{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0816EELG/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0816EELG",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-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 [IGVFSM1367KBNP](/in-vitro-systems/IGVFSM1367KBNP/) 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/IGVFSM1367KBNP/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0816EELG](/measurement-sets/IGVFDS0816EELG/) has in progress subobject auxiliary set [IGVFDS2959XNGE](/auxiliary-sets/IGVFDS2959XNGE/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0816EELG/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2959XNGE](/auxiliary-sets/IGVFDS2959XNGE/) has sequence file(s) [IGVFFI1841YGNZ](/sequence-files/IGVFFI1841YGNZ/), [IGVFFI0493WOET](/sequence-files/IGVFFI0493WOET/), [IGVFFI4416MSIX](/sequence-files/IGVFFI4416MSIX/), [IGVFFI4773WOKV](/sequence-files/IGVFFI4773WOKV/), [IGVFFI7017RBAG](/sequence-files/IGVFFI7017RBAG/), [IGVFFI2348MDAO](/sequence-files/IGVFFI2348MDAO/), [IGVFFI4258SHNG](/sequence-files/IGVFFI4258SHNG/), [IGVFFI8697CDUG](/sequence-files/IGVFFI8697CDUG/), [IGVFFI0572VUSJ](/sequence-files/IGVFFI0572VUSJ/), [IGVFFI4203QUHO](/sequence-files/IGVFFI4203QUHO/), [IGVFFI0667HDBU](/sequence-files/IGVFFI0667HDBU/), [IGVFFI1485WFBA](/sequence-files/IGVFFI1485WFBA/), [IGVFFI6291ZTLQ](/sequence-files/IGVFFI6291ZTLQ/), [IGVFFI3763KTLJ](/sequence-files/IGVFFI3763KTLJ/), [IGVFFI5614YBMK](/sequence-files/IGVFFI5614YBMK/), [IGVFFI3964TMGN](/sequence-files/IGVFFI3964TMGN/), [IGVFFI6607CURI](/sequence-files/IGVFFI6607CURI/), [IGVFFI4676UQYZ](/sequence-files/IGVFFI4676UQYZ/), [IGVFFI0674NPNR](/sequence-files/IGVFFI0674NPNR/), [IGVFFI0352EXCO](/sequence-files/IGVFFI0352EXCO/), [IGVFFI1433FEMD](/sequence-files/IGVFFI1433FEMD/), [IGVFFI8736SGYD](/sequence-files/IGVFFI8736SGYD/), [IGVFFI0034LUOS](/sequence-files/IGVFFI0034LUOS/), [IGVFFI2525WHJS](/sequence-files/IGVFFI2525WHJS/), [IGVFFI5241NFGN](/sequence-files/IGVFFI5241NFGN/), [IGVFFI5937TQYE](/sequence-files/IGVFFI5937TQYE/), [IGVFFI4436JEFG](/sequence-files/IGVFFI4436JEFG/), [IGVFFI6564QORL](/sequence-files/IGVFFI6564QORL/), [IGVFFI0700VXBP](/sequence-files/IGVFFI0700VXBP/), [IGVFFI8257ZGCV](/sequence-files/IGVFFI8257ZGCV/), [IGVFFI5992UKFB](/sequence-files/IGVFFI5992UKFB/), [IGVFFI7332BQTH](/sequence-files/IGVFFI7332BQTH/), [IGVFFI9171ZISG](/sequence-files/IGVFFI9171ZISG/), [IGVFFI7664BLBU](/sequence-files/IGVFFI7664BLBU/), [IGVFFI0996LIMM](/sequence-files/IGVFFI0996LIMM/), [IGVFFI3616TJNE](/sequence-files/IGVFFI3616TJNE/), [IGVFFI9089TGZP](/sequence-files/IGVFFI9089TGZP/), [IGVFFI4727NQVF](/sequence-files/IGVFFI4727NQVF/), [IGVFFI2467THKC](/sequence-files/IGVFFI2467THKC/), [IGVFFI8518ETUY](/sequence-files/IGVFFI8518ETUY/), [IGVFFI2524LNRT](/sequence-files/IGVFFI2524LNRT/), [IGVFFI4623FUMZ](/sequence-files/IGVFFI4623FUMZ/), [IGVFFI9767MLPW](/sequence-files/IGVFFI9767MLPW/), [IGVFFI4402JAPA](/sequence-files/IGVFFI4402JAPA/), [IGVFFI3873IXGZ](/sequence-files/IGVFFI3873IXGZ/), [IGVFFI9069HNIJ](/sequence-files/IGVFFI9069HNIJ/), [IGVFFI3972YQJR](/sequence-files/IGVFFI3972YQJR/), [IGVFFI1129VFCK](/sequence-files/IGVFFI1129VFCK/) 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/IGVFDS2959XNGE/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2959XNGE](/auxiliary-sets/IGVFDS2959XNGE/) has sequence