{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5795QOPU/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5795QOPU",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-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 in vitro system [IGVFSM1676ETUI](/in-vitro-systems/IGVFSM1676ETUI/) 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/IGVFSM1676ETUI/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS5795QOPU](/measurement-sets/IGVFDS5795QOPU/) has in progress subobject auxiliary set [IGVFDS0262VISR](/auxiliary-sets/IGVFDS0262VISR/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS5795QOPU/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS0262VISR](/auxiliary-sets/IGVFDS0262VISR/) has sequence file(s): [IGVFFI7462AKVO](/sequence-files/IGVFFI7462AKVO/), [IGVFFI9180DRLH](/sequence-files/IGVFFI9180DRLH/), [IGVFFI0284YMTU](/sequence-files/IGVFFI0284YMTU/), [IGVFFI4948UPGN](/sequence-files/IGVFFI4948UPGN/), [IGVFFI1505CICQ](/sequence-files/IGVFFI1505CICQ/), [IGVFFI5635XGRS](/sequence-files/IGVFFI5635XGRS/), [IGVFFI2774YGOD](/sequence-files/IGVFFI2774YGOD/), [IGVFFI2722NNLB](/sequence-files/IGVFFI2722NNLB/), [IGVFFI3058DBGO](/sequence-files/IGVFFI3058DBGO/), [IGVFFI8452LDVN](/sequence-files/IGVFFI8452LDVN/), [IGVFFI9866KYZN](/sequence-files/IGVFFI9866KYZN/), [IGVFFI4411WXPX](/sequence-files/IGVFFI4411WXPX/), [IGVFFI0915SBDA](/sequence-files/IGVFFI0915SBDA/), [IGVFFI8957HJAO](/sequence-files/IGVFFI8957HJAO/), [IGVFFI8128TSNE](/sequence-files/IGVFFI8128TSNE/), [IGVFFI1684KGPJ](/sequence-files/IGVFFI1684KGPJ/), [IGVFFI5318AXMA](/sequence-files/IGVFFI5318AXMA/), [IGVFFI6958XOUZ](/sequence-files/IGVFFI6958XOUZ/), [IGVFFI1054VHJG](/sequence-files/IGVFFI1054VHJG/), [IGVFFI5086TGNZ](/sequence-files/IGVFFI5086TGNZ/), [IGVFFI1090LPJK](/sequence-files/IGVFFI1090LPJK/), [IGVFFI8059CFTR](/sequence-files/IGVFFI8059CFTR/), [IGVFFI6630HQIE](/sequence-files/IGVFFI6630HQIE/), [IGVFFI6041BZDN](/sequence-files/IGVFFI6041BZDN/), [IGVFFI0903BYGD](/sequence-files/IGVFFI0903BYGD/), [IGVFFI8164GCFK](/sequence-files/IGVFFI8164GCFK/), [IGVFFI3560YQVU](/sequence-files/IGVFFI3560YQVU/), [IGVFFI8211QTUA](/sequence-files/IGVFFI8211QTUA/), [IGVFFI4272PBAR](/sequence-files/IGVFFI4272PBAR/), [IGVFFI7969IVLX](/sequence-files/IGVFFI7969IVLX/), [IGVFFI9719RWPT](/sequence-files/IGVFFI9719RWPT/), [IGVFFI6824ARGE](/sequence-files/IGVFFI6824ARGE/), [IGVFFI9536VVHV](/sequence-files/IGVFFI9536VVHV/), [IGVFFI2441DWUD](/sequence-files/IGVFFI2441DWUD/), [IGVFFI9083CPBP](/sequence-files/IGVFFI9083CPBP/), [IGVFFI8069LKOQ](/sequence-files/IGVFFI8069LKOQ/), [IGVFFI8354WGMB](/sequence-files/IGVFFI8354WGMB/), [IGVFFI7518AKRP](/sequence-files/IGVFFI7518AKRP/), [IGVFFI3787AFQI](/sequence-files/IGVFFI3787AFQI/), [IGVFFI2796VWCV](/sequence-files/IGVFFI2796VWCV/), [IGVFFI3562WJYO](/sequence-files/IGVFFI3562WJYO/), [IGVFFI1358CZQC](/sequence-files/IGVFFI1358CZQC/), [IGVFFI1109DNMJ](/sequence-files/IGVFFI1109DNMJ/), [IGVFFI0474GGLZ](/sequence-files/IGVFFI0474GGLZ/), [IGVFFI2391LBHD](/sequence-files/IGVFFI2391LBHD/), [IGVFFI6415TWYM](/sequence-files/IGVFFI6415TWYM/), [IGVFFI6344NYPV](/sequence-files/IGVFFI6344NYPV/), [IGVFFI2387SKKZ](/sequence-files/IGVFFI2387SKKZ/) 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/IGVFDS0262VISR/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5795QOPU](/measurement-sets/IGVFDS5795QOPU/) 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/IGVFDS5795QOPU/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS0262VISR](/auxiliary-sets/IGVFDS0262VISR/) has sequence