{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8736JDCM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8736JDCM",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinC_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 [IGVFSM0705YYHP](/in-vitro-systems/IGVFSM0705YYHP/) has in progress subobject construct library set [IGVFDS6982DESN](/construct-library-sets/IGVFDS6982DESN/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM0705YYHP/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS8736JDCM](/measurement-sets/IGVFDS8736JDCM/) has in progress subobject auxiliary set [IGVFDS2061JZAL](/auxiliary-sets/IGVFDS2061JZAL/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS8736JDCM/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2061JZAL](/auxiliary-sets/IGVFDS2061JZAL/) has sequence file(s): [IGVFFI2344MPYS](/sequence-files/IGVFFI2344MPYS/), [IGVFFI3218MAEC](/sequence-files/IGVFFI3218MAEC/), [IGVFFI4206TNWZ](/sequence-files/IGVFFI4206TNWZ/), [IGVFFI6739IQIO](/sequence-files/IGVFFI6739IQIO/), [IGVFFI2688SNAC](/sequence-files/IGVFFI2688SNAC/), [IGVFFI4463GBLF](/sequence-files/IGVFFI4463GBLF/), [IGVFFI1605RKIL](/sequence-files/IGVFFI1605RKIL/), [IGVFFI5088SUNH](/sequence-files/IGVFFI5088SUNH/), [IGVFFI2429ZXKM](/sequence-files/IGVFFI2429ZXKM/), [IGVFFI1579EYXF](/sequence-files/IGVFFI1579EYXF/), [IGVFFI9099LFJU](/sequence-files/IGVFFI9099LFJU/), [IGVFFI1261VPKE](/sequence-files/IGVFFI1261VPKE/), [IGVFFI2252WMRB](/sequence-files/IGVFFI2252WMRB/), [IGVFFI0446CTYE](/sequence-files/IGVFFI0446CTYE/), [IGVFFI5037OSTC](/sequence-files/IGVFFI5037OSTC/), [IGVFFI6153JLTF](/sequence-files/IGVFFI6153JLTF/), [IGVFFI8627JYIU](/sequence-files/IGVFFI8627JYIU/), [IGVFFI8352EATF](/sequence-files/IGVFFI8352EATF/), [IGVFFI8505XFDQ](/sequence-files/IGVFFI8505XFDQ/), [IGVFFI1626KEIY](/sequence-files/IGVFFI1626KEIY/), [IGVFFI6990KYYK](/sequence-files/IGVFFI6990KYYK/), [IGVFFI6764QMWO](/sequence-files/IGVFFI6764QMWO/), [IGVFFI8008AVTJ](/sequence-files/IGVFFI8008AVTJ/), [IGVFFI4108LCGL](/sequence-files/IGVFFI4108LCGL/), [IGVFFI1620IQSV](/sequence-files/IGVFFI1620IQSV/), [IGVFFI8241SECN](/sequence-files/IGVFFI8241SECN/), [IGVFFI2143YPRZ](/sequence-files/IGVFFI2143YPRZ/), [IGVFFI0302IJDC](/sequence-files/IGVFFI0302IJDC/), [IGVFFI5611GKGA](/sequence-files/IGVFFI5611GKGA/), [IGVFFI6931AEIN](/sequence-files/IGVFFI6931AEIN/), [IGVFFI8907BLPS](/sequence-files/IGVFFI8907BLPS/), [IGVFFI8471LHMT](/sequence-files/IGVFFI8471LHMT/), [IGVFFI5997XBIN](/sequence-files/IGVFFI5997XBIN/), [IGVFFI0774VUGE](/sequence-files/IGVFFI0774VUGE/), [IGVFFI4408DEAJ](/sequence-files/IGVFFI4408DEAJ/), [IGVFFI2455UNEY](/sequence-files/IGVFFI2455UNEY/), [IGVFFI9685UXUY](/sequence-files/IGVFFI9685UXUY/), [IGVFFI2220TWYV](/sequence-files/IGVFFI2220TWYV/), [IGVFFI6805LACU](/sequence-files/IGVFFI6805LACU/), [IGVFFI1380UWLD](/sequence-files/IGVFFI1380UWLD/), [IGVFFI5082PMYW](/sequence-files/IGVFFI5082PMYW/), [IGVFFI6096PQOZ](/sequence-files/IGVFFI6096PQOZ/), [IGVFFI6324OAUI](/sequence-files/IGVFFI6324OAUI/), [IGVFFI6982MJUE](/sequence-files/IGVFFI6982MJUE/), [IGVFFI9515NXDE](/sequence-files/IGVFFI9515NXDE/), [IGVFFI5588KHSS](/sequence-files/IGVFFI5588KHSS/), [IGVFFI3059ZNIK](/sequence-files/IGVFFI3059ZNIK/), [IGVFFI9226FTHE](/sequence-files/IGVFFI9226FTHE/) 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/IGVFDS2061JZAL/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS8736JDCM](/measurement-sets/IGVFDS8736JDCM/) 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/IGVFDS8736JDCM/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2061JZAL](/auxiliary-sets/IGVFDS2061JZAL/) has sequence