file(s): [IGVFFI1841YGNZ](/sequence-files/IGVFFI1841YGNZ/), [IGVFFI0493WOET](/sequence-files/IGVFFI0493WOET/), [IGVFFI4416MSIX](/sequence-files/IGVFFI4416MSIX/), [IGVFFI4773WOKV](/sequence-files/IGVFFI4773WOKV/), [IGVFFI7017RBAG](/sequence-files/IGVFFI7017RBAG/), [IGVFFI2348MDAO](/sequence-files/IGVFFI2348MDAO/), [IGVFFI4258SHNG](/sequence-files/IGVFFI4258SHNG/), [IGVFFI8697CDUG](/sequence-files/IGVFFI8697CDUG/), [IGVFFI0572VUSJ](/sequence-files/IGVFFI0572VUSJ/), [IGVFFI4203QUHO](/sequence-files/IGVFFI4203QUHO/), [IGVFFI0667HDBU](/sequence-files/IGVFFI0667HDBU/), [IGVFFI1485WFBA](/sequence-files/IGVFFI1485WFBA/), [IGVFFI6291ZTLQ](/sequence-files/IGVFFI6291ZTLQ/), [IGVFFI3763KTLJ](/sequence-files/IGVFFI3763KTLJ/), [IGVFFI5614YBMK](/sequence-files/IGVFFI5614YBMK/), [IGVFFI3964TMGN](/sequence-files/IGVFFI3964TMGN/), [IGVFFI6607CURI](/sequence-files/IGVFFI6607CURI/), [IGVFFI4676UQYZ](/sequence-files/IGVFFI4676UQYZ/), [IGVFFI0674NPNR](/sequence-files/IGVFFI0674NPNR/), [IGVFFI0352EXCO](/sequence-files/IGVFFI0352EXCO/), [IGVFFI1433FEMD](/sequence-files/IGVFFI1433FEMD/), [IGVFFI8736SGYD](/sequence-files/IGVFFI8736SGYD/), [IGVFFI0034LUOS](/sequence-files/IGVFFI0034LUOS/), [IGVFFI2525WHJS](/sequence-files/IGVFFI2525WHJS/), [IGVFFI5241NFGN](/sequence-files/IGVFFI5241NFGN/), [IGVFFI5937TQYE](/sequence-files/IGVFFI5937TQYE/), [IGVFFI4436JEFG](/sequence-files/IGVFFI4436JEFG/), [IGVFFI6564QORL](/sequence-files/IGVFFI6564QORL/), [IGVFFI0700VXBP](/sequence-files/IGVFFI0700VXBP/), [IGVFFI8257ZGCV](/sequence-files/IGVFFI8257ZGCV/), [IGVFFI5992UKFB](/sequence-files/IGVFFI5992UKFB/), [IGVFFI7332BQTH](/sequence-files/IGVFFI7332BQTH/), [IGVFFI9171ZISG](/sequence-files/IGVFFI9171ZISG/), [IGVFFI7664BLBU](/sequence-files/IGVFFI7664BLBU/), [IGVFFI0996LIMM](/sequence-files/IGVFFI0996LIMM/), [IGVFFI3616TJNE](/sequence-files/IGVFFI3616TJNE/), [IGVFFI9089TGZP](/sequence-files/IGVFFI9089TGZP/), [IGVFFI4727NQVF](/sequence-files/IGVFFI4727NQVF/), [IGVFFI2467THKC](/sequence-files/IGVFFI2467THKC/), [IGVFFI8518ETUY](/sequence-files/IGVFFI8518ETUY/), [IGVFFI2524LNRT](/sequence-files/IGVFFI2524LNRT/), [IGVFFI4623FUMZ](/sequence-files/IGVFFI4623FUMZ/), [IGVFFI9767MLPW](/sequence-files/IGVFFI9767MLPW/), [IGVFFI4402JAPA](/sequence-files/IGVFFI4402JAPA/), [IGVFFI3873IXGZ](/sequence-files/IGVFFI3873IXGZ/), [IGVFFI9069HNIJ](/sequence-files/IGVFFI9069HNIJ/), [IGVFFI3972YQJR](/sequence-files/IGVFFI3972YQJR/), [IGVFFI1129VFCK](/sequence-files/IGVFFI1129VFCK/) 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/IGVFDS2959XNGE/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0816EELG](/measurement-sets/IGVFDS0816EELG/) 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/IGVFDS0816EELG/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS2959XNGE](/auxiliary-sets/IGVFDS2959XNGE/) 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_for",
"path": "/auxiliary-sets/IGVFDS2959XNGE/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS2959XNGE/",
"accession": "IGVFDS2959XNGE",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-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/IGVFDS4989HPTW/",
"accession": "IGVFDS4989HPTW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:49:13.516935+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [],
"input_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": "2023-12-20T23:05:24.507666+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1367KBNP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1367KBNP",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinA"
],
"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 0-25% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected 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": "2023-12-05T22:20:58.428053+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": "b28c6509-1719-4d74-b014-7fa1da3af9e4"
}