), [IGVFFI0194FYDR](/sequence-files/IGVFFI0194FYDR/), [IGVFFI0381SAXZ](/sequence-files/IGVFFI0381SAXZ/), [IGVFFI0734ILOB](/sequence-files/IGVFFI0734ILOB/), [IGVFFI1656CGQI](/sequence-files/IGVFFI1656CGQI/), [IGVFFI0320WEWN](/sequence-files/IGVFFI0320WEWN/), [IGVFFI3931PIHC](/sequence-files/IGVFFI3931PIHC/), [IGVFFI0503XRRK](/sequence-files/IGVFFI0503XRRK/), [IGVFFI4060VCJN](/sequence-files/IGVFFI4060VCJN/), [IGVFFI4724UOOY](/sequence-files/IGVFFI4724UOOY/), [IGVFFI9451NYTS](/sequence-files/IGVFFI9451NYTS/), [IGVFFI1165YOSW](/sequence-files/IGVFFI1165YOSW/), [IGVFFI1160RPML](/sequence-files/IGVFFI1160RPML/), [IGVFFI5950AIVR](/sequence-files/IGVFFI5950AIVR/), [IGVFFI3723WNMK](/sequence-files/IGVFFI3723WNMK/), [IGVFFI4129TSTH](/sequence-files/IGVFFI4129TSTH/), [IGVFFI5484VQMS](/sequence-files/IGVFFI5484VQMS/), [IGVFFI0168IBTX](/sequence-files/IGVFFI0168IBTX/), [IGVFFI9388AKFK](/sequence-files/IGVFFI9388AKFK/), [IGVFFI1367EUSW](/sequence-files/IGVFFI1367EUSW/), [IGVFFI4582DSFX](/sequence-files/IGVFFI4582DSFX/), [IGVFFI6625HNRT](/sequence-files/IGVFFI6625HNRT/), [IGVFFI4412PGYQ](/sequence-files/IGVFFI4412PGYQ/), [IGVFFI0009IJSP](/sequence-files/IGVFFI0009IJSP/), [IGVFFI9954ZBDW](/sequence-files/IGVFFI9954ZBDW/), [IGVFFI0814EGXA](/sequence-files/IGVFFI0814EGXA/), [IGVFFI0476OFNB](/sequence-files/IGVFFI0476OFNB/), [IGVFFI3920KAUR](/sequence-files/IGVFFI3920KAUR/), [IGVFFI2422NMJL](/sequence-files/IGVFFI2422NMJL/), [IGVFFI6993GRZJ](/sequence-files/IGVFFI6993GRZJ/), [IGVFFI0715CNZT](/sequence-files/IGVFFI0715CNZT/), [IGVFFI0418KUEO](/sequence-files/IGVFFI0418KUEO/), [IGVFFI7706RXBE](/sequence-files/IGVFFI7706RXBE/), [IGVFFI3162LCKS](/sequence-files/IGVFFI3162LCKS/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS0637GXZD/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS0637GXZD](/auxiliary-sets/IGVFDS0637GXZD/) has sequence file(s): [IGVFFI6765PTHE](/sequence-files/IGVFFI6765PTHE/), [IGVFFI9919AMNA](/sequence-files/IGVFFI9919AMNA/), [IGVFFI2585OIQW](/sequence-files/IGVFFI2585OIQW/), [IGVFFI9306GYYW](/sequence-files/IGVFFI9306GYYW/), [IGVFFI3283PIAQ](/sequence-files/IGVFFI3283PIAQ/), [IGVFFI4896HIGG](/sequence-files/IGVFFI4896HIGG/), [IGVFFI2840YUGH](/sequence-files/IGVFFI2840YUGH/), [IGVFFI1620CPGV](/sequence-files/IGVFFI1620CPGV/), [IGVFFI3062KFNS](/sequence-files/IGVFFI3062KFNS/), [IGVFFI0092CNKX](/sequence-files/IGVFFI0092CNKX/), [IGVFFI9186LZHM](/sequence-files/IGVFFI9186LZHM/), [IGVFFI6327FKCG](/sequence-files/IGVFFI6327FKCG/), [IGVFFI0328DJZB](/sequence-files/IGVFFI0328DJZB/), [IGVFFI4104RRQF](/sequence-files/IGVFFI4104RRQF/), [IGVFFI4609BQLQ](/sequence-files/IGVFFI4609BQLQ/), [IGVFFI0194FYDR](/sequence-files/IGVFFI0194FYDR/), [IGVFFI0381SAXZ](/sequence-files