file(s) [IGVFFI7462AKVO](/sequence-files/IGVFFI7462AKVO/), [IGVFFI9180DRLH](/sequence-files/IGVFFI9180DRLH/), [IGVFFI0284YMTU](/sequence-files/IGVFFI0284YMTU/), [IGVFFI4948UPGN](/sequence-files/IGVFFI4948UPGN/), [IGVFFI1505CICQ](/sequence-files/IGVFFI1505CICQ/), [IGVFFI5635XGRS](/sequence-files/IGVFFI5635XGRS/), [IGVFFI2774YGOD](/sequence-files/IGVFFI2774YGOD/), [IGVFFI2722NNLB](/sequence-files/IGVFFI2722NNLB/), [IGVFFI3058DBGO](/sequence-files/IGVFFI3058DBGO/), [IGVFFI8452LDVN](/sequence-files/IGVFFI8452LDVN/), [IGVFFI9866KYZN](/sequence-files/IGVFFI9866KYZN/), [IGVFFI4411WXPX](/sequence-files/IGVFFI4411WXPX/), [IGVFFI0915SBDA](/sequence-files/IGVFFI0915SBDA/), [IGVFFI8957HJAO](/sequence-files/IGVFFI8957HJAO/), [IGVFFI8128TSNE](/sequence-files/IGVFFI8128TSNE/), [IGVFFI1684KGPJ](/sequence-files/IGVFFI1684KGPJ/), [IGVFFI5318AXMA](/sequence-files/IGVFFI5318AXMA/), [IGVFFI6958XOUZ](/sequence-files/IGVFFI6958XOUZ/), [IGVFFI1054VHJG](/sequence-files/IGVFFI1054VHJG/), [IGVFFI5086TGNZ](/sequence-files/IGVFFI5086TGNZ/), [IGVFFI1090LPJK](/sequence-files/IGVFFI1090LPJK/), [IGVFFI8059CFTR](/sequence-files/IGVFFI8059CFTR/), [IGVFFI6630HQIE](/sequence-files/IGVFFI6630HQIE/), [IGVFFI6041BZDN](/sequence-files/IGVFFI6041BZDN/), [IGVFFI0903BYGD](/sequence-files/IGVFFI0903BYGD/), [IGVFFI8164GCFK](/sequence-files/IGVFFI8164GCFK/), [IGVFFI3560YQVU](/sequence-files/IGVFFI3560YQVU/), [IGVFFI8211QTUA](/sequence-files/IGVFFI8211QTUA/), [IGVFFI4272PBAR](/sequence-files/IGVFFI4272PBAR/), [IGVFFI7969IVLX](/sequence-files/IGVFFI7969IVLX/), [IGVFFI9719RWPT](/sequence-files/IGVFFI9719RWPT/), [IGVFFI6824ARGE](/sequence-files/IGVFFI6824ARGE/), [IGVFFI9536VVHV](/sequence-files/IGVFFI9536VVHV/), [IGVFFI2441DWUD](/sequence-files/IGVFFI2441DWUD/), [IGVFFI9083CPBP](/sequence-files/IGVFFI9083CPBP/), [IGVFFI8069LKOQ](/sequence-files/IGVFFI8069LKOQ/), [IGVFFI8354WGMB](/sequence-files/IGVFFI8354WGMB/), [IGVFFI7518AKRP](/sequence-files/IGVFFI7518AKRP/), [IGVFFI3787AFQI](/sequence-files/IGVFFI3787AFQI/), [IGVFFI2796VWCV](/sequence-files/IGVFFI2796VWCV/), [IGVFFI3562WJYO](/sequence-files/IGVFFI3562WJYO/), [IGVFFI1358CZQC](/sequence-files/IGVFFI1358CZQC/), [IGVFFI1109DNMJ](/sequence-files/IGVFFI1109DNMJ/), [IGVFFI0474GGLZ](/sequence-files/IGVFFI0474GGLZ/), [IGVFFI2391LBHD](/sequence-files/IGVFFI2391LBHD/), [IGVFFI6415TWYM](/sequence-files/IGVFFI6415TWYM/), [IGVFFI6344NYPV](/sequence-files/IGVFFI6344NYPV/), [IGVFFI2387SKKZ](/sequence-files/IGVFFI2387SKKZ/) 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/IGVFDS0262VISR/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS0262VISR](/auxiliary-sets/IGVFDS0262VISR/) 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/IGVFDS0262VISR/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0262VISR/",
"accession": "IGVFDS0262VISR",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-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/IGVFDS5128CXIS/",
"accession": "IGVFDS5128CXIS",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-12-13T08:01:38.229708+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": "2023-12-20T23:08:04.147991+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1676ETUI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1676ETUI",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-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_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 0-25% 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": "2023-12-13T08:25:12.283933+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": "f8867dee-4d9c-4714-b3a2-53ab6e170b93"
}