{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2690TJJM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2690TJJM",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-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 [IGVFSM2310CCFV](/in-vitro-systems/IGVFSM2310CCFV/) 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/IGVFSM2310CCFV/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS2690TJJM](/measurement-sets/IGVFDS2690TJJM/) has in progress subobject auxiliary set [IGVFDS8926XVHD](/auxiliary-sets/IGVFDS8926XVHD/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS2690TJJM/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8926XVHD](/auxiliary-sets/IGVFDS8926XVHD/) has sequence file(s): [IGVFFI8093EEJC](/sequence-files/IGVFFI8093EEJC/), [IGVFFI0945MRSC](/sequence-files/IGVFFI0945MRSC/), [IGVFFI7020USLV](/sequence-files/IGVFFI7020USLV/), [IGVFFI7960CKLM](/sequence-files/IGVFFI7960CKLM/), [IGVFFI0628YAHP](/sequence-files/IGVFFI0628YAHP/), [IGVFFI4640DNSX](/sequence-files/IGVFFI4640DNSX/), [IGVFFI8474QTEK](/sequence-files/IGVFFI8474QTEK/), [IGVFFI9489VDCE](/sequence-files/IGVFFI9489VDCE/), [IGVFFI3384MZZZ](/sequence-files/IGVFFI3384MZZZ/), [IGVFFI9008GSGG](/sequence-files/IGVFFI9008GSGG/), [IGVFFI5637OPON](/sequence-files/IGVFFI5637OPON/), [IGVFFI0251NPUZ](/sequence-files/IGVFFI0251NPUZ/), [IGVFFI5516ESSK](/sequence-files/IGVFFI5516ESSK/), [IGVFFI5579JJTV](/sequence-files/IGVFFI5579JJTV/), [IGVFFI0019AJUY](/sequence-files/IGVFFI0019AJUY/), [IGVFFI2913QILN](/sequence-files/IGVFFI2913QILN/), [IGVFFI6079WMBN](/sequence-files/IGVFFI6079WMBN/), [IGVFFI2612LBPZ](/sequence-files/IGVFFI2612LBPZ/), [IGVFFI7532RIOK](/sequence-files/IGVFFI7532RIOK/), [IGVFFI5882IBBB](/sequence-files/IGVFFI5882IBBB/), [IGVFFI1560JLCV](/sequence-files/IGVFFI1560JLCV/), [IGVFFI9227RPDU](/sequence-files/IGVFFI9227RPDU/), [IGVFFI8298ECSM](/sequence-files/IGVFFI8298ECSM/), [IGVFFI4462AZJD](/sequence-files/IGVFFI4462AZJD/), [IGVFFI6277TIFA](/sequence-files/IGVFFI6277TIFA/), [IGVFFI8895CUNJ](/sequence-files/IGVFFI8895CUNJ/), [IGVFFI2379YFYC](/sequence-files/IGVFFI2379YFYC/), [IGVFFI1451FYYQ](/sequence-files/IGVFFI1451FYYQ/), [IGVFFI0556IFKJ](/sequence-files/IGVFFI0556IFKJ/), [IGVFFI5175GWLJ](/sequence-files/IGVFFI5175GWLJ/), [IGVFFI5713FJEH](/sequence-files/IGVFFI5713FJEH/), [IGVFFI5415UEDE](/sequence-files/IGVFFI5415UEDE/), [IGVFFI7980SIYV](/sequence-files/IGVFFI7980SIYV/), [IGVFFI9754KCQQ](/sequence-files/IGVFFI9754KCQQ/), [IGVFFI8554OPUE](/sequence-files/IGVFFI8554OPUE/), [IGVFFI6227XDXY](/sequence-files/IGVFFI6227XDXY/), [IGVFFI5594MYYW](/sequence-files/IGVFFI5594MYYW/), [IGVFFI4069UGKK](/sequence-files/IGVFFI4069UGKK/), [IGVFFI4240NZLI](/sequence-files/IGVFFI4240NZLI/), [IGVFFI1589OEAU](/sequence-files/IGVFFI1589OEAU/), [IGVFFI6433LVAD](/sequence-files/IGVFFI6433LVAD/), [IGVFFI8337XJYA](/sequence-files/IGVFFI8337XJYA/), [IGVFFI6882DUHO](/sequence-files/IGVFFI6882DUHO/), [IGVFFI7282SKON](/sequence-files/IGVFFI7282SKON/), [IGVFFI1977XIUI](/sequence-files/IGVFFI1977XIUI/), [IGVFFI2225VINQ](/sequence-files/IGVFFI2225VINQ/), [IGVFFI7108AVNK](/sequence-files/IGVFFI7108AVNK/), [IGVFFI2664LAQC](/sequence-files/IGVFFI2664LAQC/) 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/IGVFDS8926XVHD/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2690TJJM](/measurement-sets/IGVFDS2690TJJM/) 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/IGVFDS2690TJJM/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8926XVHD](/auxiliary-sets/IGVFDS8926XVHD/) has sequence