file(s) [IGVFFI2344MPYS](/sequence-files/IGVFFI2344MPYS/), [IGVFFI3218MAEC](/sequence-files/IGVFFI3218MAEC/), [IGVFFI4206TNWZ](/sequence-files/IGVFFI4206TNWZ/), [IGVFFI6739IQIO](/sequence-files/IGVFFI6739IQIO/), [IGVFFI2688SNAC](/sequence-files/IGVFFI2688SNAC/), [IGVFFI4463GBLF](/sequence-files/IGVFFI4463GBLF/), [IGVFFI1605RKIL](/sequence-files/IGVFFI1605RKIL/), [IGVFFI5088SUNH](/sequence-files/IGVFFI5088SUNH/), [IGVFFI2429ZXKM](/sequence-files/IGVFFI2429ZXKM/), [IGVFFI1579EYXF](/sequence-files/IGVFFI1579EYXF/), [IGVFFI9099LFJU](/sequence-files/IGVFFI9099LFJU/), [IGVFFI1261VPKE](/sequence-files/IGVFFI1261VPKE/), [IGVFFI2252WMRB](/sequence-files/IGVFFI2252WMRB/), [IGVFFI0446CTYE](/sequence-files/IGVFFI0446CTYE/), [IGVFFI5037OSTC](/sequence-files/IGVFFI5037OSTC/), [IGVFFI6153JLTF](/sequence-files/IGVFFI6153JLTF/), [IGVFFI8627JYIU](/sequence-files/IGVFFI8627JYIU/), [IGVFFI8352EATF](/sequence-files/IGVFFI8352EATF/), [IGVFFI8505XFDQ](/sequence-files/IGVFFI8505XFDQ/), [IGVFFI1626KEIY](/sequence-files/IGVFFI1626KEIY/), [IGVFFI6990KYYK](/sequence-files/IGVFFI6990KYYK/), [IGVFFI6764QMWO](/sequence-files/IGVFFI6764QMWO/), [IGVFFI8008AVTJ](/sequence-files/IGVFFI8008AVTJ/), [IGVFFI4108LCGL](/sequence-files/IGVFFI4108LCGL/), [IGVFFI1620IQSV](/sequence-files/IGVFFI1620IQSV/), [IGVFFI8241SECN](/sequence-files/IGVFFI8241SECN/), [IGVFFI2143YPRZ](/sequence-files/IGVFFI2143YPRZ/), [IGVFFI0302IJDC](/sequence-files/IGVFFI0302IJDC/), [IGVFFI5611GKGA](/sequence-files/IGVFFI5611GKGA/), [IGVFFI6931AEIN](/sequence-files/IGVFFI6931AEIN/), [IGVFFI8907BLPS](/sequence-files/IGVFFI8907BLPS/), [IGVFFI8471LHMT](/sequence-files/IGVFFI8471LHMT/), [IGVFFI5997XBIN](/sequence-files/IGVFFI5997XBIN/), [IGVFFI0774VUGE](/sequence-files/IGVFFI0774VUGE/), [IGVFFI4408DEAJ](/sequence-files/IGVFFI4408DEAJ/), [IGVFFI2455UNEY](/sequence-files/IGVFFI2455UNEY/), [IGVFFI9685UXUY](/sequence-files/IGVFFI9685UXUY/), [IGVFFI2220TWYV](/sequence-files/IGVFFI2220TWYV/), [IGVFFI6805LACU](/sequence-files/IGVFFI6805LACU/), [IGVFFI1380UWLD](/sequence-files/IGVFFI1380UWLD/), [IGVFFI5082PMYW](/sequence-files/IGVFFI5082PMYW/), [IGVFFI6096PQOZ](/sequence-files/IGVFFI6096PQOZ/), [IGVFFI6324OAUI](/sequence-files/IGVFFI6324OAUI/), [IGVFFI6982MJUE](/sequence-files/IGVFFI6982MJUE/), [IGVFFI9515NXDE](/sequence-files/IGVFFI9515NXDE/), [IGVFFI5588KHSS](/sequence-files/IGVFFI5588KHSS/), [IGVFFI3059ZNIK](/sequence-files/IGVFFI3059ZNIK/), [IGVFFI9226FTHE](/sequence-files/IGVFFI9226FTHE/) 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/IGVFDS2061JZAL/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS2061JZAL](/auxiliary-sets/IGVFDS2061JZAL/) 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/IGVFDS2061JZAL/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS2061JZAL/",
"accession": "IGVFDS2061JZAL",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinC_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/IGVFDS5864UGFT/",
"accession": "IGVFDS5864UGFT",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:50:06.248256+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/IGVFDS3423PSID/"
],
"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": "2023-12-20T23:06:05.757067+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0705YYHP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0705YYHP",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinC"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6982DESN/",
"accession": "IGVFDS6982DESN",
"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 51-75% 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": "2023-12-05T22:43:49.531628+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": "178cbb30-67ac-423b-811d-e9c77b097bd1"
}