/IGVFFI0381SAXZ/), [IGVFFI0734ILOB](/sequence-files/IGVFFI0734ILOB/), [IGVFFI1656CGQI](/sequence-files/IGVFFI1656CGQI/), [IGVFFI0320WEWN](/sequence-files/IGVFFI0320WEWN/), [IGVFFI3931PIHC](/sequence-files/IGVFFI3931PIHC/), [IGVFFI0503XRRK](/sequence-files/IGVFFI0503XRRK/), [IGVFFI4060VCJN](/sequence-files/IGVFFI4060VCJN/), [IGVFFI4724UOOY](/sequence-files/IGVFFI4724UOOY/), [IGVFFI9451NYTS](/sequence-files/IGVFFI9451NYTS/), [IGVFFI1165YOSW](/sequence-files/IGVFFI1165YOSW/), [IGVFFI1160RPML](/sequence-files/IGVFFI1160RPML/), [IGVFFI5950AIVR](/sequence-files/IGVFFI5950AIVR/), [IGVFFI3723WNMK](/sequence-files/IGVFFI3723WNMK/), [IGVFFI4129TSTH](/sequence-files/IGVFFI4129TSTH/), [IGVFFI5484VQMS](/sequence-files/IGVFFI5484VQMS/), [IGVFFI0168IBTX](/sequence-files/IGVFFI0168IBTX/), [IGVFFI9388AKFK](/sequence-files/IGVFFI9388AKFK/), [IGVFFI1367EUSW](/sequence-files/IGVFFI1367EUSW/), [IGVFFI4582DSFX](/sequence-files/IGVFFI4582DSFX/), [IGVFFI6625HNRT](/sequence-files/IGVFFI6625HNRT/), [IGVFFI4412PGYQ](/sequence-files/IGVFFI4412PGYQ/), [IGVFFI0009IJSP](/sequence-files/IGVFFI0009IJSP/), [IGVFFI9954ZBDW](/sequence-files/IGVFFI9954ZBDW/), [IGVFFI0814EGXA](/sequence-files/IGVFFI0814EGXA/), [IGVFFI0476OFNB](/sequence-files/IGVFFI0476OFNB/), [IGVFFI3920KAUR](/sequence-files/IGVFFI3920KAUR/), [IGVFFI2422NMJL](/sequence-files/IGVFFI2422NMJL/), [IGVFFI6993GRZJ](/sequence-files/IGVFFI6993GRZJ/), [IGVFFI0715CNZT](/sequence-files/IGVFFI0715CNZT/), [IGVFFI0418KUEO](/sequence-files/IGVFFI0418KUEO/), [IGVFFI7706RXBE](/sequence-files/IGVFFI7706RXBE/), [IGVFFI3162LCKS](/sequence-files/IGVFFI3162LCKS/) 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/IGVFDS0637GXZD/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS0637GXZD](/auxiliary-sets/IGVFDS0637GXZD/) 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/IGVFDS0637GXZD/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0637GXZD/",
"accession": "IGVFDS0637GXZD",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep1-BinB_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": "2023-12-13T08:48:10.193677+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": "2023-12-20T23:08:37.703865+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9828HZOI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9828HZOI",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep1-BinB"
],
"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 26-50% expression of PPIF) modified with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "22",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-13T10:00:34.900116+00:00",
"summary": "prime editing 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": "8aec074b-d6ab-4982-8dfa-cc4b88a9a512"
}