file(s) [IGVFFI8093EEJC](/sequence-files/IGVFFI8093EEJC/), [IGVFFI0945MRSC](/sequence-files/IGVFFI0945MRSC/), [IGVFFI7020USLV](/sequence-files/IGVFFI7020USLV/), [IGVFFI7960CKLM](/sequence-files/IGVFFI7960CKLM/), [IGVFFI0628YAHP](/sequence-files/IGVFFI0628YAHP/), [IGVFFI4640DNSX](/sequence-files/IGVFFI4640DNSX/), [IGVFFI8474QTEK](/sequence-files/IGVFFI8474QTEK/), [IGVFFI9489VDCE](/sequence-files/IGVFFI9489VDCE/), [IGVFFI3384MZZZ](/sequence-files/IGVFFI3384MZZZ/), [IGVFFI9008GSGG](/sequence-files/IGVFFI9008GSGG/), [IGVFFI5637OPON](/sequence-files/IGVFFI5637OPON/), [IGVFFI0251NPUZ](/sequence-files/IGVFFI0251NPUZ/), [IGVFFI5516ESSK](/sequence-files/IGVFFI5516ESSK/), [IGVFFI5579JJTV](/sequence-files/IGVFFI5579JJTV/), [IGVFFI0019AJUY](/sequence-files/IGVFFI0019AJUY/), [IGVFFI2913QILN](/sequence-files/IGVFFI2913QILN/), [IGVFFI6079WMBN](/sequence-files/IGVFFI6079WMBN/), [IGVFFI2612LBPZ](/sequence-files/IGVFFI2612LBPZ/), [IGVFFI7532RIOK](/sequence-files/IGVFFI7532RIOK/), [IGVFFI5882IBBB](/sequence-files/IGVFFI5882IBBB/), [IGVFFI1560JLCV](/sequence-files/IGVFFI1560JLCV/), [IGVFFI9227RPDU](/sequence-files/IGVFFI9227RPDU/), [IGVFFI8298ECSM](/sequence-files/IGVFFI8298ECSM/), [IGVFFI4462AZJD](/sequence-files/IGVFFI4462AZJD/), [IGVFFI6277TIFA](/sequence-files/IGVFFI6277TIFA/), [IGVFFI8895CUNJ](/sequence-files/IGVFFI8895CUNJ/), [IGVFFI2379YFYC](/sequence-files/IGVFFI2379YFYC/), [IGVFFI1451FYYQ](/sequence-files/IGVFFI1451FYYQ/), [IGVFFI0556IFKJ](/sequence-files/IGVFFI0556IFKJ/), [IGVFFI5175GWLJ](/sequence-files/IGVFFI5175GWLJ/), [IGVFFI5713FJEH](/sequence-files/IGVFFI5713FJEH/), [IGVFFI5415UEDE](/sequence-files/IGVFFI5415UEDE/), [IGVFFI7980SIYV](/sequence-files/IGVFFI7980SIYV/), [IGVFFI9754KCQQ](/sequence-files/IGVFFI9754KCQQ/), [IGVFFI8554OPUE](/sequence-files/IGVFFI8554OPUE/), [IGVFFI6227XDXY](/sequence-files/IGVFFI6227XDXY/), [IGVFFI5594MYYW](/sequence-files/IGVFFI5594MYYW/), [IGVFFI4069UGKK](/sequence-files/IGVFFI4069UGKK/), [IGVFFI4240NZLI](/sequence-files/IGVFFI4240NZLI/), [IGVFFI1589OEAU](/sequence-files/IGVFFI1589OEAU/), [IGVFFI6433LVAD](/sequence-files/IGVFFI6433LVAD/), [IGVFFI8337XJYA](/sequence-files/IGVFFI8337XJYA/), [IGVFFI6882DUHO](/sequence-files/IGVFFI6882DUHO/), [IGVFFI7282SKON](/sequence-files/IGVFFI7282SKON/), [IGVFFI1977XIUI](/sequence-files/IGVFFI1977XIUI/), [IGVFFI2225VINQ](/sequence-files/IGVFFI2225VINQ/), [IGVFFI7108AVNK](/sequence-files/IGVFFI7108AVNK/), [IGVFFI2664LAQC](/sequence-files/IGVFFI2664LAQC/) 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/IGVFDS8926XVHD/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS8926XVHD](/auxiliary-sets/IGVFDS8926XVHD/) 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/IGVFDS8926XVHD/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8926XVHD/",
"accession": "IGVFDS8926XVHD",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-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/IGVFDS4989HPTW/",
"accession": "IGVFDS4989HPTW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:49:28.833568+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": "2023-12-20T23:05:20.186150+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2310CCFV/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2310CCFV",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinD"
],
"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 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": "2023-12-05T23:46:44.483431+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": "4e61fb64-f131-490e-bcc4-5ca0a2ed11f9"
}